diff --git a/.devcontainer.json b/.devcontainer.json index 38b751e..497dc21 100644 --- a/.devcontainer.json +++ b/.devcontainer.json @@ -18,20 +18,32 @@ // "forwardPorts": [], // Use 'postCreateCommand' to run commands after the container is created. - "postCreateCommand": "mamba env create -n core -f dev-env.yml && conda run -n core poetry install", + "postCreateCommand": "mamba env create -n core -f dev-env.yml && conda run -n core poetry config virtualenvs.in-project true && conda run -n core poetry install", // Configure tool-specific properties. "customizations": { "vscode": { - "extensions": ["ms-python.python"], + "extensions": [ + "ms-python.python", + "ms-vscode.live-server", + "ms-python.black-formatter" + ], "settings": { + "python.analysis.typeCheckingMode": "strict", "python.condaPath": "/opt/conda/condabin/conda", - "python.defaultInterpreterPath": "/opt/conda/envs/core/bin/python", "python.terminal.activateEnvironment": true, "python.terminal.activateEnvInCurrentTerminal": true, - "python.venvFolders": ["/home/vscode/.cache/pypoetry/virtualenvs"], + "python.venvPath": "/workspaces/core/.venv", + "python.defaultInterpreterPath": "/workspaces/core/.venv/bin/python", + "python.testing.pytestArgs": [ + "tests" + ], + "python.testing.pytestEnabled": true, + "python.testing.unittestEnabled": false, "terminal.integrated.environmentChangesRelaunch": true, - "terminal.integrated.hideOnStartup": "always" + "editor.defaultFormatter": "ms-python.black-formatter", + "terminal.integrated.hideOnStartup": "always", + "files.eol": "\n" } } } diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index b14a946..be87540 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -22,7 +22,8 @@ jobs: - { python: "3.11", os: "ubuntu-latest", session: "tests" } - { python: "3.12", os: "ubuntu-latest", session: "tests" } # - { python: "3.11", os: "windows-latest", session: "tests" } - - { python: "3.8", os: "macos-latest", session: "tests" } + - { python: "3.9", os: "macos-13", session: "tests" } + - { python: "3.11", os: "macos-latest", session: "tests" } - { python: "3.8", os: "ubuntu-latest", session: "size" } - { python: "3.8", os: "ubuntu-latest", session: "coverage" } @@ -86,7 +87,7 @@ jobs: run: | export NOXSESSION=tests # check that code coverage is not lower than specific percent - nox --verbose --python=${{ matrix.python }} -- --cov=. --cov-report=term-missing --cov-fail-under=93 + nox --verbose --python=${{ matrix.python }} -- --cov-fail-under=92.5 - name: Run tests with nox if: matrix.session == 'tests' || matrix.session == 'lint' diff --git a/core/genotypes.py b/core/genotypes.py index d0377ac..8e25c95 100644 --- a/core/genotypes.py +++ b/core/genotypes.py @@ -13,12 +13,8 @@ from pysam import VariantFile from cyvcf2 import VCF, Variant -try: - import trtools.utils.tr_harmonizer as trh -except ModuleNotFoundError: - from . import tr_harmonizer as trh - from .data import Data +from . import tr_harmonizer as trh class Genotypes(Data): diff --git a/core/logging.py b/core/logging.py new file mode 100755 index 0000000..fd7918b --- /dev/null +++ b/core/logging.py @@ -0,0 +1,46 @@ +from __future__ import annotations +import logging + + +def getLogger(name: str = None, level: str = "ERROR", exact_time=False): + """ + Retrieve a Logger object + + Parameters + ---------- + name : str, optional + The name of the logging object + level : str, optional + The level of verbosity for the logger + """ + if name is None: + name = "" + else: + name = "." + name + + # create logger + logger = logging.getLogger("core" + name) + logger.setLevel(level) + + # create console handler and set level to debug + ch = logging.StreamHandler() + ch.setLevel(level) + + # create formatter + db_time = ( + ("|%(asctime)s" + (".%(msecs)03d" if exact_time else "")) + if level == "DEBUG" + else "" + ) + formatter = logging.Formatter( + fmt="[%(levelname)8s" + db_time + "] %(message)s (%(filename)s:%(lineno)s)", + datefmt="%H:%M:%S", + ) + + # add formatter to ch + ch.setFormatter(formatter) + + # add ch to logger + logger.addHandler(ch) + + return logger diff --git a/core/tr_harmonizer.py b/core/tr_harmonizer.py old mode 100644 new mode 100755 index 6fcd1b2..1c493e4 --- a/core/tr_harmonizer.py +++ b/core/tr_harmonizer.py @@ -1,1721 +1,1845 @@ -""" -Utilities for harmonizing tandem repeat VCF records. -Handles VCFs generated by various TR genotyping tools -""" -import re -import enum -import warnings -from typing import ( - Any, - Callable, - Dict, - Generator, - Iterator, - List, - Optional, - Set, - Tuple, - Union, -) - -import cyvcf2 -import numpy as np - -# List of supported VCF types -# TODO: add Beagle -# TODO: add support for tool version numbers - -_beagle_error = ( - "If this file was imputed by Beagle, did you remember to copy the info fields over?" -) - - -def GetCanonicalOneStrand(repseq): - r"""Get canonical STR sequence, considering one strand - The canonical sequence is the first alphabetically - out of all possible rotations. e.g. CAG -> AGC. - Parameters - ---------- - repseq : str - String giving a STR motif (repeat unit sequence) - Returns - ------- - canon : str - The canonical sequence of the STR motif - Examples - -------- - >>> GetCanonicalOneStrand("CAG") - "AGC" - """ - nucToNumber = {"A": 0, "C": 1, "G": 2, "T": 3} - repseq = repseq.upper() - size = len(repseq) - canonical = repseq - for i in range(size): - newseq = repseq[size - i :] + repseq[0 : size - i] - for j in range(size): - if nucToNumber[newseq[j]] < nucToNumber[canonical[j]]: - canonical = newseq - elif nucToNumber[newseq[j]] > nucToNumber[canonical[j]]: - break - return canonical - - -def InferRepeatSequence(seq, period): - """ - TODO change to dynamic programming approach - Infer the repeated sequence in a string - Parameters - ---------- - seq : str - A string of nucleotides - period : int - Length of the repeat unit - Returns - ------- - repseq : str - The inferred repeat unit (motif). - If the input sequence is smaller than the period, - repseq consists of all N's. - Examples - -------- - >>> InferRepeatSequence('ATATATAT', 2) - 'AT' - """ - if period > len(seq): - return "N" * period - best_kmer = None - best_copies = 0 - for offset in range(0, period): - kmers = {} - start_idx = 0 - while start_idx + period <= len(seq): - kmer = seq[start_idx : (start_idx + period)] - if kmer not in kmers: - kmers[kmer] = 1 - else: - kmers[kmer] += 1 - start_idx += period - current_best_kmer = max(kmers, key=lambda k: kmers[k]) - current_best_copies = kmers[current_best_kmer] - if current_best_copies > best_copies: - best_kmer = current_best_kmer - best_copies = current_best_copies - return GetCanonicalOneStrand(best_kmer) - - -def FabricateAllele(motif, length): - """ - Fabricate an allele with the given motif and length. - Parameters - ---------- - motif : str - the motif to build the allele from - length : float - the number of times to copy the motif - (noninteger implies partial repeats). - This does NOT specify the desired length of the - returned string. - Return - ------ - str - the fabricated allele string - Notes - ----- - The allele is fabricated with the given motif orientation - (e.g. motif = 'ACG' could produce 'ACGACGACG' but not 'CGACGACGA'). - Fabricated alleles will contain no impurities nor flanking base pairs. - In the case of length being a noninteger float (because of partial - repeats) and where it is unclear if the last nucleotide should be - included in the fabricated repeat or not due to imprecision in the - length float, the last nucleotide will always be left off (the - length of the returned string will always be rounded down). - """ - fab = math.floor(length) * motif - idx = 0 - while (len(fab) + 1) / len(motif) < length: - fab += motif[idx] - idx += 1 - - return fab - - -class VcfTypes(enum.Enum): - """The different tr callers that tr_harmonizer supports.""" - - # enum constants must have values, so given them - # redundant values - gangstr = "gangstr" - advntr = "advntr" - hipstr = "hipstr" - eh = "eh" - popstr = "popstr" - - # Don't include the redundant values - # in how enums are printed out - def __repr__(self): - return "<{}.{}>".format(self.__class__.__name__, self.name) - - -def _ToVCFType(vcftype: Union[str, VcfTypes]): - # Convert the input to a VcfTypes enum. - # - # If it is a string, look up the VcfTypes enum. - # If it is already a VcfTypes enum, return it. - # Otherwise, error - - if isinstance(vcftype, str): - if vcftype not in VcfTypes.__members__: - raise ValueError( - ("{} is not an excepted TR vcf type. Expected one of {}").format( - vcftype, list(VcfTypes.__members__) - ) - ) - return VcfTypes[vcftype] - elif isinstance(vcftype, VcfTypes): - return vcftype - else: - raise TypeError( - "{} (of type {}) is not a vcftype".format(vcftype, type(vcftype)) - ) - - -def MayHaveImpureRepeats(vcftype: Union[str, VcfTypes]): - """ - Determine if any of the alleles in this VCF may contain impure repeats. - Specifically, impure repeats include: - * impurities in the underlying sequence (e.g. AAATAAAAA) - * partial repeats (e.g. AATAATAATAA) - This is a guarantee that the caller attempted to call impure repeats, - not that it found any. It also does not guarantee that - all impurities present were identified and called. - Returns - ------- - bool - Indicates whether repeat sequences may be impure - """ - vcftype = _ToVCFType(vcftype) - if vcftype == VcfTypes.gangstr: - return False - if vcftype == VcfTypes.hipstr: - return True - if vcftype == VcfTypes.advntr: - return True - if vcftype == VcfTypes.popstr: - return True - if vcftype == VcfTypes.eh: - return False - - # Can't cover this line because it is future proofing. - # (It explicitly is not reachable now, - # would only be reachable if VcfTypes is expanded in the future) - _UnexpectedTypeError(vcftype) # pragma: no cover - - -def HasLengthRefGenotype(vcftype: Union[str, VcfTypes]): - """ - Determine if the reference alleles of variants are given by length. - If True, then reference alleles for all variants produced by this - caller are specified by length and not by sequence. Sequences are - fabricated according to :py:func:`FabricateAllele`. - If True, then :py:meth:`HasLengthAltGenotypes` will also be true - Returns - ------- - bool - Indicates whether ref alleles are specified by length - """ - vcftype = _ToVCFType(vcftype) - if vcftype == VcfTypes.gangstr: - return False - if vcftype == VcfTypes.hipstr: - return False - if vcftype == VcfTypes.advntr: - return False - if vcftype == VcfTypes.popstr: - return False - if vcftype == VcfTypes.eh: - return True - - # Can't cover this line because it is future proofing. - # (It explicitly is not reachable now, - # would only be reachable if VcfTypes is expanded in the future) - _UnexpectedTypeError(vcftype) # pragma: no cover - - -def HasLengthAltGenotypes(vcftype: Union[str, VcfTypes]): - """ - Determine if the alt alleles of variants are given by length. - If True, then alt alleles for all variants produced by this - caller are specified by length and not by sequence. Sequences are - fabricated according to :py:func:`FabricateAllele`. - Returns - ------- - bool - Indicates whether alt alleles are specified by length - """ - vcftype = _ToVCFType(vcftype) - if vcftype == VcfTypes.gangstr: - return False - if vcftype == VcfTypes.hipstr: - return False - if vcftype == VcfTypes.advntr: - return False - if vcftype == VcfTypes.popstr: - return True - if vcftype == VcfTypes.eh: - return True - - # Can't cover this line because it is future proofing. - # (It explicitly is not reachable now, - # would only be reachable if VcfTypes is expanded in the future) - _UnexpectedTypeError(vcftype) # pragma: no cover - - -def _UnexpectedTypeError(vcftype: Union[str, VcfTypes]): - raise ValueError("self.vcftype is the unexpected type {}".format(vcftype)) - - -def InferVCFType( - vcffile: cyvcf2.VCF, vcftype: Union[str, VcfTypes] = "auto" -) -> VcfTypes: - """ - Infer the genotyping tool used to create the VCF. - When we can, infer from header metadata. - Otherwise, try to infer the type from the ALT field. - Parameters - ---------- - vcffile : - The input VCF file - vcftype : - If it is unclear which of a few VCF callers produced the underlying - VCF (because the output markings of those VCF callers are similar) - this string can be supplied by the user to choose from among - those callers. - Returns - ------- - vcftype : VcfTypes - Type of the VCF file - Raises - ------ - TypeError - If this VCF does not look like it was produced by any supported TR - caller, or if it looks like it could have been produced by more than one - supported TR caller and vcftype == 'auto', or if vcftype doesn't match - any of the callers that could have produced this VCF. - """ - possible_vcf_types = set() - header = vcffile.raw_header.lower() - if "command=" in header and "gangstr" in header: - possible_vcf_types.add(VcfTypes.gangstr) - if "command=" in header and "hipstr" in header: - possible_vcf_types.add(VcfTypes.hipstr) - if "source=advntr" in header: - possible_vcf_types.add(VcfTypes.advntr) - if "source=popstr" in header: - possible_vcf_types.add(VcfTypes.popstr) - if re.search(r"ALT= bool: - """ - Is this a VCF produced by running the Beagle software to impute STRs from a panel generated by an TR genotyper, - or does it consist of STRs directly called by a TR genotyper? - Parameters - ---------- - vcffile : - The input VCF file - Returns - ------- - bool - Whether this is a VCF produced by Beagle - """ - - return bool(re.search("##source=('|\")beagle", vcffile.raw_header.lower())) - - -def HarmonizeRecord(vcftype: Union[str, VcfTypes], vcfrecord: cyvcf2.Variant): - """ - Create a standardized TRRecord object out of a cyvcf2.Variant - object of possibly unknown type. - Parameters - ---------- - vcftype : - Type of vcf to harmonize from. - vcfrecord : - A cyvcf2.Variant Object - Returns - ------- - TRRecord - A TRRecord object built out of the input record - """ - vcftype = _ToVCFType(vcftype) - if vcftype == VcfTypes.gangstr: - return _HarmonizeGangSTRRecord(vcfrecord) - if vcftype == VcfTypes.hipstr: - return _HarmonizeHipSTRRecord(vcfrecord) - if vcftype == VcfTypes.advntr: - return _HarmonizeAdVNTRRecord(vcfrecord) - if vcftype == VcfTypes.eh: - return _HarmonizeEHRecord(vcfrecord) - if vcftype == VcfTypes.popstr: - return _HarmonizePopSTRRecord(vcfrecord) - - # Can't cover this line because it is future proofing. - # (It explicitly is not reachable now, - # would only be reachable if VcfTypes is expanded in the future) - _UnexpectedTypeError(vcftype) # pragma: no cover - - -def _HarmonizeGangSTRRecord(vcfrecord: cyvcf2.Variant): - """ - Turn a cyvcf2.Variant with GangSTR content into a TRRecord. - Parameters - ---------- - vcfrecord : - A cyvcf2.Variant Object - Returns - ------- - TRRecord - """ - if vcfrecord.INFO.get("RU") is None: - raise TypeError( - "Record at {}:{} is missing mandatory GangSTR info field RU. ".format( - vcfrecord.CHROM, vcfrecord.POS - ) - + _beagle_error - ) - if vcfrecord.INFO.get("VID") is not None: - raise TypeError( - "Trying to read an AdVNTR record as a GangSTR record {}:{}".format( - vcfrecord.CHROM, vcfrecord.POS - ) - ) - if vcfrecord.INFO.get("VARID") is not None: - raise TypeError( - "Trying to read an EH record as a GangSTR record {}:{}".format( - vcfrecord.CHROM, vcfrecord.POS - ) - ) - ref_allele = vcfrecord.REF.upper() - if vcfrecord.ALT: - alt_alleles = _UpperCaseAlleles(vcfrecord.ALT) - else: - alt_alleles = [] - motif = vcfrecord.INFO["RU"].upper() - record_id = None - - return TRRecord( - vcfrecord, - ref_allele, - alt_alleles, - motif, - record_id, - "Q" if vcfrecord.INFO.get("IMP") is None else None, - ) - - -def _HarmonizeHipSTRRecord(vcfrecord: cyvcf2.Variant): - """ - Turn a cyvcf2.Variant with HipSTR content into a TRRecord. - Parameters - ---------- - vcfrecord : - A cyvcf2.Variant Object - Returns - ------- - TRRecord - """ - if ( - vcfrecord.INFO.get("START") is None - or vcfrecord.INFO.get("END") is None - or vcfrecord.INFO.get("PERIOD") is None - ): - raise TypeError( - "Record at {}:{} is missing one of the mandatory HipSTR info fields START," - " END, PERIOD. ".format(vcfrecord.CHROM, vcfrecord.POS) - + _beagle_error - ) - # determine full alleles and trimmed alleles - pos = int(vcfrecord.POS) - start_offset = int(vcfrecord.INFO["START"]) - pos - pos_end_offset = int(vcfrecord.INFO["END"]) - pos - neg_end_offset = pos_end_offset + 1 - len(vcfrecord.REF) - - if start_offset == 0 and neg_end_offset == 0: - full_alleles = None - else: - if vcfrecord.ALT: - full_alts = _UpperCaseAlleles(vcfrecord.ALT) - else: - full_alts = [] - - full_alleles = (vcfrecord.REF.upper(), full_alts) - - # neg_end_offset is the number of flanking non repeat bp to remove - # from the end of each allele - # e.g. 'AAAT'[0:-1] == 'AAA' - # however, if neg_end_offset == 0, then we would get - # 'AAAA'[1:0] == '' which is not the intent - # so we need an if statement to instead write 'AAAA'[0:] - # which gives us 'AAAA' - if neg_end_offset == 0: - ref_allele = vcfrecord.REF[start_offset:].upper() - if vcfrecord.ALT: - alt_alleles = [] - for alt in vcfrecord.ALT: - alt_alleles.append(str(alt)[start_offset:].upper()) - else: - alt_alleles = [] - else: - ref_allele = vcfrecord.REF[start_offset:neg_end_offset].upper() - if vcfrecord.ALT: - alt_alleles = [] - for alt in vcfrecord.ALT: - alt_alleles.append(str(alt)[start_offset:neg_end_offset].upper()) - else: - alt_alleles = [] - - # Get the motif. - # Hipstr doesn't tell us this explicitly, so figure it out - motif = InferRepeatSequence(ref_allele[start_offset:], vcfrecord.INFO["PERIOD"]) - record_id = vcfrecord.ID - - return TRRecord( - vcfrecord, - ref_allele, - alt_alleles, - motif, - record_id, - "Q" if vcfrecord.INFO.get("IMP") is None else None, - harmonized_pos=int(vcfrecord.INFO["START"]), - full_alleles=full_alleles, - ) - - -def _HarmonizeAdVNTRRecord(vcfrecord: cyvcf2.Variant): - """ - Turn a cyvcf2.Variant with adVNTR content into a TRRecord. - Parameters - ---------- - vcfrecord : - A cyvcf2.Variant Object - Returns - ------- - TRRecord - """ - if vcfrecord.INFO.get("RU") is None or vcfrecord.INFO.get("VID") is None: - raise TypeError( - "Record at {}:{} is missing one of the mandatory ADVNTR info fields RU," - " VID. ".format(vcfrecord.CHROM, vcfrecord.POS) - + _beagle_error - ) - ref_allele = vcfrecord.REF.upper() - if vcfrecord.ALT: - alt_alleles = _UpperCaseAlleles(vcfrecord.ALT) - else: - alt_alleles = [] - motif = vcfrecord.INFO["RU"].upper() - record_id = vcfrecord.INFO["VID"] - - return TRRecord( - vcfrecord, - ref_allele, - alt_alleles, - motif, - record_id, - "ML" if vcfrecord.INFO.get("IMP") is None else None, - ) - - -# def _PHREDtoProb(phred: int) -> float: -# """Convert PHRED score to probability -# -# Notes -# ----- -# Per https://en.wikipedia.org/wiki/Phred_quality_score -# """ -# return 10**(-phred/10) - - -# def _ConvertPLtoQualityProb(PL: List[int]) -> float: -# """ -# Convert a list of PHRED-scaled genotype probabilities to the -# unscaled probability of the single most likely genotype.# -# -# Notes -# ----- -# PHRED scaling is not very accurate around numbers close to 1 -# unfortunately, so for PHRED score of 0, instead calculate the probability -# by 1 - sum(probabilities of other genotypes) -# """ -# -# max_likelihood = min(PL) -# if max_likelihood != 0: -# return _PHREDtoProb(max_likelihood) -# -# sum_other_likelihoods = 0.0 -# for phred_likelihood in PL: -# if phred_likelihood == 0: -# continue -# sum_other_likelihoods += _PHREDtoProb(phred_likelihood) -# return max(_PHREDtoProb(1), 1 - sum_other_likelihoods) - - -def _HarmonizePopSTRRecord(vcfrecord: cyvcf2.Variant): - """ - Turn a cyvcf2.Variant with popSTR content into a TRRecord. - Parameters - ---------- - vcfrecord : - A cyvcf2.Variant Object - Returns - ------- - TRRecord - """ - if vcfrecord.INFO.get("Motif") is None: - raise TypeError( - "Record at {}:{} is missing mandatory PopSTR info field MOTIF".format( - vcfrecord.CHROM, vcfrecord.POS - ) - ) - ref_allele = vcfrecord.REF.upper() - motif = vcfrecord.INFO["Motif"].upper() - record_id = vcfrecord.ID - - if vcfrecord.ALT: - alt_allele_lengths = [] - for alt in vcfrecord.ALT: - alt = str(alt) - if alt[0] != "<" or alt[-1] != ">": - raise TypeError( - "This record does not look like a PopSTR" - " record. Alt alleles were not formatted" - " as expected" - ) - alt_allele_lengths.append(float(alt[1:-1])) - else: - alt_allele_lengths = [] - - return TRRecord( - vcfrecord, - ref_allele, - None, - motif, - record_id, - None, - alt_allele_lengths=alt_allele_lengths, - ) - - -def _HarmonizeEHRecord(vcfrecord: cyvcf2.Variant): - """ - Turn a cyvcf2.Variant with EH content into a TRRecord. - Parameters - ---------- - vcfrecord : - A cyvcf2.Variant Object - Returns - ------- - TRRecord - """ - if vcfrecord.INFO.get("VARID") is None or vcfrecord.INFO.get("RU") is None: - raise TypeError( - "Record at {}:{} is missing one of the mandatory ExpansionHunter info" - " fields VARID, RU. ".format(vcfrecord.CHROM, vcfrecord.POS) - + _beagle_error - ) - record_id = vcfrecord.INFO["VARID"] - motif = vcfrecord.INFO["RU"].upper() - ref_allele_length = int(vcfrecord.INFO["RL"]) / len(motif) - if vcfrecord.ALT: - alt_allele_lengths = [] - for alt in vcfrecord.ALT: - alt = str(alt) - if alt[:4] != " int: - """ - Return the maximum ploidy of any sample at this locus. - All genotypes will be a tuple of that many haplotypes, - where samples with a smaller ploidy than that - will have haplotypes at the end of the tuple set to ',' - (for string genotypes) or -2 (for index or length genotypes) - """ - return self.vcfrecord.ploidy - - def GetNumSamples(self) -> int: - """ - Return the number of samples at this locus (called or not). - Same as the number of samples in the overall vcf - """ - return self.vcfrecord.genotype.n_samples - - def GetGenotypeIndicies(self) -> Optional[np.ndarray]: - """ - Get an array of genotype indicies across all samples. - A genotype index is a number 0, 1, 2 ... - where 0 corresponds to the reference allele, - 1 to the first alt allele, 2 to the second, etc. - The array is an array of ints with one row per sample. - The number of columns is the maximum ploidy of any sample - (normally 2) plus 1 for phasing. - All but the final column represent the index of the genotypes - of each call. - The final column has values 0 for unphased sampels or 1 for phased. - So a sample with gt '0|2' would be represented by the row [0, 2, 1] - and a sample with gt '3/0' would be represented by the row [3, 0, 0]. - Uncalled haplotypes (represented by '.' in the VCF) are represented - by '-1' genotypes. If the sample has fewer haplotypes than the - maximum ploidy of all samples at this locus, then the row is padded - with -2s, so a haploid sample with gt '1' where other samples - are diploid would be represented by the row [1, -2, 0]. - If all the genotype columns for a sample are negative then the - sample is a no call. Note: the value of the phasing - column is unspecified for haploid or no-call samples. - Returns - ------- - Optional[np.ndarray] - The numpy array described above, of type int. - If there are no samples in the vcf this record comes from - then return None instead - """ - if self.vcfrecord.genotype is None: - return None - return self.vcfrecord.genotype.array() - - def GetCalledSamples(self, strict: bool = True) -> Optional[np.ndarray]: - """ - Get an array listing which samples have been called at this locus. - Parameters - ---------- - strict : - By default genotypes such as '1/.' are considered not called - because at least one of the haplotypes present is not called. - Set strict = False to mark these as being called. - Note: genotypes having lesser ploidy will not be marked - as no calls even when strict = True (e.g. if some samples - have tetraploid genotypes at this locus, a genotype of '1/2/2' - will be marked as called even though it is triploid) - Returns - ------- - Optional[np.ndarray] - A bool array of length equal to the number of samples, - where true indicates a sample has been called - and false indicates otherwise. - If there are no samples in the vcf this record comes from - then return None instead - """ - gt_idxs = self.GetGenotypeIndicies() - if gt_idxs is None: - return None - - if strict: - return ~np.any(gt_idxs[:, :-1] == -1, axis=1) - else: - return ~np.all( - np.logical_or(gt_idxs[:, :-1] == -1, gt_idxs[:, :-1] == -2), axis=1 - ) - - def GetSamplePloidies(self) -> Optional[np.ndarray]: - """ - Get an array listing the ploidies of each sample - Returns - ------- - Optional[np.ndarray] - An array of positive ints with length equal to the - number of samples where each entry denotes the - number of genotypes for each sample at this locus - (including no calls) - If there are no samples in the vcf this record comes from - then return None instead - """ - gt_idxs = self.GetGenotypeIndicies() - if gt_idxs is None: - return None - - return gt_idxs.shape[1] - 1 - np.sum(gt_idxs[:, :-1] == -2, axis=1) - - def GetCallRate(self, strict: bool = True) -> float: - """ - Return the call rate at this locus. - Parameters - ---------- - strict : - By default genotypes such as '1/.' are considered not called - because at least one of the haplotypes present is not called. - Set strict = False to mark these as being called. - Note: genotypes having lesser ploidy will not be marked - as no calls even when strict = True (e.g. if some samples - have tetraploid genotypes at this locus, a genotype of '1/2/2' - will be marked as called even though it is triploid) - Returns - ------- - The fraction of the samples at this locus that have been - called. If there are no samples in the vcf this record comes from - then return np.nan instead - """ - called_samples = self.GetCalledSamples(strict=strict) - if called_samples is None: - return None - else: - return np.sum(called_samples) / called_samples.shape[0] - - def _GetStringGenotypeArray(self, idx_gts: np.ndarray, seq_alleles: List[str]): - max_len = max(len(allele) for allele in seq_alleles) - seq_array = np.empty(idx_gts.shape, dtype=" Optional[np.ndarray]: - """ - Get an array of string genotypes for each sample. - The array is as described in :py:meth:`GetGenotypeIndicies` - except that the indicies are replaced by their corresponding - sequences, -1 indicies (nocalls) are replaced by '.', - -2 indicies (not present due to smaller ploidy) are replaced - by ',', and the phasing bits (0 or 1) are replaced by the strings - '0' or '1'. - Will not include flanking base pairs. To get genotypes that include - flanking base pairs (for callers that call those), use - :py:meth:`GetFullStringGenotypes`. For callers that include flanking base pairs - it is possible that some of the alleles in the regular string genotypes - (with the flanks stripped) will be identical. In this case, you may - use :py:meth:`UniqueStringGenotypeMapping` to get a canonical unique subset - of indicies which represent all possible alleles. - Note that some TR callers will only call allele lengths, not allele - sequences. In such a case, this method will return a fabricated - sequence based on the called length (see - :py:meth:`FabricateAllele`) and - a warning will be raised. This may not be intended - - use :py:meth:`GetLengthGenotypes` for a fully caller agnostic - way of handling genotypes. - This method is inefficient for many samples, consider either using - length genotypes (:py:meth:`GetLengthGenotypes`), or - using genotype indicies (:py:meth:`GetGenotypeIndicies`) and - accessing string genotypes as needed through the fields ref_allele and - alt_alleles, instead. - Returns - ------- - Optional[np.ndarray] - The numpy array described above, of type ' Optional[np.ndarray]: - """ - Get an array of full string genotypes for each sample. - See :py:meth:`GetStringGenotypes` for details and - limitations of string genotypes. - If the sample does not have full genotypes that are distinct - from its regular string genotypes (because no flanking base pairs - were called) then the regular string genotypes are returned. - Returns - ------- - Optional[np.ndarray] - The numpy array described above, of type ' Dict[int, int]: - """ - Get a mapping whose values are unique string genotype indicies. - Return - ------ - Dict[int, int] - A mapping allele idx -> allele idx - whose keys are all allele indicies and whose values are a - subset of indicies which represents all the unique regular - string alleles for this variant. For almost all records, - this will be a mapping from each index to itself. For some - records with full string genotypes that include flanking base - pairs, some of the regular string alleles will be identical. - In this case, only one of those allele's indicies will be in the - set of values of this dictionary, and all identical alleles - will map to that one index. - """ - mapping = {} - if not self.HasFullStringGenotypes(): - for idx in range(len(self.alt_alleles) + 1): - mapping[idx] = idx - else: - allele_to_idx = {} - alleles = [self.ref_allele] - alleles.extend(self.alt_alleles) - for idx, allele in enumerate(alleles): - if allele not in allele_to_idx: - allele_to_idx[allele] = idx - mapping[idx] = idx - else: - mapping[idx] = allele_to_idx[allele] - - return mapping - - def UniqueStringGenotypes(self) -> Set[int]: - """ - Find allele indicies corresponding to the unique alleles. - Equivalent to calling - :code:`set(UniqueStringGenotypeMapping().values())` - Returns - ------- - Set[int] - The indicies of the unique string alleles - """ - return set(self.UniqueStringGenotypeMapping().values()) - - def GetLengthGenotypes(self) -> Optional[np.ndarray]: - """ - Get an array of length genotypes for each sample. - Represents the sample's genotype in terms of the number - of repeats of the motif in each allele. - Returns a pair of floats - alleles including partial repeats - or other impurities may have noninteger lengths. - The array is as described in :py:meth:`GetGenotypeIndicies` - except that indicies are replaced by their length genotypes. - -1s, -2s and the phasing bits are not modified. - For records with both regular and full sequences (those with flanking - bps), this returns the length of the regular sequences - Returns - ------- - Optional[np.ndarray] - The numpy array described above, of type float - If there are no samples in the vcf this record comes from - then return None instead - """ - idx_gts = self.GetGenotypeIndicies() - if idx_gts is None: - return None - - len_gts = np.empty(idx_gts.shape) - len_gts[:, -1] = idx_gts[:, -1] - - allele_lens = [] - allele_lens.append(self.ref_allele_length) - allele_lens.extend(self.alt_allele_lengths) - - for idx, allele_len in enumerate(allele_lens): - len_gts[:, :-1][idx_gts[:, :-1] == idx] = allele_len - - len_gts[idx_gts == -1] = -1 - len_gts[idx_gts == -2] = -2 - - return len_gts - - def UniqueLengthGenotypeMapping(self) -> Dict[int, int]: - """ - Get a mapping whose values are unique string genotype indicies. - Return - ------ - genotypeMapping : Dict[int, int] - A mapping allele idx -> allele idx - whose keys are all allele indicies and whose values are a - subset of indicies which represents all the unique - length alleles for this variant. For variants where - multiple alleles have the same length, all will map to - a single index from among those alleles. - """ - mapping = {} - allele_to_idx = {} - alleles = [self.ref_allele] - alleles.extend(self.alt_alleles) - for idx, allele in enumerate(alleles): - allele = len(allele) - if allele not in allele_to_idx: - allele_to_idx[allele] = idx - mapping[idx] = idx - else: - mapping[idx] = allele_to_idx[allele] - - return mapping - - def UniqueLengthGenotypes(self) -> Set[int]: - """ - Find allele indicies corresponding to the unique length alleles. - Equivalent to calling - :code:`set(UniqueLengthGenotypeMapping().values())` - Returns - ------- - Set[int] - The indicies of the unique string alleles - """ - return set(self.UniqueLengthGenotypeMapping().values()) - - def HasFullStringGenotypes(self) -> bool: - """ - Determine if this record has full string genotypes. - Returns - ------- - bool: - True iff :py:meth:`GetFullStringGenotypes` will return - a different value than :py:meth:`GetStringGenotypes` for some - alleles. - """ - return self.full_alleles is not None - - def HasFabricatedRefAllele(self) -> bool: - """ - Determine if this record has a fabricated ref allels. - Returns - ------- - bool: - True iff ref_allele_length was passed to this - record's constructor. - """ - return self.has_fabricated_ref_allele - - def HasFabricatedAltAlleles(self) -> bool: - """ - Determine if this record has fabricated alt alleles. - Returns - ------- - bool: - True iff alt_allele_lengths was passed to this - record's constructor. - """ - return self.has_fabricated_alt_alleles - - def GetGenotypeCounts( - self, - sample_index: Optional[Any] = None, - uselength: bool = True, - index: bool = False, - fullgenotypes: bool = False, - include_nocalls: bool = False, - ) -> Dict[tuple, int]: - """ - Get the counts of each genotype for a record. - For samples with a lower ploidy than the max ploidy among all samples, - the -2 placeholder haplotypes are sorted to the beginning of the call - (e.g. (-2, 5) instead of (5, -2)) - This currently returns unphased genotypes (with no phasing column), it could be - extend to have an option to respect phasing - Parameters - ---------- - sample_index : - Used to index the numpy array of samples. So can be a numpy array - of sample indicies, or a bool array with length of the number - of samples, etc. - If None, then all samples are included. - uselength : - If True, represent alleles as lengths - else represent as strings - index : - If True, represent alleles as indexes (0 = ref, 1 = first_alt, - etc.) instead of sequences or lengths - fullgenotypes : - If True, include flanking basepairs in allele representations. - Only makes sense when expliictly stating uselength=False. - Cannot be combined with index. - include_nocalls: - If False, all genotypes with one or more uncalled haplotypes - (-1 or '.') are excluded from the returned dictionary, - they are included if True. Genotypes with lower ploidy (-2 or ',') - are included regardless. - Returns - ------- - genotype_counts: Dict[tuple, int] - Gives the count of each genotype. - Genotypes are represented as tuples of alleles, - where the type of allele representation is determined by the uselength, index - and fullgenotypes optional parameters. - """ - # TODO test these - if uselength and fullgenotypes: - raise ValueError("Can't specify both uselength and fullgenotypes") - if index and not uselength: - raise ValueError( - "Specified uselength=False and index at the same" - " time, these are mutually exclusive options" - ) - - if index: - gts = self.GetGenotypeIndicies() - nocall_entry = -1 - elif uselength and not index: - gts = self.GetLengthGenotypes() - nocall_entry = -1 - elif not uselength and not fullgenotypes: - gts = self.GetStringGenotypes() - nocall_entry = "." - elif fullgenotypes: - gts = self.GetFullStringGenotypes() - nocall_entry = "." - - if gts is None: - return {} - - gts = gts[:, :-1] # remove phasing - gts = np.sort(gts, axis=1) - - if sample_index is not None: - gts = gts[sample_index, :] - - genotypes, counts = np.unique(gts, axis=0, return_counts=True) - count_dict = dict(zip(tuple(map(tuple, genotypes)), counts)) - - if not include_nocalls: - gts_to_remove = set() - for genotype in count_dict: - if nocall_entry in genotype: - gts_to_remove.add(genotype) - for gt in gts_to_remove: - del count_dict[gt] - - return count_dict - - def GetAlleleCounts( - self, - sample_index: Optional[Any] = None, - *, - uselength: bool = True, - index: bool = False, - fullgenotypes: bool = False - ) -> Dict[Any, int]: - """ - Get the counts of each allele for a record. - This does not return counts of no calls as it is not - clear how many 'no call alleles' would be present per no call - Alleles that are not called in any sample are not present - in the returned dictionary - Parameters - ---------- - sample_index : - Used to index the numpy array of samples. So can be a numpy array - of sample indicies, or a bool array with length of the number - of samples, etc. - If None, then all samples are included. - uselength : bool, optional - If True, represent alleles a lengths - else represent as strings - index : - If True, represent alleles as indexes (0 = ref, 1 = first_alt, - etc.) instead of sequences or lengths - fullgenotypes : - If True, include flanking basepairs in allele representations - Only makes sense when expliictly stating uselength=False. - Cannot be combined with index. - Returns - ------- - allele_counts: Dict[Any, int] - Gives the count of each allele. - The type of allele representation is determined by the uselength, index - and fullgenotypes optional parameters. - """ - # TODO test these - if uselength and fullgenotypes: - raise ValueError("Can't specify both uselength and fullgenotypes") - if index and not uselength: - raise ValueError( - "Specified uselength=False and index at the same" - " time, these are mutually exclusive options" - ) - if index: - gts = self.GetGenotypeIndicies() - nocall_entry = -1 - lowploidy_entry = -2 - elif uselength and not index: - gts = self.GetLengthGenotypes() - nocall_entry = -1 - lowploidy_entry = -2 - elif not uselength and not fullgenotypes: - gts = self.GetStringGenotypes() - nocall_entry = "." - lowploidy_entry = "," - elif fullgenotypes: - gts = self.GetFullStringGenotypes() - nocall_entry = "." - lowploidy_entry = "," - - if gts is None: - return {} - - gts = gts[:, :-1] # remove phasing - - if sample_index is not None: - gts = gts[sample_index, :] - - # remove no calls and missing haplotypes - gts = gts[gts != nocall_entry] - gts = gts[gts != lowploidy_entry] - - alleles, counts = np.unique(gts, return_counts=True) - return dict(zip(alleles, counts)) - - def GetAlleleFreqs( - self, - sample_index: Optional[Any] = None, - *, - uselength: bool = True, - index: bool = False, - fullgenotypes: bool = False - ) -> Dict[Any, float]: - """ - Get the frequencies of each allele for a record. - Parameters - ---------- - sample_index : - Used to index the numpy array of samples. So can be a numpy array - of sample indicies, or a bool array with length of the number - of samples, etc. - If None, then all samples are included. - uselength : - If True, represent alleles a lengths - else represent as strings - index : - If True, represent alleles as indexes (0 = ref, 1 = first_alt, - etc.) instead of sequences or lengths - fullgenotypes : - If True, include flanking basepairs in allele representations. - Only makes sense when expliictly stating uselength=False. - Cannot be combined with index. - Returns - ------- - allele_freqs: Dict[Any, float] - Gives the frequency of each allele among called samples - The type of allele representation is determined by the uselength, index - and fullgenotypes optional parameters. - """ - allele_counts = self.GetAlleleCounts( - uselength=uselength, - index=index, - fullgenotypes=fullgenotypes, - sample_index=sample_index, - ) - total = float(sum(allele_counts.values())) - return {key: value / total for key, value in allele_counts.items()} - - def GetMaxAllele(self, sample_index: Optional[Any] = None) -> float: - """ - Get the maximum allele length called in a record. - - Represents lengths in terms of the number of repeats of the motif. - The longest allele may have a noninteger length if it includes - partial repeats or other impurities. - For records with both regular and full sequences (those with flanking - bps), this returns the length of the regular sequences - Parameters - ---------- - sample_index : - Used to index the numpy array of samples. So can be a numpy array - of sample indicies, or a bool array with length of the number - of samples, etc. - If None, then all samples are included. - Returns - ------- - maxallele : float - The maximum allele length called (in number of repeat units), - or nan if no alleles called - """ - # TODO should we have GetMinAllele too? - # TODO should we have an option for grabbing - # the index of the longest allele? - alleles = self.GetAlleleCounts(uselength=True, sample_index=sample_index).keys() - if len(alleles) == 0: - return np.nan - return max(alleles) - - def HasQualityScores(self) -> bool: - """ - Does this TRRecord contain quality scores for each of its calls? - If present, the meaning and reliability of these scores is - genotyper dependent, see the doc section :ref:`Quality Scores`. - Return - ------ - boolean: - Whether or not a FORMAT field that could be interpreted as a - quality score has been identified - """ - return self.quality_field is not None and self.quality_field in self.format - - def GetQualityScores(self) -> np.ndarray: - """ - Get the quality scores of the calls for each sample. - The meaning and reliability of these scores is genotyper - dependent, see the doc section :ref:`Quality Scores`. - Returns - ------- - np.ndarray : - An array of quality score floats, one row per sample - Samples which were not called have the value np.nan - """ - if not self.HasQualityScores(): - raise TypeError( - "This TRRecord does not have a corresponding quality score field" - ) - quality_val = self.format[self.quality_field] - transform = self.quality_score_transform - if transform is None: - return quality_val - else: - return np.apply_along_axis(transform, 0, quality_val) - - def __str__(self): - """Generate a summary of the variant described by this record.""" - record_id = self.record_id - if record_id is None: - record_id = "{}:{}".format(self.vcfrecord.CHROM, self.vcfrecord.POS) - if self.HasFullStringGenotypes(): - string = "{} {} {} ".format(record_id, self.motif, self.full_alleles[0]) - string += ",".join(self.full_alleles[1]) - return string - - if self.HasFabricatedRefAllele(): - string = "{} {} n_reps:{} ".format( - record_id, self.motif, self.ref_allele_length - ) - else: - string = "{} {} {} ".format(record_id, self.motif, self.ref_allele) - - if len(self.alt_alleles) == 0: - string += "." - elif self.HasFabricatedAltAlleles(): - string += ",".join( - "n_reps:" + str(length) for length in self.alt_allele_lengths - ) - else: - string += ",".join(self.alt_alleles) - - return string - - -class TRRecordHarmonizer: - """ - Class producing a uniform interface for accessing TR VCF records. - Produces the same output interface regardless of the - tool that created the input VCF. - The main purpose of this class is to infer which tool - a VCF came from, and appropriately convert its records - to TRRecord objects. - This class provides the object oriented paradigm for iterating - through a TR vcf. If you wish to use the functional paradigm and - provide the cyvcf2.Variant objects yourself, use the top-level - functions in this module. - Parameters - ---------- - vcffile : cyvcf2.VCF instance - vcftype : {'auto', 'gangstr', 'advntr', 'hipstr', 'eh', 'popstr'}, optional - Type of the VCF file. Default='auto'. - If vcftype=='auto', attempts to infer the type. - Attributes - ---------- - vcffile : cyvcf2.VCF instance - vcftype : enum - Type of the VCF file. Must be included in VcfTypes - Raises - ------ - TypeError - If the type of the VCF cannot be properly inferred. - See :py:meth:`InferVCFType` for more details. - """ - - def __init__(self, vcffile: cyvcf2.VCF, vcftype: Union[str, VcfTypes] = "auto"): - self.vcffile = vcffile - self.vcftype = InferVCFType(vcffile, vcftype) - - def MayHaveImpureRepeats(self) -> bool: - """ - Determine if any of the alleles in this VCF may contain impure repeats. - See Also - -------- - tr_harmonizer.MayHaveImpureRepeats - """ - return MayHaveImpureRepeats(self.vcftype) - - def HasLengthRefGenotype(self) -> bool: - """ - Determine if the reference alleles of variants are given by length. - See Also - -------- - tr_harmonizer.HasLengthRefGenotype - """ - return HasLengthRefGenotype(self.vcftype) - - def HasLengthAltGenotypes(self) -> bool: - """ - Determine if the alt alleles of variants are given by length. - See Also - -------- - tr_harmonizer.HasLengthAltGenotypes - """ - return HasLengthAltGenotypes(self.vcftype) - - def HasQualityScore(self) -> bool: - """ - Does this VCF contain quality scores for each of its calls? - If present, the meaning and reliability of these scores is - genotyper dependent, see the doc section :ref:`Quality Scores`. - Returns - ------- - bool - Whether or not a FORMAT field that could be interpreted as a - quality score has been identified - """ - if self.vcftype == VcfTypes.gangstr: - return "FORMAT= bool: - """ - Is this a VCF produced by running the Beagle software to impute STRs from a panel generated by an TR genotyper? - See Also - -------- - tr_harmonizer.IsBeagleVCF - """ - return IsBeagleVCF(self.vcffile) - - def __iter__(self) -> Iterator[TRRecord]: - """Iterate over TRRecords produced from the underlying vcf.""" - return self - - def __next__(self) -> TRRecord: - """Iterate over TRRecord produced from the underlying vcf.""" - return HarmonizeRecord(self.vcftype, next(self.vcffile)) - - -# TODO check all users of this class for new options +# type: ignore +""" +Utilities for harmonizing tandem repeat VCF records. + +Handles VCFs generated by various TR genotyping tools +""" +import re +import enum +import warnings +from typing import ( + Any, + Callable, + Dict, + Generator, + Iterator, + List, + Optional, + Set, + Tuple, + Union, +) + +import cyvcf2 +import numpy as np + +from . import utils + + +# List of supported VCF types +# TODO: add Beagle +# TODO: add support for tool version numbers + +_beagle_error = ( + "If this file was imputed by Beagle, did you remember to copy the info fields over?" +) + + +class VcfTypes(enum.Enum): + """The different tr callers that tr_harmonizer supports.""" + + # enum constants must have values, so given them + # redundant values + gangstr = "gangstr" + advntr = "advntr" + hipstr = "hipstr" + eh = "eh" + popstr = "popstr" + + # Don't include the redundant values + # in how enums are printed out + def __repr__(self): + return "<{}.{}>".format(self.__class__.__name__, self.name) + + +class TRDosageTypes(enum.Enum): + """Ways to compute TR dosages.""" + + bestguess = "bestguess" + beagleap = "beagleap" + bestguess_norm = "bestguess_norm" + beagleap_norm = "beagleap_norm" + + def __repr__(self): + return "<{}.{}>".format(self.__class__.__name__, self.name) + + +def _ToVCFType(vcftype: Union[str, VcfTypes]): + # Convert the input to a VcfTypes enum. + # + # If it is a string, look up the VcfTypes enum. + # If it is already a VcfTypes enum, return it. + # Otherwise, error + + if isinstance(vcftype, str): + if vcftype not in VcfTypes.__members__: + raise ValueError( + ("{} is not an excepted TR vcf type. Expected one of {}").format( + vcftype, list(VcfTypes.__members__) + ) + ) + return VcfTypes[vcftype] + elif isinstance(vcftype, VcfTypes): + return vcftype + else: + raise TypeError( + "{} (of type {}) is not a vcftype".format(vcftype, type(vcftype)) + ) + + +def MayHaveImpureRepeats(vcftype: Union[str, VcfTypes]): + """ + Determine if any of the alleles in this VCF may contain impure repeats. + + Specifically, impure repeats include: + + * impurities in the underlying sequence (e.g. AAATAAAAA) + * partial repeats (e.g. AATAATAATAA) + + This is a guarantee that the caller attempted to call impure repeats, + not that it found any. It also does not guarantee that + all impurities present were identified and called. + + Returns + ------- + bool + Indicates whether repeat sequences may be impure + """ + vcftype = _ToVCFType(vcftype) + if vcftype == VcfTypes.gangstr: + return False + if vcftype == VcfTypes.hipstr: + return True + if vcftype == VcfTypes.advntr: + return True + if vcftype == VcfTypes.popstr: + return True + if vcftype == VcfTypes.eh: + return False + + # Can't cover this line because it is future proofing. + # (It explicitly is not reachable now, + # would only be reachable if VcfTypes is expanded in the future) + _UnexpectedTypeError(vcftype) # pragma: no cover + + +def HasLengthRefGenotype(vcftype: Union[str, VcfTypes]): + """ + Determine if the reference alleles of variants are given by length. + + If True, then reference alleles for all variants produced by this + caller are specified by length and not by sequence. Sequences are + fabricated according to :py:func:`trtools.utils.utils.FabricateAllele`. + + If True, then :py:meth:`HasLengthAltGenotypes` will also be true + + Returns + ------- + bool + Indicates whether ref alleles are specified by length + """ + vcftype = _ToVCFType(vcftype) + if vcftype == VcfTypes.gangstr: + return False + if vcftype == VcfTypes.hipstr: + return False + if vcftype == VcfTypes.advntr: + return False + if vcftype == VcfTypes.popstr: + return False + if vcftype == VcfTypes.eh: + return True + + # Can't cover this line because it is future proofing. + # (It explicitly is not reachable now, + # would only be reachable if VcfTypes is expanded in the future) + _UnexpectedTypeError(vcftype) # pragma: no cover + + +def HasLengthAltGenotypes(vcftype: Union[str, VcfTypes]): + """ + Determine if the alt alleles of variants are given by length. + + If True, then alt alleles for all variants produced by this + caller are specified by length and not by sequence. Sequences are + fabricated according to :py:func:`trtools.utils.utils.FabricateAllele`. + + Returns + ------- + bool + Indicates whether alt alleles are specified by length + """ + vcftype = _ToVCFType(vcftype) + if vcftype == VcfTypes.gangstr: + return False + if vcftype == VcfTypes.hipstr: + return False + if vcftype == VcfTypes.advntr: + return False + if vcftype == VcfTypes.popstr: + return True + if vcftype == VcfTypes.eh: + return True + + # Can't cover this line because it is future proofing. + # (It explicitly is not reachable now, + # would only be reachable if VcfTypes is expanded in the future) + _UnexpectedTypeError(vcftype) # pragma: no cover + + +def _UnexpectedTypeError(vcftype: Union[str, VcfTypes]): + raise ValueError("self.vcftype is the unexpected type {}".format(vcftype)) + + +def InferVCFType( + vcffile: cyvcf2.VCF, vcftype: Union[str, VcfTypes] = "auto" +) -> VcfTypes: + """ + Infer the genotyping tool used to create the VCF. + + When we can, infer from header metadata. + Otherwise, try to infer the type from the ALT field. + + Parameters + ---------- + vcffile : + The input VCF file + vcftype : + If it is unclear which of a few VCF callers produced the underlying + VCF (because the output markings of those VCF callers are similar) + this string can be supplied by the user to choose from among + those callers. + + Returns + ------- + vcftype : VcfTypes + Type of the VCF file + + Raises + ------ + TypeError + If this VCF does not look like it was produced by any supported TR + caller, or if it looks like it could have been produced by more than one + supported TR caller and vcftype == 'auto', or if vcftype doesn't match + any of the callers that could have produced this VCF. + """ + possible_vcf_types = set() + header = vcffile.raw_header.lower() + if "command=" in header and "gangstr" in header: + possible_vcf_types.add(VcfTypes.gangstr) + if "command=" in header and "hipstr" in header: + possible_vcf_types.add(VcfTypes.hipstr) + if "source=advntr" in header: + possible_vcf_types.add(VcfTypes.advntr) + if "source=popstr" in header: + possible_vcf_types.add(VcfTypes.popstr) + if re.search(r"ALT= bool: + """ + Is this a VCF produced by running the Beagle software to impute STRs from a panel generated by an TR genotyper, + or does it consist of STRs directly called by a TR genotyper? + + Parameters + ---------- + vcffile : + The input VCF file + + Returns + ------- + bool + Whether this is a VCF produced by Beagle + """ + + return bool(re.search("##source=('|\")beagle", vcffile.raw_header.lower())) + + +def HarmonizeRecord(vcftype: Union[str, VcfTypes], vcfrecord: cyvcf2.Variant): + """ + Create a standardized TRRecord object out of a cyvcf2.Variant + object of possibly unknown type. + + Parameters + ---------- + vcfrecord : + A cyvcf2.Variant Object + + Returns + ------- + trrecord : TRRecord + A TRRecord object built out of the input record + """ + vcftype = _ToVCFType(vcftype) + if vcftype == VcfTypes.gangstr: + return _HarmonizeGangSTRRecord(vcfrecord) + if vcftype == VcfTypes.hipstr: + return _HarmonizeHipSTRRecord(vcfrecord) + if vcftype == VcfTypes.advntr: + return _HarmonizeAdVNTRRecord(vcfrecord) + if vcftype == VcfTypes.eh: + return _HarmonizeEHRecord(vcfrecord) + if vcftype == VcfTypes.popstr: + return _HarmonizePopSTRRecord(vcfrecord) + + # Can't cover this line because it is future proofing. + # (It explicitly is not reachable now, + # would only be reachable if VcfTypes is expanded in the future) + _UnexpectedTypeError(vcftype) # pragma: no cover + + +def _HarmonizeGangSTRRecord(vcfrecord: cyvcf2.Variant): + """ + Turn a cyvcf2.Variant with GangSTR content into a TRRecord. + + Parameters + ---------- + vcfrecord : + A cyvcf2.Variant Object + + Returns + ------- + TRRecord + """ + if vcfrecord.INFO.get("RU") is None: + raise TypeError( + "Record at {}:{} is missing mandatory GangSTR info field RU. ".format( + vcfrecord.CHROM, vcfrecord.POS + ) + + _beagle_error + ) + if vcfrecord.INFO.get("VID") is not None: + raise TypeError( + "Trying to read an AdVNTR record as a GangSTR record {}:{}".format( + vcfrecord.CHROM, vcfrecord.POS + ) + ) + if vcfrecord.INFO.get("VARID") is not None: + raise TypeError( + "Trying to read an EH record as a GangSTR record {}:{}".format( + vcfrecord.CHROM, vcfrecord.POS + ) + ) + ref_allele = vcfrecord.REF.upper() + if vcfrecord.ALT: + alt_alleles = _UpperCaseAlleles(vcfrecord.ALT) + else: + alt_alleles = [] + motif = vcfrecord.INFO["RU"].upper() + record_id = None + + return TRRecord( + vcfrecord, + ref_allele, + alt_alleles, + motif, + record_id, + "Q" if vcfrecord.INFO.get("IMP") is None else None, + ) + + +def _HarmonizeHipSTRRecord(vcfrecord: cyvcf2.Variant): + """ + Turn a cyvcf2.Variant with HipSTR content into a TRRecord. + + Parameters + ---------- + vcfrecord : + A cyvcf2.Variant Object + + Returns + ------- + TRRecord + """ + if ( + vcfrecord.INFO.get("START") is None + or vcfrecord.INFO.get("END") is None + or vcfrecord.INFO.get("PERIOD") is None + ): + raise TypeError( + "Record at {}:{} is missing one of the mandatory HipSTR info fields START," + " END, PERIOD. ".format(vcfrecord.CHROM, vcfrecord.POS) + + _beagle_error + ) + # determine full alleles and trimmed alleles + pos = int(vcfrecord.POS) + start_offset = int(vcfrecord.INFO["START"]) - pos + pos_end_offset = int(vcfrecord.INFO["END"]) - pos + neg_end_offset = pos_end_offset + 1 - len(vcfrecord.REF) + + if start_offset == 0 and neg_end_offset == 0: + full_alleles = None + else: + if vcfrecord.ALT: + full_alts = _UpperCaseAlleles(vcfrecord.ALT) + else: + full_alts = [] + + full_alleles = (vcfrecord.REF.upper(), full_alts) + + # neg_end_offset is the number of flanking non repeat bp to remove + # from the end of each allele + # e.g. 'AAAT'[0:-1] == 'AAA' + # however, if neg_end_offset == 0, then we would get + # 'AAAA'[1:0] == '' which is not the intent + # so we need an if statement to instead write 'AAAA'[0:] + # which gives us 'AAAA' + if neg_end_offset == 0: + ref_allele = vcfrecord.REF[start_offset:].upper() + if vcfrecord.ALT: + alt_alleles = [] + for alt in vcfrecord.ALT: + alt_alleles.append(str(alt)[start_offset:].upper()) + else: + alt_alleles = [] + else: + ref_allele = vcfrecord.REF[start_offset:neg_end_offset].upper() + if vcfrecord.ALT: + alt_alleles = [] + for alt in vcfrecord.ALT: + alt_alleles.append(str(alt)[start_offset:neg_end_offset].upper()) + else: + alt_alleles = [] + + # Get the motif. + # Hipstr doesn't tell us this explicitly, so figure it out + motif = utils.InferRepeatSequence( + ref_allele[start_offset:], vcfrecord.INFO["PERIOD"] + ) + record_id = vcfrecord.ID + + return TRRecord( + vcfrecord, + ref_allele, + alt_alleles, + motif, + record_id, + "Q" if vcfrecord.INFO.get("IMP") is None else None, + harmonized_pos=int(vcfrecord.INFO["START"]), + full_alleles=full_alleles, + ) + + +def _HarmonizeAdVNTRRecord(vcfrecord: cyvcf2.Variant): + """ + Turn a cyvcf2.Variant with adVNTR content into a TRRecord. + + Parameters + ---------- + vcfrecord : + A cyvcf2.Variant Object + + Returns + ------- + TRRecord + """ + if vcfrecord.INFO.get("RU") is None or vcfrecord.INFO.get("VID") is None: + raise TypeError( + "Record at {}:{} is missing one of the mandatory ADVNTR info fields RU," + " VID. ".format(vcfrecord.CHROM, vcfrecord.POS) + + _beagle_error + ) + ref_allele = vcfrecord.REF.upper() + if vcfrecord.ALT: + alt_alleles = _UpperCaseAlleles(vcfrecord.ALT) + else: + alt_alleles = [] + motif = vcfrecord.INFO["RU"].upper() + record_id = vcfrecord.INFO["VID"] + + return TRRecord( + vcfrecord, + ref_allele, + alt_alleles, + motif, + record_id, + "ML" if vcfrecord.INFO.get("IMP") is None else None, + ) + + +# def _PHREDtoProb(phred: int) -> float: +# """Convert PHRED score to probability +# +# Notes +# ----- +# Per https://en.wikipedia.org/wiki/Phred_quality_score +# """ +# return 10**(-phred/10) + + +# def _ConvertPLtoQualityProb(PL: List[int]) -> float: +# """ +# Convert a list of PHRED-scaled genotype probabilities to the +# unscaled probability of the single most likely genotype.# +# +# Notes +# ----- +# PHRED scaling is not very accurate around numbers close to 1 +# unfortunately, so for PHRED score of 0, instead calculate the probability +# by 1 - sum(probabilities of other genotypes) +# """ +# +# max_likelihood = min(PL) +# if max_likelihood != 0: +# return _PHREDtoProb(max_likelihood) +# +# sum_other_likelihoods = 0.0 +# for phred_likelihood in PL: +# if phred_likelihood == 0: +# continue +# sum_other_likelihoods += _PHREDtoProb(phred_likelihood) +# return max(_PHREDtoProb(1), 1 - sum_other_likelihoods) + + +def _HarmonizePopSTRRecord(vcfrecord: cyvcf2.Variant): + """ + Turn a cyvcf2.Variant with popSTR content into a TRRecord. + + Parameters + ---------- + vcfrecord : + A cyvcf2.Variant Object + + Returns + ------- + TRRecord + """ + if vcfrecord.INFO.get("Motif") is None: + raise TypeError( + "Record at {}:{} is missing mandatory PopSTR info field MOTIF".format( + vcfrecord.CHROM, vcfrecord.POS + ) + ) + ref_allele = vcfrecord.REF.upper() + motif = vcfrecord.INFO["Motif"].upper() + record_id = vcfrecord.ID + + if vcfrecord.ALT: + alt_allele_lengths = [] + for alt in vcfrecord.ALT: + alt = str(alt) + if alt[0] != "<" or alt[-1] != ">": + raise TypeError( + "This record does not look like a PopSTR" + " record. Alt alleles were not formatted" + " as expected" + ) + alt_allele_lengths.append(float(alt[1:-1])) + else: + alt_allele_lengths = [] + + return TRRecord( + vcfrecord, + ref_allele, + None, + motif, + record_id, + None, + alt_allele_lengths=alt_allele_lengths, + ) + + +def _HarmonizeEHRecord(vcfrecord: cyvcf2.Variant): + """ + Turn a cyvcf2.Variant with EH content into a TRRecord. + + Parameters + ---------- + vcfrecord : + A cyvcf2.Variant Object + + Returns + ------- + TRRecord + """ + if vcfrecord.INFO.get("VARID") is None or vcfrecord.INFO.get("RU") is None: + raise TypeError( + "Record at {}:{} is missing one of the mandatory ExpansionHunter info" + " fields VARID, RU. ".format(vcfrecord.CHROM, vcfrecord.POS) + + _beagle_error + ) + record_id = vcfrecord.INFO["VARID"] + motif = vcfrecord.INFO["RU"].upper() + ref_allele_length = int(vcfrecord.INFO["RL"]) / len(motif) + if vcfrecord.ALT: + alt_allele_lengths = [] + for alt in vcfrecord.ALT: + alt = str(alt) + if alt[:4] != " 0: + self.min_allele_length = min( + self.ref_allele_length, min(self.alt_allele_lengths) + ) + self.max_allele_length = max( + self.ref_allele_length, max(self.alt_allele_lengths) + ) + else: + self.min_allele_length = self.ref_allele_length + self.max_allele_length = self.ref_allele_length + + try: + self._CheckRecord() + except ValueError as e: + raise ValueError( + ("Invalid TRRecord. TRRecord: {} Original record: {}").format( + str(self), str(self.vcfrecord) + ), + e, + ) + + def _CheckRecord(self): + """ + Check that this record is properly constructed. + + Checks that the same number of alt alleles were specified + as in the underlying record and that the full_alleles, if supplied, + contain their corresponding standard alleles + + Raises an error if a check fails + """ + if len(self.alt_alleles) != len(self.vcfrecord.ALT): + raise ValueError( + "Underlying record does not have the same " + "number of alt alleles as given to the TRRecord " + "constructor. Underlying alt alleles: {}, " + " constructor alt alleles: {}".format( + self.vcfrecord.ALT, self.alt_alleles + ) + ) + + if self.full_alleles: + if len(self.full_alleles) != 2: + raise ValueError( + "full_alleles doesn't have both a ref allele and alt alleles" + ) + full_ref, full_alts = self.full_alleles + if len(full_alts) != len(self.alt_alleles): + raise ValueError( + "Different number of full alternate alleles than normal alt alleles" + ) + if self.ref_allele not in full_ref: + raise ValueError("could not find ref allele inside full ref allele") + for idx, (full_alt, alt) in enumerate(zip(full_alts, self.alt_alleles)): + if alt not in full_alt: + raise ValueError( + ( + "Could not find alt allele {} inside its full alt allele" + ).format(idx) + ) + + def GetMaxPloidy(self) -> int: + """ + Return the maximum ploidy of any sample at this locus. + + All genotypes will be a tuple of that many haplotypes, + where samples with a smaller ploidy than that + will have haplotypes at the end of the tuple set to ',' + (for string genotypes) or -2 (for index or length genotypes) + """ + return self.vcfrecord.ploidy + + def GetNumSamples(self) -> int: + """ + Return the number of samples at this locus (called or not). + + Same as the number of samples in the overall vcf + """ + return self.vcfrecord.genotype.n_samples + + def GetGenotypeIndicies(self) -> Optional[np.ndarray]: + """ + Get an array of genotype indicies across all samples. + + A genotype index is a number 0, 1, 2 ... + where 0 corresponds to the reference allele, + 1 to the first alt allele, 2 to the second, etc. + The array is an array of ints with one row per sample. + The number of columns is the maximum ploidy of any sample + (normally 2) plus 1 for phasing. + All but the final column represent the index of the genotypes + of each call. + The final column has values 0 for unphased sampels or 1 for phased. + So a sample with gt '0|2' would be represented by the row [0, 2, 1] + and a sample with gt '3/0' would be represented by the row [3, 0, 0]. + Uncalled haplotypes (represented by '.' in the VCF) are represented + by '-1' genotypes. If the sample has fewer haplotypes than the + maximum ploidy of all samples at this locus, then the row is padded + with -2s, so a haploid sample with gt '1' where other samples + are diploid would be represented by the row [1, -2, 0]. + If all the genotype columns for a sample are negative then the + sample is a no call. Note: the value of the phasing + column is unspecified for haploid or no-call samples. + + Returns + ------- + Optional[np.ndarray] + The numpy array described above, of type int. + If there are no samples in the vcf this record comes from + then return None instead + """ + if self.vcfrecord.genotype is None: + return None + return self.vcfrecord.genotype.array().astype(int) + + def GetCalledSamples(self, strict: bool = True) -> Optional[np.ndarray]: + """ + Get an array listing which samples have been called at this locus. + + Parameters + ---------- + strict : + By default genotypes such as '1/.' are considered not called + because at least one of the haplotypes present is not called. + Set strict = False to mark these as being called. + Note: genotypes having lesser ploidy will not be marked + as no calls even when strict = True (e.g. if some samples + have tetraploid genotypes at this locus, a genotype of '1/2/2' + will be marked as called even though it is triploid) + + Returns + ------- + Optional[np.ndarray] + A bool array of length equal to the number of samples, + where true indicates a sample has been called + and false indicates otherwise. + If there are no samples in the vcf this record comes from + then return None instead + """ + gt_idxs = self.GetGenotypeIndicies() + if gt_idxs is None: + return None + + if strict: + return ~np.any(gt_idxs[:, :-1] == -1, axis=1) + else: + return ~np.all( + np.logical_or(gt_idxs[:, :-1] == -1, gt_idxs[:, :-1] == -2), axis=1 + ) + + def GetSamplePloidies(self) -> Optional[np.ndarray]: + """ + Get an array listing the ploidies of each sample + + Returns + ------- + Optional[np.ndarray] + An array of positive ints with length equal to the + number of samples where each entry denotes the + number of genotypes for each sample at this locus + (including no calls) + If there are no samples in the vcf this record comes from + then return None instead + """ + gt_idxs = self.GetGenotypeIndicies() + if gt_idxs is None: + return None + + return gt_idxs.shape[1] - 1 - np.sum(gt_idxs[:, :-1] == -2, axis=1) + + def GetCallRate(self, strict: bool = True) -> float: + """ + Return the call rate at this locus. + + Parameters + ---------- + strict : + By default genotypes such as '1/.' are considered not called + because at least one of the haplotypes present is not called. + Set strict = False to mark these as being called. + Note: genotypes having lesser ploidy will not be marked + as no calls even when strict = True (e.g. if some samples + have tetraploid genotypes at this locus, a genotype of '1/2/2' + will be marked as called even though it is triploid) + + Returns + ------- + The fraction of the samples at this locus that have been + called. If there are no samples in the vcf this record comes from + then return np.nan instead + """ + called_samples = self.GetCalledSamples(strict=strict) + if called_samples is None: + return None + else: + return np.sum(called_samples) / called_samples.shape[0] + + def _GetStringGenotypeArray(self, idx_gts: np.ndarray, seq_alleles: List[str]): + max_len = max(len(allele) for allele in seq_alleles) + seq_array = np.empty(idx_gts.shape, dtype=" Optional[np.ndarray]: + """ + Get an array of string genotypes for each sample. + + The array is as described in :py:meth:`GetGenotypeIndicies` + except that the indicies are replaced by their corresponding + sequences, -1 indicies (nocalls) are replaced by '.', + -2 indicies (not present due to smaller ploidy) are replaced + by ',', and the phasing bits (0 or 1) are replaced by the strings + '0' or '1'. + + Will not include flanking base pairs. To get genotypes that include + flanking base pairs (for callers that call those), use + :py:meth:`GetFullStringGenotypes`. For callers that include flanking base pairs + it is possible that some of the alleles in the regular string genotypes + (with the flanks stripped) will be identical. In this case, you may + use :py:meth:`UniqueStringGenotypeMapping` to get a canonical unique subset + of indicies which represent all possible alleles. + + Note that some TR callers will only call allele lengths, not allele + sequences. In such a case, this method will return a fabricated + sequence based on the called length (see + :py:meth:`trtools.utils.utils.FabricateAllele`) and + a warning will be raised. This may not be intended - + use :py:meth:`GetLengthGenotypes` for a fully caller agnostic + way of handling genotypes. + + This method is inefficient for many samples, consider either using + length genotypes (:py:meth:`GetLengthGenotypes`), or + using genotype indicies (:py:meth:`GetGenotypeIndicies`) and + accessing string genotypes as needed through the fields ref_allele and + alt_alleles, instead. + + Returns + ------- + Optional[np.ndarray] + The numpy array described above, of type ' Optional[np.ndarray]: + """ + Get an array of full string genotypes for each sample. + See :py:meth:`GetStringGenotypes` for details and + limitations of string genotypes. + + If the sample does not have full genotypes that are distinct + from its regular string genotypes (because no flanking base pairs + were called) then the regular string genotypes are returned. + + Returns + ------- + Optional[np.ndarray] + The numpy array described above, of type ' Dict[int, int]: + """ + Get a mapping whose values are unique string genotype indicies. + + Return + ------ + Dict[int, int] + A mapping allele idx -> allele idx + whose keys are all allele indicies and whose values are a + subset of indicies which represents all the unique regular + string alleles for this variant. For almost all records, + this will be a mapping from each index to itself. For some + records with full string genotypes that include flanking base + pairs, some of the regular string alleles will be identical. + In this case, only one of those allele's indicies will be in the + set of values of this dictionary, and all identical alleles + will map to that one index. + """ + mapping = {} + if not self.HasFullStringGenotypes(): + for idx in range(len(self.alt_alleles) + 1): + mapping[idx] = idx + else: + allele_to_idx = {} + alleles = [self.ref_allele] + alleles.extend(self.alt_alleles) + for idx, allele in enumerate(alleles): + if allele not in allele_to_idx: + allele_to_idx[allele] = idx + mapping[idx] = idx + else: + mapping[idx] = allele_to_idx[allele] + + return mapping + + def UniqueStringGenotypes(self) -> Set[int]: + """ + Find allele indicies corresponding to the unique alleles. + + Equivalent to calling + :code:`set(UniqueStringGenotypeMapping().values())` + + Returns + ------- + Set[int] + The indicies of the unique string alleles + """ + return set(self.UniqueStringGenotypeMapping().values()) + + def GetDosages( + self, dosagetype: TRDosageTypes = TRDosageTypes.bestguess + ) -> Optional[np.ndarray]: + """ + Get an array of genotype dosages for each sample. + + Multiple strategies are used to compute dosages: + + - bestguess - Sum of the length (in num. rpt units) of alleles + - beagleap - For each haplotype, dosage is computed as: + sum_a len(a) x p(a) where len(a) is the length (in rpt. units) + of each allele a, and p(a) is the allele probability (from Beagle AP1/AP2 fields) + The total dosage is this value summed across the two haplotypes + - bestguess_norm - Same as bestguess but scaled to be between 0 and 2 + - beagleap_norm - Same as beagleap but scaled to be between 0 and 2 + + Note: normalized dosages currently not supported for haploid calls + Those are set to np.nan in the output dosages if using a _norm option + + Parameters + ---------- + dosagetype : Enum + Which TRDosageType to compute. Default bestguess + + Returns + ------- + dosages : npt.NDArray[np.float32] + A numpy array of dosages, of type float + If no samples are in the array, return None + """ + if self.GetNumSamples() == 0: + return None + if (dosagetype in [TRDosageTypes.beagleap, TRDosageTypes.beagleap_norm]) and ( + self.vcfrecord.format("AP1") is None or self.vcfrecord.format("AP2") is None + ): + raise ValueError( + "Requested Beagle dosages for record at {}:{} but AP1/AP2 fields not" + " found.".format(self.chrom, self.pos) + ) + if dosagetype in [TRDosageTypes.bestguess, TRDosageTypes.bestguess_norm]: + # Get length gts and replace -1 (missing) and -2 (low ploidy) with 0 + # But if normalizing set those to np.nan since unclear + # how to normalize haploid dosages which end up negative + # under the current method... + lengts = self.GetLengthGenotypes() + if dosagetype == TRDosageTypes.bestguess_norm: + lengts[lengts == -1] = np.nan + lengts[lengts == -2] = np.nan + else: + lengts[lengts == -1] = 0 + lengts[lengts == -2] = 0 + unnorm_dosages = lengts[:, :-1].sum(axis=1).astype(np.float32) + elif dosagetype in [TRDosageTypes.beagleap, TRDosageTypes.beagleap_norm]: + # Extract allele probabilities + ap1 = self.vcfrecord.format("AP1") + ref1 = np.clip( + 1 - np.sum(ap1, axis=1), 0, 1 + ) # If neg due to rounding, cutoff at 0 + ap2 = self.vcfrecord.format("AP2") + ref2 = np.clip(1 - np.sum(ap2, axis=1), 0, 1) + + # Check AP field. allow wiggle room for rounding + if np.any(np.sum(ap1, axis=1) > 1.1) or np.any(np.sum(ap2, axis=1) > 1.1): + raise ValueError("AP1 or AP2 field summing to more than 1 detected") + if np.any(ap1 < 0) or np.any(ap2 < 0): + raise ValueError("Negative AP1 or AP2 fields detected") + + # Get haplotype dosages + if len(self.alt_allele_lengths) > 0: + max_alt_len = max(self.alt_allele_lengths) + h1_dos = np.clip(np.dot(ap1, self.alt_allele_lengths), 0, max_alt_len) + h2_dos = np.clip(np.dot(ap2, self.alt_allele_lengths), 0, max_alt_len) + else: + h1_dos = 0 + h2_dos = 0 + ref1_dos = ref1 * self.ref_allele_length + ref2_dos = ref2 * self.ref_allele_length + + # Add together for final dosage + unnorm_dosages = (h1_dos + h2_dos + ref1_dos + ref2_dos).astype(np.float32) + else: + raise ValueError("Unsupported dosagetype") + if dosagetype in [TRDosageTypes.bestguess_norm, TRDosageTypes.beagleap_norm]: + if self.min_allele_length == self.max_allele_length: + # Can't normalize, just set all to 0 + dosages = np.zeros(self.GetNumSamples(), dtype=np.float32) + else: + # Normalize to be between 0 and 2 + dosages = (unnorm_dosages - 2 * self.min_allele_length) / ( + self.max_allele_length - self.min_allele_length + ) + assert not (np.any(dosages >= 2.1) or np.any(dosages <= -0.1)) + dosages = np.clip(dosages, 0, 2) + else: + dosages = unnorm_dosages + return dosages + + def GetLengthGenotypes(self) -> Optional[np.ndarray]: + """ + Get an array of length genotypes for each sample. + + Represents the sample's genotype in terms of the number + of repeats of the motif in each allele. + Returns a pair of floats - alleles including partial repeats + or other impurities may have noninteger lengths. + + The array is as described in :py:meth:`GetGenotypeIndicies` + except that indicies are replaced by their length genotypes. + -1s, -2s and the phasing bits are not modified. + + For records with both regular and full sequences (those with flanking + bps), this returns the length of the regular sequences + + Returns + ------- + Optional[np.ndarray] + The numpy array described above, of type float + If there are no samples in the vcf this record comes from + then return None instead + """ + idx_gts = self.GetGenotypeIndicies() + if idx_gts is None: + return None + + # store allele lengths in a numpy array + # and add fake alleles for -2 and -1 missing values + allele_lens = np.array( + [self.ref_allele_length, *self.alt_allele_lengths, -2, -1] + ) + + # copy repeats lengths and phasing for each sample + len_gts = allele_lens[idx_gts] + len_gts[:, -1] = idx_gts[:, -1] + + return len_gts + + def UniqueLengthGenotypeMapping(self) -> Dict[int, int]: + """ + Get a mapping whose values are unique string genotype indicies. + + Return + ------ + genotypeMapping : Dict[int, int] + A mapping allele idx -> allele idx + whose keys are all allele indicies and whose values are a + subset of indicies which represents all the unique + length alleles for this variant. For variants where + multiple alleles have the same length, all will map to + a single index from among those alleles. + """ + mapping = {} + allele_to_idx = {} + alleles = [self.ref_allele] + alleles.extend(self.alt_alleles) + for idx, allele in enumerate(alleles): + allele = len(allele) + if allele not in allele_to_idx: + allele_to_idx[allele] = idx + mapping[idx] = idx + else: + mapping[idx] = allele_to_idx[allele] + + return mapping + + def UniqueLengthGenotypes(self) -> Set[int]: + """ + Find allele indicies corresponding to the unique length alleles. + + Equivalent to calling + :code:`set(UniqueLengthGenotypeMapping().values())` + + Returns + ------- + Set[int] + The indicies of the unique string alleles + """ + return set(self.UniqueLengthGenotypeMapping().values()) + + def HasFullStringGenotypes(self) -> bool: + """ + Determine if this record has full string genotypes. + + Returns + ------- + bool: + True iff :py:meth:`GetFullStringGenotypes` will return + a different value than :py:meth:`GetStringGenotypes` for some + alleles. + """ + return self.full_alleles is not None + + def HasFabricatedRefAllele(self) -> bool: + """ + Determine if this record has a fabricated ref allels. + + Returns + ------- + bool: + True iff ref_allele_length was passed to this + record's constructor. + """ + return self.has_fabricated_ref_allele + + def HasFabricatedAltAlleles(self) -> bool: + """ + Determine if this record has fabricated alt alleles. + + Returns + ------- + bool: + True iff alt_allele_lengths was passed to this + record's constructor. + """ + return self.has_fabricated_alt_alleles + + def GetGenotypeCounts( + self, + sample_index: Optional[Any] = None, + uselength: bool = True, + index: bool = False, + fullgenotypes: bool = False, + include_nocalls: bool = False, + ) -> Dict[tuple, int]: + """ + Get the counts of each genotype for a record. + + For samples with a lower ploidy than the max ploidy among all samples, + the -2 placeholder haplotypes are sorted to the beginning of the call + (e.g. (-2, 5) instead of (5, -2)) + + This currently returns unphased genotypes (with no phasing column), it could be + extend to have an option to respect phasing + + Parameters + ---------- + sample_index : + Used to index the numpy array of samples. So can be a numpy array + of sample indicies, or a bool array with length of the number + of samples, etc. + If None, then all samples are included. + uselength : + If True, represent alleles as lengths + else represent as strings + index : + If True, represent alleles as indexes (0 = ref, 1 = first_alt, + etc.) instead of sequences or lengths + fullgenotypes : + If True, include flanking basepairs in allele representations. + Only makes sense when expliictly stating uselength=False. + Cannot be combined with index. + include_nocalls: + If False, all genotypes with one or more uncalled haplotypes + (-1 or '.') are excluded from the returned dictionary, + they are included if True. Genotypes with lower ploidy (-2 or ',') + are included regardless. + + Returns + ------- + genotype_counts: Dict[tuple, int] + Gives the count of each genotype. + Genotypes are represented as tuples of alleles, + where the type of allele representation is determined by the uselength, index + and fullgenotypes optional parameters. + """ + # TODO test these + if uselength and fullgenotypes: + raise ValueError("Can't specify both uselength and fullgenotypes") + if index and not uselength: + raise ValueError( + "Specified uselength=False and index at the same" + " time, these are mutually exclusive options" + ) + + if index: + gts = self.GetGenotypeIndicies() + nocall_entry = -1 + elif uselength and not index: + gts = self.GetLengthGenotypes() + nocall_entry = -1 + elif not uselength and not fullgenotypes: + gts = self.GetStringGenotypes() + nocall_entry = "." + elif fullgenotypes: + gts = self.GetFullStringGenotypes() + nocall_entry = "." + + if gts is None: + return {} + + gts = gts[:, :-1] # remove phasing + gts = np.sort(gts, axis=1) + + if sample_index is not None: + gts = gts[sample_index, :] + + genotypes, counts = np.unique(gts, axis=0, return_counts=True) + count_dict = dict(zip(tuple(map(tuple, genotypes)), counts)) + + if not include_nocalls: + gts_to_remove = set() + for genotype in count_dict: + if nocall_entry in genotype: + gts_to_remove.add(genotype) + for gt in gts_to_remove: + del count_dict[gt] + + return count_dict + + def GetAlleleCounts( + self, + sample_index: Optional[Any] = None, + *, + uselength: bool = True, + index: bool = False, + fullgenotypes: bool = False + ) -> Dict[Any, int]: + """ + Get the counts of each allele for a record. + + This does not return counts of no calls as it is not + clear how many 'no call alleles' would be present per no call + + Alleles that are not called in any sample are not present + in the returned dictionary + + Parameters + ---------- + sample_index : + Used to index the numpy array of samples. So can be a numpy array + of sample indicies, or a bool array with length of the number + of samples, etc. + If None, then all samples are included. + uselength : bool, optional + If True, represent alleles a lengths + else represent as strings + index : + If True, represent alleles as indexes (0 = ref, 1 = first_alt, + etc.) instead of sequences or lengths + fullgenotypes : + If True, include flanking basepairs in allele representations + Only makes sense when expliictly stating uselength=False. + Cannot be combined with index. + + Returns + ------- + allele_counts: Dict[Any, int] + Gives the count of each allele. + The type of allele representation is determined by the uselength, index + and fullgenotypes optional parameters. + """ + # TODO test these + if uselength and fullgenotypes: + raise ValueError("Can't specify both uselength and fullgenotypes") + if index and not uselength: + raise ValueError( + "Specified uselength=False and index at the same" + " time, these are mutually exclusive options" + ) + if index: + gts = self.GetGenotypeIndicies() + nocall_entry = -1 + lowploidy_entry = -2 + elif uselength and not index: + gts = self.GetLengthGenotypes() + nocall_entry = -1 + lowploidy_entry = -2 + elif not uselength and not fullgenotypes: + gts = self.GetStringGenotypes() + nocall_entry = "." + lowploidy_entry = "," + elif fullgenotypes: + gts = self.GetFullStringGenotypes() + nocall_entry = "." + lowploidy_entry = "," + + if gts is None: + return {} + + gts = gts[:, :-1] # remove phasing + + if sample_index is not None: + gts = gts[sample_index, :] + + # remove no calls and missing haplotypes + gts = gts[gts != nocall_entry] + gts = gts[gts != lowploidy_entry] + + alleles, counts = np.unique(gts, return_counts=True) + return dict(zip(alleles, counts)) + + def GetAlleleFreqs( + self, + sample_index: Optional[Any] = None, + *, + uselength: bool = True, + index: bool = False, + fullgenotypes: bool = False + ) -> Dict[Any, float]: + """ + Get the frequencies of each allele for a record. + + Parameters + ---------- + sample_index : + Used to index the numpy array of samples. So can be a numpy array + of sample indicies, or a bool array with length of the number + of samples, etc. + If None, then all samples are included. + uselength : + If True, represent alleles a lengths + else represent as strings + index : + If True, represent alleles as indexes (0 = ref, 1 = first_alt, + etc.) instead of sequences or lengths + fullgenotypes : + If True, include flanking basepairs in allele representations. + Only makes sense when expliictly stating uselength=False. + Cannot be combined with index. + + Returns + ------- + allele_freqs: Dict[Any, float] + Gives the frequency of each allele among called samples + The type of allele representation is determined by the uselength, index + and fullgenotypes optional parameters. + """ + allele_counts = self.GetAlleleCounts( + uselength=uselength, + index=index, + fullgenotypes=fullgenotypes, + sample_index=sample_index, + ) + total = float(sum(allele_counts.values())) + return {key: value / total for key, value in allele_counts.items()} + + def GetMaxAllele(self, sample_index: Optional[Any] = None) -> float: + """ + Get the maximum allele length called in a record. + + Represents lengths in terms of the number of repeats of the motif. + The longest allele may have a noninteger length if it includes + partial repeats or other impurities. + + For records with both regular and full sequences (those with flanking + bps), this returns the length of the regular sequences + + Parameters + ---------- + sample_index : + Used to index the numpy array of samples. So can be a numpy array + of sample indicies, or a bool array with length of the number + of samples, etc. + If None, then all samples are included. + + Returns + ------- + maxallele : float + The maximum allele length called (in number of repeat units), + or nan if no alleles called + """ + # TODO should we have GetMinAllele too? + # TODO should we have an option for grabbing + # the index of the longest allele? + alleles = self.GetAlleleCounts(uselength=True, sample_index=sample_index).keys() + if len(alleles) == 0: + return np.nan + return max(alleles) + + def HasQualityScores(self) -> bool: + """ + Does this TRRecord contain quality scores for each of its calls? + If present, the meaning and reliability of these scores is + genotyper dependent, see the doc section :ref:`Quality Scores`. + + Return + ------ + boolean: + Whether or not a FORMAT field that could be interpreted as a + quality score has been identified + """ + return self.quality_field is not None and self.quality_field in self.format + + def GetQualityScores(self) -> np.ndarray: + """ + Get the quality scores of the calls for each sample. + + The meaning and reliability of these scores is genotyper + dependent, see the doc section :ref:`Quality Scores`. + + Returns + ------- + np.ndarray : + An array of quality score floats, one row per sample + Samples which were not called have the value np.nan + """ + if not self.HasQualityScores(): + raise TypeError( + "This TRRecord does not have a corresponding quality score field" + ) + quality_val = self.format[self.quality_field] + transform = self.quality_score_transform + if transform is None: + return quality_val + else: + return np.apply_along_axis(transform, 0, quality_val) + + def __str__(self): + """Generate a summary of the variant described by this record.""" + record_id = self.record_id + if record_id is None: + record_id = "{}:{}".format(self.vcfrecord.CHROM, self.vcfrecord.POS) + if self.HasFullStringGenotypes(): + string = "{} {} {} ".format(record_id, self.motif, self.full_alleles[0]) + string += ",".join(self.full_alleles[1]) + return string + + if self.HasFabricatedRefAllele(): + string = "{} {} n_reps:{} ".format( + record_id, self.motif, self.ref_allele_length + ) + else: + string = "{} {} {} ".format(record_id, self.motif, self.ref_allele) + + if len(self.alt_alleles) == 0: + string += "." + elif self.HasFabricatedAltAlleles(): + string += ",".join( + "n_reps:" + str(length) for length in self.alt_allele_lengths + ) + else: + string += ",".join(self.alt_alleles) + + return string + + +class TRRecordHarmonizer: + """ + Class producing a uniform interface for accessing TR VCF records. + + Produces the same output interface regardless of the + tool that created the input VCF. + + The main purpose of this class is to infer which tool + a VCF came from, and appropriately convert its records + to TRRecord objects. + + This class provides the object oriented paradigm for iterating + through a TR vcf. If you wish to use the functional paradigm and + provide the cyvcf2.Variant objects yourself, use the top-level + functions in this module. + + Parameters + ---------- + vcffile : cyvcf2.VCF instance + vcftype : {'auto', 'gangstr', 'advntr', 'hipstr', 'eh', 'popstr'}, optional + Type of the VCF file. Default='auto'. + If vcftype=='auto', attempts to infer the type. + + Attributes + ---------- + vcffile : cyvcf2.VCF instance + vcftype : enum + Type of the VCF file. Must be included in VcfTypes + + Raises + ------ + TypeError + If the type of the VCF cannot be properly inferred. + See :py:meth:`InferVCFType` for more details. + """ + + def __init__(self, vcffile: cyvcf2.VCF, vcftype: Union[str, VcfTypes] = "auto"): + self.vcffile = vcffile + self.vcftype = InferVCFType(vcffile, vcftype) + self._record_idx = None + + def MayHaveImpureRepeats(self) -> bool: + """ + Determine if any of the alleles in this VCF may contain impure repeats. + + See Also + -------- + tr_harmonizer.MayHaveImpureRepeats + """ + return MayHaveImpureRepeats(self.vcftype) + + def HasLengthRefGenotype(self) -> bool: + """ + Determine if the reference alleles of variants are given by length. + + See Also + -------- + tr_harmonizer.HasLengthRefGenotype + """ + return HasLengthRefGenotype(self.vcftype) + + def HasLengthAltGenotypes(self) -> bool: + """ + Determine if the alt alleles of variants are given by length. + + See Also + -------- + tr_harmonizer.HasLengthAltGenotypes + """ + return HasLengthAltGenotypes(self.vcftype) + + def HasQualityScore(self) -> bool: + """ + Does this VCF contain quality scores for each of its calls? + If present, the meaning and reliability of these scores is + genotyper dependent, see the doc section :ref:`Quality Scores`. + + Returns + ------- + bool + Whether or not a FORMAT field that could be interpreted as a + quality score has been identified + """ + if self.vcftype == VcfTypes.gangstr: + return "FORMAT= bool: + """ + Is this a VCF produced by running the Beagle software to impute STRs from a panel generated by an TR genotyper? + + See Also + -------- + tr_harmonizer.IsBeagleVCF + """ + return IsBeagleVCF(self.vcffile) + + def __iter__(self) -> Iterator[TRRecord]: + """Iterate over TRRecords produced from the underlying vcf.""" + return self + + def __next__(self) -> TRRecord: + """Iterate over TRRecord produced from the underlying vcf.""" + if self._record_idx is None: + self._record_idx = 1 + self._record_idx += 1 + try: + record = next(self.vcffile) + except StopIteration: + raise + except Exception: + raise ValueError( + "Unable to parse the " + + str(self._record_idx) + + "th tandem " + "repeat in the provided VCF. Check that it is properly formatted." + ) + return HarmonizeRecord(self.vcftype, record) + + +# TODO check all users of this class for new options diff --git a/core/utils.py b/core/utils.py new file mode 100755 index 0000000..886c158 --- /dev/null +++ b/core/utils.py @@ -0,0 +1,643 @@ +# type: ignore +""" +Util functions for calculating summary STR statistics +and performing basic string operations on STR alleles. +""" +# import argparse +# import itertools +import math + +# import os +# from typing import Any, Dict, List, Optional, Set + +# import cyvcf2 +# import numpy as np + +# from . import common + +nucToNumber = {"A": 0, "C": 1, "G": 2, "T": 3} + + +# def LoadSingleReader( +# vcf_loc: str, checkgz: bool = True, lazy: bool = False, samples: Set[str] = None +# ) -> Optional[cyvcf2.VCF]: +# """ +# Return a VCF reader + +# Parameters +# ---------- +# vcf_loc : +# The location of the VCF file to read +# checkgz: +# Check whether VCF file is gzipped and indexed, +# if not return None +# lazy: +# if True, then don’t unpack (parse) the underlying record until needed. +# Default: False +# samples: +# List of samples to include. If None, load all samples + +# Returns +# ------- +# reader : Optional[cyvcf2.VCF] +# The cyvcf2.VCF instance, or None if the VCF is not present +# or could not be opened +# """ +# # check that vcf_loc is a file or file descriptor (ex: '/dev/stdin') +# if not os.path.exists(vcf_loc) or os.path.isdir(vcf_loc): +# common.WARNING("Could not find VCF file %s" % vcf_loc) +# return None +# if checkgz: +# if not vcf_loc.endswith(".vcf.gz") and not vcf_loc.endswith(".vcf.bgz"): +# common.WARNING("Make sure %s is bgzipped and indexed" % vcf_loc) +# return None +# if not os.path.isfile(vcf_loc + ".tbi"): +# common.WARNING("Could not find VCF index %s.tbi" % vcf_loc) +# return None +# if samples is not None: +# if not isinstance(samples, set): +# common.WARNING( +# "Samples cannot be loaded in a particular order. Order will be ignored" +# ) +# samples = list(samples) +# try: +# return cyvcf2.VCF(vcf_loc, lazy=lazy, samples=samples) +# except OSError: +# common.WARNING("Could not open VCF file %s. Is it really VCF?" % vcf_loc) +# return None + + +# def LoadReaders( +# vcf_locs: List[str], checkgz: bool = True +# ) -> Optional[List[cyvcf2.VCF]]: +# """ +# Return a list of VCF readers + +# Parameters +# ---------- +# vcf_locs : +# A list of vcf locations +# checkgz: +# Check if each VCF file is gzipped and indexed + +# Returns +# ------- +# readers : Optional[List[cvycf2.VCF]] +# A list of VCF readers, or None if any of them could not be found. +# If checkgz, then also return None if any of the VCF readers +# were not gzipped and tabix indexed. +# """ +# readers = [] +# for f in vcf_locs: +# rdr = LoadSingleReader(f, checkgz) +# if rdr is None: +# return None +# readers.append(rdr) + +# return readers + + +# def GetContigs(vcf: cyvcf2.VCF) -> List[str]: +# """ +# Returns the contig IDs in the VCF. + +# Parameters +# ---------- +# vcf : +# The vcf to get contigs from + +# Returns +# ------- +# List[str] : +# A list of contig IDs +# """ +# contigs = [] +# for header_line in vcf.header_iter(): +# if header_line["HeaderType"].lower() == "contig": +# contigs.append(header_line["ID"]) +# return contigs + + +# def ValidateAlleleFreqs(allele_freqs): +# r"""Check that the allele frequency distribution is valid. + +# Allele frequencies must sum to 1. + +# Parameters +# ---------- +# allele_freqs : dict of object: float +# Dictionary of allele frequencies for each allele. +# Alleles are typically strings (sequences) or floats (num. repeats) + +# Returns +# ------- +# is_valid : bool +# Return True if the distribution is valid, else False + +# Examples +# -------- +# >>> ValidateAlleleFreqs({0:0.5, 1:0.5}) +# True +# """ +# if len(allele_freqs.keys()) == 0: +# return False +# return abs(1 - sum(allele_freqs.values())) <= 0.001 + + +# def GetHeterozygosity(allele_freqs): +# r"""Compute heterozygosity of a locus + +# Heterozygosity is defined as the probability +# that two randomly drawn alleles are different. + +# Parameters +# ---------- +# allele_freqs : dict of object: float +# Dictionary of allele frequencies for each allele. +# Alleles are typically strings (sequences) or floats (num. repeats) + +# Returns +# ------- +# heterozygosity : float +# The heterozygosity of the locus. +# If the allele frequencies dictionary is invalid, return np.nan + +# Notes +# ----- +# Heterzygosity is computed as: + +# .. math:: H = 1-\sum_{i=1..n} p_i^2 + +# where `p_i` is the frequency of allele `i` and `n` is the number of alleles. + +# Examples +# -------- +# >>> GetHeterozygosity({0:0.5, 1:0.5}) +# 0.5 +# """ +# if not ValidateAlleleFreqs(allele_freqs): +# return np.nan +# return 1 - sum([freq**2 for freq in allele_freqs.values()]) + + +# def GetEntropy(allele_freqs: Dict[Any, float]) -> float: +# r"""Compute the (bit) entropy of a locus + +# Entropy is defined as the +# `entropy _` +# of the distribution of allele frequencies. + +# Parameters +# ---------- +# allele_freqs : dict of object: float +# Dictionary of allele frequencies for each allele. +# Alleles are typically strings (sequences) or floats (num. repeats) + +# Returns +# ------- +# entropy: float +# The entropy of the locus. +# If the allele frequencies dictionary is invalid, return np.nan + +# Notes +# ----- +# Entropy is computed as: + +# .. math:: E = -\sum_{i=1..n} -p_i*log_2(p_i) + +# where `p_i` is the frequency of allele `i` and `n` is the number of alleles. + +# Examples +# -------- +# >>> GetEntropy({0:0.5, 1:0.5}) +# 1.0 +# """ +# if not ValidateAlleleFreqs(allele_freqs): +# return np.nan +# return float(scipy.stats.entropy(list(x for x in allele_freqs.values()), base=2)) + + +# def GetMean(allele_freqs): +# r"""Compute the mean allele length + +# Parameters +# ---------- +# allele_freqs : dict of object: float +# Dictionary of allele frequencies for each allele. +# Alleles must be given in lengths (numbers, not strings) + +# Returns +# ------- +# mean: float +# Return mean if allele frequencies dictionary is valid + +# Examples +# -------- +# >>> GetMean({0:0.5, 1:0.5}) +# 0.5 +# """ +# if not ValidateAlleleFreqs(allele_freqs): +# return np.nan +# return sum([key * allele_freqs[key] for key in allele_freqs]) + + +# def GetMode(allele_freqs): +# """ +# Compute the mode allele length. + +# If more than one allele has the maximum number of copies out of all +# alleles, choose one at random (but reproducibly) + +# Parameters +# ---------- +# allele_freqs : dict of object: float +# Dictionary of allele frequencies for each allele. +# Alleles must be given in lengths (numbers, not strings) + +# Returns +# ------- +# mode: float +# Return mode if allele frequencies dictionary is valid + +# Examples +# -------- +# >>> GetMode({0:0.1, 1:0.9}) +# 1 +# """ +# if not ValidateAlleleFreqs(allele_freqs): +# return np.nan +# mode_freq = -1 +# modes = set() +# for allele, freq in allele_freqs.items(): +# if freq > mode_freq: +# modes = {allele} +# mode_freq = freq +# if freq == mode_freq: +# modes.add(allele) +# return min(modes) # use min to make this arbitrary selection reproducible + + +# def GetVariance(allele_freqs): +# r"""Compute the variance of the allele lengths + +# Parameters +# ---------- +# allele_freqs : dict of object: float +# Dictionary of allele frequencies for each allele. +# Alleles must be given in lengths (numbers, not strings) + +# Returns +# ------- +# variance: float +# Return variance if allele frequencies dictionary is valid +# np.nan otherwise. + +# Examples +# -------- +# >>> GetVariance({0:1}) +# 0 +# """ +# if not ValidateAlleleFreqs(allele_freqs): +# return np.nan +# mean = GetMean(allele_freqs) +# return sum([allele_freqs[key] * (key - mean) ** 2 for key in allele_freqs.keys()]) + + +# def GetHardyWeinbergBinomialTest(allele_freqs, genotype_counts): +# r"""Compute Hardy Weinberg p-value + +# Tests whether the number of observed heterozygous vs. +# homozygous individuals is different than expected +# under Hardy Weinberg Equilibrium given the observed +# allele frequencies, based on a binomial test. + +# Parameters +# ---------- +# allele_freqs : dict of object: float +# Dictionary of allele frequencies for each allele. +# Alleles are typically strings (sequences) or floats (num. repeats) +# genotype_counts : dict of (object, object): int +# Dictionary of counts of each genotype. Genotypes are defined +# as tuples of alleles. Alleles must be the same as those given in +# allele_freqs + +# Returns +# ------- +# p-value : float +# The two-sided p-value returned by a binomial test (scipy.stats.binom_test) +# If the allele frequencies dictionary is invalid, return np.nan +# If genotype alleles not included in frequencies dictionary, return np.nan +# """ +# if not ValidateAlleleFreqs(allele_freqs): +# return np.nan +# exp_hom_frac = sum([val**2 for val in allele_freqs.values()]) +# total_samples = sum(genotype_counts.values()) +# num_hom = 0 +# for gt in genotype_counts: +# if gt[0] not in allele_freqs.keys(): +# return np.nan +# if gt[1] not in allele_freqs.keys(): +# return np.nan +# if gt[0] == gt[1]: +# num_hom += genotype_counts[gt] +# try: +# return scipy.stats.binom_test(num_hom, n=total_samples, p=exp_hom_frac) +# except AttributeError: +# # binom_test was deprecated in favor of binomtest in scipy 1.12.0 +# return scipy.stats.binomtest(num_hom, n=total_samples, p=exp_hom_frac).pvalue + + +# def GetHomopolymerRun(seq): +# r"""Compute the maximum homopolymer run length in a sequence + +# Parameters +# ---------- +# seq : str +# String giving a sequence of nucleotides + +# Returns +# ------- +# runlength : int +# The length of the longest homopolymer run + +# Examples +# -------- +# >>> GetHomopolymerRun("AATAAAATAAAAAT") +# 5 +# """ +# if len(seq) == 0: +# return 0 +# seq = seq.upper() +# return max(len(list(y)) for (c, y) in itertools.groupby(seq)) + + +# def GetCanonicalMotif(repseq): +# r"""Get canonical STR sequence, considering both strands + +# The canonical sequence is the first alphabetically +# out of all possible rotations on + and - strands +# of the sequence. e.g. "TG" canonical sequence is "AC". + +# Parameters +# ---------- +# repseq : str +# String giving a STR motif (repeat unit sequence) + +# Returns +# ------- +# canon : str +# The canonical sequence of the STR motif + +# Examples +# -------- +# >>> GetCanonicalMotif("TG") +# 'AC' +# """ +# repseq = repseq.upper() +# # Get canonical sequence of each strand +# repseq_f = GetCanonicalOneStrand(repseq) +# repseq_r = GetCanonicalOneStrand(ReverseComplement(repseq)) +# # choose first seq alphabetically +# for i in range(len(repseq_f)): +# if nucToNumber[repseq_f[i]] < nucToNumber[repseq_r[i]]: +# return repseq_f +# if nucToNumber[repseq_r[i]] < nucToNumber[repseq_f[i]]: +# return repseq_r +# return repseq_f + + +def GetCanonicalOneStrand(repseq): + r"""Get canonical STR sequence, considering one strand + + The canonical sequence is the first alphabetically + out of all possible rotations. e.g. CAG -> AGC. + + Parameters + ---------- + repseq : str + String giving a STR motif (repeat unit sequence) + + Returns + ------- + canon : str + The canonical sequence of the STR motif + + Examples + -------- + >>> GetCanonicalOneStrand("CAG") + 'AGC' + """ + repseq = repseq.upper() + size = len(repseq) + canonical = repseq + for i in range(size): + newseq = repseq[size - i :] + repseq[0 : size - i] + for j in range(size): + if nucToNumber[newseq[j]] < nucToNumber[canonical[j]]: + canonical = newseq + elif nucToNumber[newseq[j]] > nucToNumber[canonical[j]]: + break + return canonical + + +# def ReverseComplement(seq): +# r"""Get reverse complement of a sequence. + +# Converts everything to uppsercase. + +# Parameters +# ---------- +# seq : str +# String of nucleotides. + +# Returns +# ------- +# revcompseq : str +# Reverse complement of the input sequence. + +# Examples +# -------- +# >>> ReverseComplement("AGGCT") +# 'AGCCT' +# """ +# seq = seq.upper() +# newseq = "" +# size = len(seq) +# for i in range(len(seq)): +# char = seq[len(seq) - i - 1] +# if char == "A": +# newseq += "T" +# elif char == "G": +# newseq += "C" +# elif char == "C": +# newseq += "G" +# elif char == "T": +# newseq += "A" +# else: +# newseq += "N" +# return newseq + + +def InferRepeatSequence(seq, period): + """ + TODO change to dynamic programming approach + Infer the repeated sequence in a string + + Parameters + ---------- + seq : str + A string of nucleotides + period : int + Length of the repeat unit + + Returns + ------- + repseq : str + The inferred repeat unit (motif). + If the input sequence is smaller than the period, + repseq consists of all N's. + + Examples + -------- + >>> InferRepeatSequence('ATATATAT', 2) + 'AT' + """ + if period > len(seq): + return "N" * period + best_kmer = None + best_copies = 0 + for offset in range(0, period): + kmers = {} + start_idx = 0 + while start_idx + period <= len(seq): + kmer = seq[start_idx : (start_idx + period)] + if kmer not in kmers: + kmers[kmer] = 1 + else: + kmers[kmer] += 1 + start_idx += period + current_best_kmer = max(kmers, key=lambda k: kmers[k]) + current_best_copies = kmers[current_best_kmer] + if current_best_copies > best_copies: + best_kmer = current_best_kmer + best_copies = current_best_copies + return GetCanonicalOneStrand(best_kmer) + + +# def LongestPerfectRepeat(seq, motif, check_reverse=True): +# r""" +# Determine the length (bp) of the longest +# perfect repeat stretch + +# Credit: function originally written by +# Helyaneh Ziaei-Jam + +# Parameters +# ---------- +# seq : str +# Repeat region sequence +# motif : str +# Repeat unit sequence +# check_reverse : bool (optional) +# If False, don't check reverse complement + +# Returns +# ------- +# max_match : int +# Number of bp of longest perfect stretch +# """ +# max_matches = [] +# seq = seq.upper() +# checkseqs = [seq] +# if check_reverse: +# strand_seq = ReverseComplement(seq) +# checkseqs.append(strand_seq) +# for ref_ in checkseqs: +# for mot in [motif, motif[::-1]]: +# i = 0 +# match = 0 +# max_match = 0 +# while True: +# if i >= len(ref_): +# break +# for j in range(0, len(motif)): +# k = i +# while True: +# while j < len(mot) and k < len(ref_) and ref_[k] == mot[j]: +# k += 1 +# j += 1 +# match += 1 +# max_match = max(max_match, match) +# if j == len(motif): +# j = 0 +# i = k +# else: +# if j == len(motif) - 1: +# i += 1 +# match = 0 +# break +# j = 0 +# max_matches.append(max_match) +# return max(max_matches) + + +def FabricateAllele(motif, length): + """ + Fabricate an allele with the given motif and length. + + Parameters + ---------- + motif : str + the motif to build the allele from + length : float + the number of times to copy the motif + (noninteger implies partial repeats). + This does NOT specify the desired length of the + returned string. + + Return + ------ + str + the fabricated allele string + + Notes + ----- + The allele is fabricated with the given motif orientation + (e.g. motif = 'ACG' could produce 'ACGACGACG' but not 'CGACGACGA'). + Fabricated alleles will contain no impurities nor flanking base pairs. + In the case of length being a noninteger float (because of partial + repeats) and where it is unclear if the last nucleotide should be + included in the fabricated repeat or not due to imprecision in the + length float, the last nucleotide will always be left off (the + length of the returned string will always be rounded down). + """ + fab = math.floor(length) * motif + idx = 0 + while (len(fab) + 1) / len(motif) < length: + fab += motif[idx] + idx += 1 + + return fab + + +# class ArgumentDefaultsHelpFormatter(argparse.HelpFormatter): # pragma: no cover +# """ +# Build a custom argument parser that works just like +# argparse.ArgumentDefaultsHelpFormatter except that it +# doesn't display None defaults. Everything below +# is copied from the python library source except for that. + +# Help message formatter which adds default values to argument help. + +# Only the name of this class is considered a public API. All the methods +# provided by the class are considered an implementation detail. +# """ + +# def _get_help_string(self, action): +# help = action.help +# if "%(default)" not in action.help: +# if action.default is not argparse.SUPPRESS and action.default is not None: +# defaulting_nargs = [argparse.OPTIONAL, argparse.ZERO_OR_MORE] +# if action.option_strings or action.nargs in defaulting_nargs: +# help += " (default: %(default)s)" +# return help diff --git a/noxfile.py b/noxfile.py index 1cce100..9a0a7f0 100644 --- a/noxfile.py +++ b/noxfile.py @@ -1,3 +1,4 @@ +# type: ignore """Nox sessions.""" import os import shutil diff --git a/poetry.lock b/poetry.lock index 74db166..b5861a9 100644 --- a/poetry.lock +++ b/poetry.lock @@ -102,13 +102,13 @@ uvloop = ["uvloop (>=0.15.2)"] [[package]] name = "certifi" -version = "2024.2.2" +version = "2024.8.30" description = "Python package for providing Mozilla's CA Bundle." optional = false python-versions = ">=3.6" files = [ - {file = 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">=0.90.1" [tool.poetry.group.docs.dependencies] Sphinx = ">=4.3.2" @@ -50,6 +50,7 @@ log_cli_format = "%(asctime)s [%(levelname)8s] %(message)s (%(filename)s:%(linen log_cli_date_format = "%Y-%m-%d %H:%M:%S" addopts = """ --ignore noxfile.py +-p tests.dataloader """ [tool.coverage.run] @@ -57,10 +58,13 @@ omit = [ ".nox/*", "noxfile.py", "core/__init__.py", - "core/tr_harmonizer.py", ] [tool.coverage.report] exclude_lines = [ "pragma: no cover", ] + +[tool.pyright] +strictParameterNoneValue = false +ignore = ["**/tests/**"] diff --git a/tests/data/beagle/advntr_imputed.vcf.gz b/tests/data/beagle/advntr_imputed.vcf.gz new file mode 100644 index 0000000..2a37fee Binary files /dev/null and b/tests/data/beagle/advntr_imputed.vcf.gz differ diff --git a/tests/data/beagle/advntr_imputed_missing_infos.vcf.gz b/tests/data/beagle/advntr_imputed_missing_infos.vcf.gz new file mode 100644 index 0000000..1d99321 Binary files /dev/null and b/tests/data/beagle/advntr_imputed_missing_infos.vcf.gz differ diff --git a/tests/data/beagle/eh_imputed.vcf.gz b/tests/data/beagle/eh_imputed.vcf.gz new file mode 100644 index 0000000..5e85b20 Binary files /dev/null and b/tests/data/beagle/eh_imputed.vcf.gz differ diff --git a/tests/data/beagle/eh_imputed_missing_infos.vcf.gz b/tests/data/beagle/eh_imputed_missing_infos.vcf.gz new file mode 100644 index 0000000..4fa8807 Binary files /dev/null and b/tests/data/beagle/eh_imputed_missing_infos.vcf.gz differ diff --git a/tests/data/beagle/gangstr_imputed.vcf.gz b/tests/data/beagle/gangstr_imputed.vcf.gz new file mode 100644 index 0000000..e180adb Binary files /dev/null and b/tests/data/beagle/gangstr_imputed.vcf.gz differ diff --git a/tests/data/beagle/gangstr_imputed_missing_infos.vcf.gz b/tests/data/beagle/gangstr_imputed_missing_infos.vcf.gz new file mode 100644 index 0000000..ec175b6 Binary files /dev/null and b/tests/data/beagle/gangstr_imputed_missing_infos.vcf.gz differ diff --git a/tests/data/beagle/hipstr_imputed.vcf.gz b/tests/data/beagle/hipstr_imputed.vcf.gz new file mode 100644 index 0000000..7d43cb7 Binary files /dev/null and b/tests/data/beagle/hipstr_imputed.vcf.gz differ diff --git a/tests/data/beagle/hipstr_imputed_missing_infos.vcf.gz b/tests/data/beagle/hipstr_imputed_missing_infos.vcf.gz new file mode 100644 index 0000000..7aeb38a Binary files /dev/null and b/tests/data/beagle/hipstr_imputed_missing_infos.vcf.gz differ diff --git a/tests/data/snps.vcf b/tests/data/snps.vcf new file mode 100644 index 0000000..2b1320e --- /dev/null +++ b/tests/data/snps.vcf @@ -0,0 +1,30 @@ +##fileformat=VCFv4.1 +##FILTER= +##fileDate=15082017_02h10m46s +##source=SHAPEIT2.v837 +##log_file=shapeit_15082017_02h10m46s_d9e4b88d-2500-460c-9753-e6c2ac3bcb15.log +##FORMAT= +##contig= +##INFO= +##INFO= +##bcftools_viewVersion=1.6-49-ga2ffda9-dirty+htslib-1.7-1-gaf40c73 +##bcftools_viewCommand=view --samples SS0012978,SS0012979,SS0013012 -r 22:16050115-16052271 -Oz -o snps.vcf.gz 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PASS AC=0;AN=6 GT 0|0 0|0 0|0 +22 16052080 rs4965031 G A . PASS AC=1;AN=6 GT 0|0 0|0 1|0 +22 16052271 rs188996808 G A . PASS AC=0;AN=6 GT 0|0 0|0 0|0 diff --git a/tests/data/test_ExpansionHunter.vcf b/tests/data/test_ExpansionHunter.vcf new file mode 100644 index 0000000..7e98679 --- /dev/null +++ b/tests/data/test_ExpansionHunter.vcf @@ -0,0 +1,21 @@ +##fileformat=VCFv4.1 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878_S1_HTT +chr4 3076603 . C , . PASS END=3076660;REF=19;RL=57;RU=CAG;VARID=HTT;REPID=HTT GT:SO:REPCN:REPCI:ADSP:ADFL:ADIR:LC 1/2:SPANNING/SPANNING:16/18:16-16/18-18:4/7:319/320:0/0:34.624013 diff --git a/tests/data/test_advntr.vcf b/tests/data/test_advntr.vcf new file mode 100644 index 0000000..f76aee8 --- /dev/null +++ b/tests/data/test_advntr.vcf @@ -0,0 +1,13 @@ +##fileformat=VCFv4.3 +##source=adVNTR ver. 1.3.3 +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CSTB_2_5_testdata.bam +chr21 45196323 . GCGCGGGGCGGGGCGCGGGGCGGGGCGCGGGGCGGG GCGCGGGGCGGGGCGCGGGGCGGG,GCGCGGGGCGGGGCGCGGGGCGGGGCGCGGGGCGGGGCGCGGGGCGGGGCGCGGGGCGGG . . END=45196359;VID=301645;RU=GCGCGGGGCGGG;RC=3 GT:DP:SR:FR:ML 1/2:60:39:21:0.863 diff --git a/tests/data/test_file_gangstr_unindexed1.vcf.gz b/tests/data/test_file_gangstr_unindexed1.vcf.gz new file mode 100644 index 0000000..3e04c56 Binary files /dev/null and b/tests/data/test_file_gangstr_unindexed1.vcf.gz differ diff --git a/tests/data/test_gangstr.vcf b/tests/data/test_gangstr.vcf new file mode 100644 index 0000000..686b6f9 --- /dev/null +++ b/tests/data/test_gangstr.vcf @@ -0,0 +1,1400 @@ +##fileformat=VCFv4.1 +##FILTER= +##command=GangSTR-2.4.2.12-9da7 --bam /scratch/bams/drive3/4512-JFI-0366_BXD196_phased_possorted_bam.bam --regions /scratch/regions/0705_mm10.bed --ref /scratch/ref/mm10.fa --str-info /scratch/strinfo/100519_mm10_strinfo_wo_stutt_recalc_many_samples.bed --chrom chr1 --trim-to-readlength 128 --drop-dupes --out result/4512-JFI-0366_BXD196/res_chr1 +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##bcftools_filterVersion=1.6-49-ga2ffda9-dirty+htslib-1.7-1-gaf40c73 +##bcftools_filterCommand=filter -r chr1:3000000-10000000 /storage/mikhail/100919_BXD_all_drive1_drive3_rep_stutt_model/result/4512-JFI-0366_BXD196/res_chr1.vcf.gz; Date=Sun Nov 24 18:06:49 2019 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BXD196_0366 +chr1 3004986 . tctgtctgtctg . . PASS END=3004997;RU=tctg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000632591;STUTTERDOWN=0.000632591;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:0.999912:3,3:3-3,3-3:17,12,0,2:3,17:2,2:193.56:366.612,131.36:0,0:0,5.1188e-05,0.999949 +chr1 3005549 . aaaacaaaacaaaacaaaac . . PASS END=3005568;RU=aaaac;PERIOD=5;REF=4;GRID=1,7;STUTTERUP=0.000661;STUTTERDOWN=0.00264397;STUTTERP=0.987382;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:1:4,4:4-4,4-4:20,11,0,0:4,20:NULL:181.959:366.612,131.36:0,0:0,8.11654e-06,0.999994 +chr1 3009351 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=3009402;RU=tg;PERIOD=2;REF=26;GRID=19,27;STUTTERUP=0.0752532;STUTTERDOWN=0.287761;STUTTERP=0.73575;EXPTHRESH=26 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:28:0.597778:24,24:22-24,22-24:7,10,0,10:23,2|24,5:5,1|6,2|7,1|8,3|9,1|11,1|12,1:204.961:366.612,131.36:0.647588,0.647588:0.977848,0.0221963,7.63327e-09 +chr1 3011925 . tatatatatatatatatatatatatatatatatatatatatatata tatatatatatatatatatatatata . PASS END=3011970;RU=ta;PERIOD=2;REF=23;GRID=8,17;STUTTERUP=0.159106;STUTTERDOWN=0.180648;STUTTERP=0.664826;EXPTHRESH=23 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:24:0.941159:13,13:11-13,11-13:9,12,0,0:13,9:NULL:154.4:366.612,131.36:0.623055,0.623055:1,0,0 +chr1 3013640 . tttgtttgtttgtttg . . PASS END=3013655;RU=tttg;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000570832;STUTTERDOWN=0.00971689;STUTTERP=0.970764;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:27:0.999747:4,4:3-4,3-4:15,9,0,2:4,15:3,2:152.109:366.612,131.36:0.298675,0.298675:0,0.000127996,0.999873 +chr1 3021480 . atgatgatgatg . . PASS END=3021491;RU=atg;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000391733;STUTTERDOWN=0.00156691;STUTTERP=0.987382;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:27:0.999619:4,4:4-4,4-4:15,12,0,0:4,15:NULL:172.657:366.612,131.36:0,0:0,0.000249006,0.999751 +chr1 3029298 . agagagagagag agagagagagagagagagag . PASS END=3029309;RU=ag;PERIOD=2;REF=6;GRID=1,13;STUTTERUP=0.00656231;STUTTERDOWN=0.015725;STUTTERP=0.716953;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:11:0.0250924:10,10:1-13,1-13:0,9,0,2:NULL:10,2:102.272:366.612,131.36:4.66296,4.66296:4.77053e-15,0.489352,0.510706 +chr1 3030350 . tttatttattta . . PASS END=3030361;RU=ttta;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000572302;STUTTERDOWN=0.000572302;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:1:3,3:3-3,3-3:18,16,0,2:3,18:2,2:235.97:366.612,131.36:0,0:0,6.94948e-06,0.999994 +chr1 3034212 . atctatctatct . . PASS END=3034223;RU=atct;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00053027;STUTTERDOWN=0.00053027;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:1:3,3:3-3,3-3:20,15,0,0:3,20:NULL:216.349:366.612,131.36:0,0:0,7.31421e-06,0.999994 +chr1 3045469 . cacacacacacacacacacacacacaca cacacacacacacacacacacacacacacacacacacacaca . PASS END=3045496;RU=ca;PERIOD=2;REF=14;GRID=16,24;STUTTERUP=0.0650522;STUTTERDOWN=0.138148;STUTTERP=0.728435;EXPTHRESH=14 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:16:0.219972:21,21:19-21,19-21:3,9,0,2:21,3:14,2:117.372:366.612,131.36:0.822319,0.822319:0,0,1 +chr1 3050738 . tatttatttatttatttatttatttatt tatttatttatt . PASS END=3050765;RU=tatt;PERIOD=4;REF=7;GRID=1,6;STUTTERUP=0.00261671;STUTTERDOWN=0.0166551;STUTTERP=0.640408;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:14:0.0818061:3,3:1-6,1-6:0,12,0,2:NULL:3,2:123.205:366.612,131.36:1.27442,1.27442:1,0,0 +chr1 3050955 . acacacacacacacacacacacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacac . PASS END=3051002;RU=ac;PERIOD=2;REF=24;GRID=14,23;STUTTERUP=0.0649655;STUTTERDOWN=0.244322;STUTTERP=0.718977;EXPTHRESH=24 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:32:0.569695:19,19:17-20,17-20:15,8,0,8:17,3|18,2|19,10:6,1|7,2|12,1|13,2|16,1|17,1:221.818:366.612,131.36:0.927845,0.927845:1,0,0 +chr1 3051394 . tttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttgg tttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttgg,tttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttggtttttgg . PASS END=3051533;RU=tttttgg;PERIOD=7;REF=20;GRID=9,55;STUTTERUP=0.05;STUTTERDOWN=0.05;STUTTERP=0.9;EXPTHRESH=20 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:44:0.271392:17,33:12-22,27-40:0,8,11,24:NULL:3,3|4,2|5,2|6,1|7,1|8,1|9,1|10,1|11,3|12,1|14,1|15,2|16,1|17,4:373:366.612,131.36:3.3949,3.70244:0,0.99537,0.00464368 +chr1 3062124 . atacatacatacatacatacatacatacatacatacatacatac . . PASS END=3062167;RU=atac;PERIOD=4;REF=11;GRID=8,19;STUTTERUP=0.0109539;STUTTERDOWN=0.034804;STUTTERP=0.750815;EXPTHRESH=11 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:46:0.999926:11,11:11-16,11-16:16,17,0,12:11,16:4,2|5,5|6,1|7,1|10,3:309.428:366.612,131.36:1.95404,1.95404:9.34602e-34,3.55638e-05,0.999964 +chr1 3063324 . atttatttatttatttatttatttatttatttatttatttattt atttatttatttatttatttatttattt . PASS END=3063367;RU=attt;PERIOD=4;REF=11;GRID=7,13;STUTTERUP=0.0108517;STUTTERDOWN=0.0430953;STUTTERP=0.532319;EXPTHRESH=11 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:11:0.0401205:7,7:7-10,7-10:0,6,0,4:NULL:3,3|4,1:84.8502:366.612,131.36:1.35575,1.35575:0.460155,0.439871,0.100118 +chr1 3068357 . tgtgtgtgtgtg tgtgtgtgtg . PASS END=3068368;RU=tg;PERIOD=2;REF=6;GRID=2,8;STUTTERUP=0.00837821;STUTTERDOWN=0.015849;STUTTERP=0.98956;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:42:1:5,5:5-5,5-5:28,14,0,0:5,28:NULL:237.617:366.612,131.36:0,0:1,3.0363e-08,0 +chr1 3072369 . tttatttattta . . PASS END=3072380;RU=ttta;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000447124;STUTTERDOWN=0.00215882;STUTTERP=0.984306;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:0.999994:3,3:3-3,3-3:19,18,0,0:3,19:NULL:243.124:366.612,131.36:0,0:0,1.2668e-05,0.999987 +chr1 3072798 . ttttgttttgttttgttttgttttg . . PASS END=3072822;RU=ttttg;PERIOD=5;REF=5;GRID=2,8;STUTTERUP=0.000598337;STUTTERDOWN=0.0062851;STUTTERP=0.535057;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:0.999778:5,5:5-5,5-5:14,17,0,5:5,14:3,3|4,2:248.589:366.612,131.36:0,0:0,0.000141535,0.999858 +chr1 3074617 . gaaagaaagaaa . . PASS END=3074628;RU=gaaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000471948;STUTTERDOWN=0.00227867;STUTTERP=0.984306;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:1:3,3:3-3,3-3:31,7,0,0:3,31:NULL:187.183:366.612,131.36:0,0:0,1.99785e-09,1 +chr1 3074661 . catgcatgcatgcatg catgcatgcatgcatgcatg . PASS END=3074676;RU=catg;PERIOD=4;REF=4;GRID=2,8;STUTTERUP=0.000496248;STUTTERDOWN=0.0113372;STUTTERP=0.978623;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:31:0.999956:5,5:5-5,5-5:18,13,0,0:5,18:NULL:190.145:366.612,131.36:0,0:0,2.90782e-05,0.999972 +chr1 3078669 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=3078700;RU=tg;PERIOD=2;REF=16;GRID=33,39;STUTTERUP=0.0723727;STUTTERDOWN=0.133573;STUTTERP=0.823877;EXPTHRESH=16 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:31:0.0317504:36,36:33-36,33-36:0,9,0,21:NULL:6,2|7,1|12,4|15,1|18,2|19,1|21,1|22,1|25,2|26,1|30,2|31,1|33,2:249.104:366.612,131.36:0.717805,0.717805:0,0,1 +chr1 3079448 . taaataaataaa . . PASS END=3079459;RU=taaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00051765;STUTTERDOWN=0.0010353;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:30:0.993512:3,3:3-3,3-3:9,19,0,2:3,9:2,1|3,1:217.894:366.612,131.36:0,0:6.05535e-38,0.00285955,0.997148 +chr1 3079495 . aagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaag aagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaag . PASS END=3079545;RU=aag;PERIOD=3;REF=17;GRID=21,27;STUTTERUP=0.0113951;STUTTERDOWN=0.135689;STUTTERP=0.735614;EXPTHRESH=17 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:26:0.313861:24,24:22-25,22-25:2,16,0,8:24,2:8,1|10,1|11,1|15,1|20,2|22,1|24,1:218.24:366.612,131.36:0.736676,0.736676:0,0,1 +chr1 3083387 . tgacttgacttgact . . PASS END=3083401;RU=tgact;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000529595;STUTTERDOWN=0.00105919;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:45:1:3,3:3-3,3-3:23,22,0,0:3,23:NULL:298.503:366.612,131.36:0,0:0,7.11885e-07,1 +chr1 3086726 . acccacccaccc . . PASS END=3086737;RU=accc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00081144;STUTTERDOWN=0.00081144;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:43:0.99608:3,3:3-3,3-3:11,32,0,0:3,11:NULL:333.133:366.612,131.36:0,0:2.92855e-34,0.00311361,0.996897 +chr1 3086953 . aacaacaacaacaac aacaacaacaacaacaac . PASS END=3086967;RU=aac;PERIOD=3;REF=5;GRID=3,9;STUTTERUP=0.00268351;STUTTERDOWN=0.0324385;STUTTERP=0.975669;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:47:0.999987:6,6:6-6,6-6:19,24,0,4:6,19:3,1|4,3:327.885:366.612,131.36:0,0:0,1.24015e-05,0.999987 +chr1 3087313 . ggttggttggtt . . PASS END=3087324;RU=ggtt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00118886;STUTTERDOWN=0.00237769;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:0.267226:3,3:1-3,1-3:2,31,0,0:3,2:NULL:290.32:366.612,131.36:0.697862,0.697862:2.84597e-06,0.590135,0.40994 +chr1 3091604 . gggtgggtgggt . . PASS END=3091615;RU=gggt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00127785;STUTTERDOWN=0.00127785;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:13:0.930378:3,3:3-3,3-3:7,6,0,0:3,7:NULL:80.4305:366.612,131.36:0,0:5.49869e-21,0.0321949,0.967864 +chr1 3095754 . tctctctctctc . . PASS END=3095765;RU=tc;PERIOD=2;REF=6;GRID=3,9;STUTTERUP=0.00399009;STUTTERDOWN=0.00868085;STUTTERP=0.949753;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:43:1:6,6:6-6,6-6:25,18,0,0:6,25:NULL:259.181:366.612,131.36:0,0:0,1.55939e-07,1 +chr1 3095926 . aaaataaaataaaataaaat aaaataaaataaaataaaataaaat . PASS END=3095945;RU=aaaat;PERIOD=5;REF=4;GRID=2,8;STUTTERUP=0.00213409;STUTTERDOWN=0.0178079;STUTTERP=0.801178;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:45:1:5,5:5-5,5-5:28,14,0,3:5,28:2,1|3,1|4,1:267.093:366.612,131.36:0,0:0,1.22478e-08,1 +chr1 3095965 . caaacaaacaaa . . PASS END=3095976;RU=caaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000955391;STUTTERDOWN=0.00161478;STUTTERP=0.949235;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:24:0.845777:3,3:3-3,3-3:5,17,0,2:3,5:2,2:186.828:366.612,131.36:0,0:6.79616e-16,0.074876,0.92522 +chr1 3097482 . ttgttgttgttgttg . . PASS END=3097496;RU=ttg;PERIOD=3;REF=5;GRID=2,8;STUTTERUP=0.00150659;STUTTERDOWN=0.0119338;STUTTERP=0.978331;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:1:5,5:5-5,5-5:20,11,0,0:5,20:NULL:182.636:366.612,131.36:0,0:0,6.53813e-06,0.999994 +chr1 3099936 . gggtgggtgggt . . PASS END=3099947;RU=gggt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000860538;STUTTERDOWN=0.000860538;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:30:0.995606:3,3:3-3,3-3:11,19,0,0:3,11:NULL:210.358:366.612,131.36:0,0:1.47805e-34,0.00247729,0.997527 +chr1 3105146 . ggaaggaaggaa ggaaggaa . PASS END=3105157;RU=ggaa;PERIOD=4;REF=3;GRID=1,5;STUTTERUP=0.000538242;STUTTERDOWN=0.00615004;STUTTERP=0.976204;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:17:0.101965:2,2:2-3,2-3:0,15,0,2:NULL:2,2:149.768:366.612,131.36:0.390807,0.390807:0.150094,0.489507,0.360547 +chr1 3116455 . atatatatatatatatatatatatatatatatatatatatatatatatatatatatat atatatatatatatatatatatatatatatatatatatatatat . PASS END=3116512;RU=at;PERIOD=2;REF=29;GRID=19,25;STUTTERUP=0.105251;STUTTERDOWN=0.31819;STUTTERP=0.644287;EXPTHRESH=29 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:9:0.138491:22,22:19-22,19-22:2,7,0,0:22,2:NULL:72.0894:366.612,131.36:1.39572,1.39572:1,0,0 +chr1 3120976 . ttgttgttgttg . . PASS END=3120987;RU=ttg;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000414234;STUTTERDOWN=0.00128833;STUTTERP=0.92706;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:42:1:4,4:4-4,4-4:21,21,0,0:4,21:NULL:271.316:366.612,131.36:0,0:0,4.39296e-06,0.999995 +chr1 3122158 . agagagagagagagagagagagagagagagagag agagagagagagagagagagagagagagagagagagag . PASS END=3122191;RU=ag;PERIOD=2;REF=17;GRID=16,23;STUTTERUP=0.0557325;STUTTERDOWN=0.202188;STUTTERP=0.659533;EXPTHRESH=17 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:37:0.385809:19,19:19-20,19-20:4,29,0,3:19,4:7,1|9,1|17,1:298.939:366.612,131.36:0.696174,0.696174:5.99569e-16,0.144868,0.855214 +chr1 3122249 . cagacagacaga . . PASS END=3122260;RU=caga;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000305431;STUTTERDOWN=0.00147469;STUTTERP=0.984306;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:46:1:3,3:3-3,3-3:37,9,0,0:3,37:NULL:227.276:366.612,131.36:0,0:0,3.83981e-11,1 +chr1 3125367 . aacaaacaaacaaaca aaca . PASS END=3125382;RU=aaca;PERIOD=4;REF=4;GRID=1,103;STUTTERUP=0.00145196;STUTTERDOWN=0.00291806;STUTTERP=0.753251;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:15:0.0664576:1,1:1-1,1-1:0,15,0,0:NULL:NULL:131.572:366.612,131.36:0,0:0.296148,0.540177,0.1637 +chr1 3125745 . ttattattattatta ttattattattattattatta . PASS END=3125759;RU=tta;PERIOD=3;REF=5;GRID=7,13;STUTTERUP=0.00167017;STUTTERDOWN=0.0227472;STUTTERP=0.459907;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:6:0.0303655:7,7:7-10,7-10:0,5,0,0:NULL:NULL:44.1227:366.612,131.36:1.34223,1.34223:0,0,1 +chr1 3130290 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=3130337;RU=gt;PERIOD=2;REF=24;GRID=20,43;STUTTERUP=0.0714026;STUTTERDOWN=0.254426;STUTTERP=0.689813;EXPTHRESH=24 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/1:37:0.382746:24,42:24-25,23-42:15,17,0,5:23,4|24,8|25,3:14,1|17,1|19,1|21,1|40,1:291.567:366.612,131.36:0.358902,8.71943:5.58835e-11,0.00100609,0.998998 +chr1 3131093 . tgactgactgac . . PASS END=3131104;RU=tgac;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000439253;STUTTERDOWN=0.000439253;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:45:1:3,3:3-3,3-3:21,24,0,0:3,21:NULL:299.824:366.612,131.36:0,0:0,4.24596e-06,0.999995 +chr1 3132979 . ctccctccctcc . . PASS END=3132990;RU=ctcc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000435421;STUTTERDOWN=0.000870842;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:1:3,3:3-3,3-3:21,16,0,0:3,21:NULL:232.377:366.612,131.36:0,0:0,4.51274e-06,0.999995 +chr1 3134119 . ttgttgttgttgttgttgttgttgttgttgttgttgttgttg . . PASS END=3134160;RU=ttg;PERIOD=3;REF=14;GRID=10,17;STUTTERUP=0.0125024;STUTTERDOWN=0.0664097;STUTTERP=0.665703;EXPTHRESH=14 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:0.978038:14,14:13-14,13-14:9,18,0,11:14,9:3,1|4,1|6,2|7,1|8,1|10,1|12,2|13,2:291.17:366.612,131.36:0.390807,0.390807:1.78453e-18,0.0105156,0.989507 +chr1 3153384 . aataaataaata . . PASS END=3153395;RU=aata;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000846944;STUTTERDOWN=0.00572588;STUTTERP=0.964325;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:1:3,3:3-3,3-3:29,6,0,0:3,29:NULL:172.88:366.612,131.36:0,0:0,1.09816e-08,1 +chr1 3161509 . gggtgggtgggt . . PASS END=3161520;RU=gggt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00121178;STUTTERDOWN=0.00119178;STUTTERP=0.947003;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:22:0.994566:3,3:3-3,3-3:11,11,0,0:3,11:NULL:145.407:366.612,131.36:0,0:7.00828e-33,0.00300606,0.997003 +chr1 3162873 . tgctgctgctgc tgctgctgctgctgctgc . PASS END=3162884;RU=tgc;PERIOD=3;REF=4;GRID=3,9;STUTTERUP=0.00123317;STUTTERDOWN=0.0149159;STUTTERP=0.786764;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:20:0.999286:6,6:6-6,6-6:14,6,0,0:6,14:NULL:113.711:366.612,131.36:0,0:0,0.000160033,0.999842 +chr1 3163213 . attctattctattct . . PASS END=3163227;RU=attct;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000687725;STUTTERDOWN=0.00196458;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:25:0.999547:3,3:3-3,3-3:14,11,0,0:3,14:NULL:153.89:366.612,131.36:0,0:2.8026e-45,0.000269175,0.999735 +chr1 3164426 . tcttcctcttcctcttcc . . PASS END=3164443;RU=tcttcc;PERIOD=6;REF=3;GRID=1,6;STUTTERUP=0.000511617;STUTTERDOWN=0.0014615;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:40:1:3,3:3-3,3-3:24,16,0,0:3,24:NULL:247.76:366.612,131.36:0,0:0,8.32048e-07,1 +chr1 3164472 . tcatcatcatcatca . . PASS END=3164486;RU=tca;PERIOD=3;REF=5;GRID=2,8;STUTTERUP=0.00411803;STUTTERDOWN=0.0089592;STUTTERP=0.849679;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:44:1:5,5:5-5,5-5:31,13,0,0:5,31:NULL:245.878:366.612,131.36:0,0:0,5.79757e-09,1 +chr1 3166251 . aaacaaacaaac . . PASS END=3166262;RU=aaac;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000484016;STUTTERDOWN=0.00138266;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:1:3,3:3-3,3-3:24,15,0,0:3,24:NULL:232.352:366.612,131.36:0,0:0,4.06024e-07,1 +chr1 3169195 . gtagtagtagta . . PASS END=3169206;RU=gta;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000393482;STUTTERDOWN=0.000786963;STUTTERP=0.999;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:1:4,4:4-4,4-4:23,12,0,2:4,23:3,2:215.508:366.612,131.36:0,0:0,3.28087e-07,1 +chr1 3169225 . acacacacacacacacacacacacacacacacac acacacacacacacacacacacacac . PASS END=3169258;RU=ac;PERIOD=2;REF=17;GRID=9,17;STUTTERUP=0.0474585;STUTTERDOWN=0.116816;STUTTERP=0.871257;EXPTHRESH=17 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:44:0.98882:13,13:13-14,13-14:11,15,0,16:13,11:5,1|6,3|7,1|8,2|9,3|10,1|11,1|12,4:311.885:366.612,131.36:0.341835,0.341835:0.998596,0.00140777,2.52175e-40 +chr1 3169275 . aataaataaata . . PASS END=3169286;RU=aata;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000587388;STUTTERDOWN=0.00117477;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:23:0.98337:3,3:3-3,3-3:9,14,0,0:3,9:NULL:164.015:366.612,131.36:0,0:2.11896e-29,0.0105485,0.989476 +chr1 3170541 . acaaaacaaaacaaaacaaa . . PASS END=3170560;RU=acaaa;PERIOD=5;REF=4;GRID=1,7;STUTTERUP=0.00102565;STUTTERDOWN=0.00205129;STUTTERP=0.627854;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:46:1:4,4:4-4,4-4:23,21,0,2:4,23:2,1|3,1:294.167:366.612,131.36:0,0:0,7.87942e-07,1 +chr1 3180457 . gggtgggtgggt . . PASS END=3180468;RU=gggt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00107064;STUTTERDOWN=0.00107064;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:27:0.927026:3,3:3-3,3-3:7,20,0,0:3,7:NULL:201.976:366.612,131.36:0,0:2.07325e-21,0.0459557,0.95412 +chr1 3184125 . acacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacac . PASS END=3184152;RU=ac;PERIOD=2;REF=14;GRID=16,23;STUTTERUP=0.05108;STUTTERDOWN=0.164228;STUTTERP=0.762858;EXPTHRESH=14 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:32:0.972076:19,19:19-20,19-20:9,9,0,13:19,9:5,1|6,2|7,2|9,1|11,1|12,1|13,2|15,1|17,2:230.576:366.612,131.36:0.398507,0.398507:0,0,1 +chr1 3184524 . ttgttgttgttgttgttg . . PASS END=3184541;RU=ttg;PERIOD=3;REF=6;GRID=3,9;STUTTERUP=0.000452284;STUTTERDOWN=0.00873488;STUTTERP=0.804035;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:0.999765:6,6:6-6,6-6:15,19,0,3:6,15:5,3:255.504:366.612,131.36:0,0:0,0.000105367,0.999895 +chr1 3185654 . agagagagagag . . PASS END=3185665;RU=ag;PERIOD=2;REF=6;GRID=3,9;STUTTERUP=0.00442668;STUTTERDOWN=0.0123968;STUTTERP=0.963303;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:30:0.999571:6,6:6-6,6-6:14,16,0,0:6,14:NULL:206.063:366.612,131.36:0,0:5.27875e-34,0.000291058,0.999712 +chr1 3188551 . gctttttgctttttgctttttgctttttgctttttgctttttgctttttgcttttt gctttttgctttttgctttttgctttttgctttttgctttttgcttttt . PASS END=3188606;RU=gcttttt;PERIOD=7;REF=8;GRID=4,10;STUTTERUP=0.0374646;STUTTERDOWN=0.0116903;STUTTERP=0.78626;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:22:0.98448:7,7:7-7,7-7:9,9,0,4:7,9:5,2|6,1|7,1:146.862:366.612,131.36:0,0:0.990598,0.00942173,4.03629e-19 +chr1 3189480 . ttattattattattattattattattattattattattattattatta ttattattattattattattattattattattattattattattattatta . PASS END=3189527;RU=tta;PERIOD=3;REF=16;GRID=14,23;STUTTERUP=0.0672182;STUTTERDOWN=0.0679338;STUTTERP=0.673379;EXPTHRESH=16 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:30:0.627346:17,17:17-20,17-20:5,14,0,9:17,5:5,1|9,2|10,2|11,3|15,1:227.535:366.612,131.36:1.36051,1.36051:3.08894e-09,0.0980891,0.902012 +chr1 3190239 . tttgtttgtttgtttg . . PASS END=3190254;RU=tttg;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.0019452;STUTTERDOWN=0.0019452;STUTTERP=0.95916;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:1.00001:4,4:4-4,4-4:21,12,0,5:4,21:3,5:231.473:366.612,131.36:0,0:0,9.58837e-07,1 +chr1 3192683 . gtgtgtgtgtgtgt . . PASS END=3192696;RU=gt;PERIOD=2;REF=7;GRID=3,11;STUTTERUP=0.0132672;STUTTERDOWN=0.0241373;STUTTERP=0.855381;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:1.00001:7,7:7-8,7-8:20,8,0,5:7,20:4,1|5,1|6,3:190.257:366.612,131.36:0.195027,0.195027:3.28507e-39,2.62655e-06,1 +chr1 3192934 . tatatatatatata . . PASS END=3192947;RU=ta;PERIOD=2;REF=7;GRID=4,11;STUTTERUP=0.0299674;STUTTERDOWN=0.0498574;STUTTERP=0.637761;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:1:7,7:7-7,7-7:24,8,0,0:7,24:NULL:166.924:366.612,131.36:0,0:7.62517e-41,5.24495e-07,1 +chr1 3193519 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg,tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=3193554;RU=tg;PERIOD=2;REF=18;GRID=22,29;STUTTERUP=0.0571216;STUTTERDOWN=0.188217;STUTTERP=0.590402;EXPTHRESH=18 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:16:0.896001:25,26:25-26,25-26:5,6,0,5:25,3|26,2:6,1|8,1|14,1|17,1|18,1:130.22:366.612,131.36:0.363246,0.374147:0,0,1 +chr1 3194182 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg,tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=3194229;RU=tg;PERIOD=2;REF=24;GRID=22,29;STUTTERUP=0.041669;STUTTERDOWN=0.309525;STUTTERP=0.442848;EXPTHRESH=24 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:41:0.881189:25,26:25-26,26-26:9,14,0,18:25,4|26,5:6,1|7,1|8,1|10,1|14,4|15,2|16,1|17,1|18,1|19,3|23,1|24,1:322.102:366.612,131.36:0.431574,0:4.54279e-23,0.000752893,0.999249 +chr1 3194304 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg,tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=3194333;RU=tg;PERIOD=2;REF=15;GRID=11,36;STUTTERUP=0.0456538;STUTTERDOWN=0.211879;STUTTERP=0.828231;EXPTHRESH=15 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:44:0.281101:16,36:16-16,16-36:21,11,0,11:15,7|16,14:5,1|6,1|9,1|13,1|14,1|15,1|16,1|19,2|22,1|33,1:312.349:366.612,131.36:0,7.03249:0,9.98693e-29,1 +chr1 3198131 . aaaaaacaaaaaacaaaaaac aaaaaacaaaaaacaaaaaacaaaaaac . PASS END=3198151;RU=aaaaaac;PERIOD=7;REF=3;GRID=1,7;STUTTERUP=0.00049065;STUTTERDOWN=0.00573035;STUTTERP=0.71264;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:20:0.379613:4,4:3-4,3-4:2,11,0,6:4,2:2,2|3,4:152.071:366.612,131.36:0.469019,0.469019:5.91913e-40,0.0394766,0.960594 +chr1 3207640 . tttgtttgtttgtttgtttgtttg tttgtttgtttgtttgtttgtttgtttgtttgtttgtttgtttg . PASS END=3207663;RU=tttg;PERIOD=4;REF=6;GRID=1,13;STUTTERUP=0.00180877;STUTTERDOWN=0.0224933;STUTTERP=0.705329;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:21:0.0797823:11,11:6-12,6-12:0,11,0,10:NULL:2,3|3,1|4,1|6,3|9,1|10,1:178.745:366.612,131.36:2.00988,2.00988:4.63405e-39,0.0583273,0.941757 +chr1 3209528 . aaaaacaaaaacaaaaacaaaaac . . PASS END=3209551;RU=aaaaac;PERIOD=6;REF=4;GRID=1,7;STUTTERUP=0.000545992;STUTTERDOWN=0.00433416;STUTTERP=0.824224;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:21:0.916764:4,4:1-4,1-4:7,14,0,0:4,7:NULL:163.65:366.612,131.36:0.5093,0.5093:4.93839e-24,0.0720031,0.92809 +chr1 3209577 . aacaaaacaaaacaa . . PASS END=3209591;RU=aacaa;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000506006;STUTTERDOWN=0.002024;STUTTERP=0.844424;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:24:0.999471:3,3:3-3,3-3:14,10,0,0:3,14:NULL:149.919:366.612,131.36:0,0:0,0.000357457,0.999644 +chr1 3212208 . tatttatttatt . . PASS END=3212219;RU=tatt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00040913;STUTTERDOWN=0.00116873;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:0.999776:3,3:3-3,3-3:15,22,0,2:3,15:2,2:275.853:366.612,131.36:0,0:0,0.000127184,0.999873 +chr1 3219276 . attattattattattattattattattattatt attattattattattattattattattatt . PASS END=3219308;RU=att;PERIOD=3;REF=11;GRID=6,13;STUTTERUP=0.0326382;STUTTERDOWN=0.0584049;STUTTERP=0.795636;EXPTHRESH=11 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:23:0.993726:10,10:9-10,9-10:11,8,0,3:10,11:3,1|9,2:143.553:366.612,131.36:0.21692,0.21692:0.996844,0.00316656,1.55989e-15 +chr1 3224265 . aaacaaacaaac . . PASS END=3224276;RU=aaac;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000582895;STUTTERDOWN=0.00116579;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:1.00001:3,3:3-3,3-3:21,10,0,0:3,21:NULL:173.555:366.612,131.36:0,0:0,3.11222e-06,1 +chr1 3229231 . aacaaaacaaaacaaaacaaaacaa aacaaaacaaaacaaaacaa . PASS END=3229255;RU=aacaa;PERIOD=5;REF=5;GRID=1,7;STUTTERUP=0.00410225;STUTTERDOWN=0.00614075;STUTTERP=0.608941;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:18:0.969771:4,4:4-4,4-4:9,9,0,0:4,9:NULL:117.579:366.612,131.36:0,0:0.990731,0.00929149,1.05996e-22 +chr1 3230661 . acacacacacacacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacacacacacacacacacacacac . PASS END=3230700;RU=ac;PERIOD=2;REF=20;GRID=18,30;STUTTERUP=0.0495699;STUTTERDOWN=0.152459;STUTTERP=0.782277;EXPTHRESH=20 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:16:0.0246166:29,29:18-29,18-29:0,9,0,6:NULL:11,1|12,1|17,1|20,1|22,1|27,1:132.661:366.612,131.36:2.88399,2.88399:3.81652e-23,0.111212,0.888885 +chr1 3247218 . aaaacaaaacaaaac . . PASS END=3247232;RU=aaaac;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000659758;STUTTERDOWN=0.00188469;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:0.999292:3,3:3-3,3-3:13,15,0,3:3,13:2,3:213.981:366.612,131.36:0,0:4.88072e-42,0.000339974,0.99966 +chr1 3248425 . ttgcttgcttgcttgc . . PASS END=3248440;RU=ttgc;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000389733;STUTTERDOWN=0.00263484;STUTTERP=0.958596;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:50:1:4,4:4-4,4-4:32,16,0,2:4,32:2,1|3,1:292.716:366.612,131.36:0,0:0,9.84893e-10,1 +chr1 3250571 . accaccaccaccacc accaccaccacc . PASS END=3250585;RU=acc;PERIOD=3;REF=5;GRID=1,7;STUTTERUP=0.0125677;STUTTERDOWN=0.00580437;STUTTERP=0.899359;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:39:1:4,4:4-4,4-4:21,18,0,0:4,21:NULL:250.656:366.612,131.36:0,0:1,2.14843e-06,0 +chr1 3256241 . aaacaaacaaac . . PASS END=3256252;RU=aaac;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000432338;STUTTERDOWN=0.00123503;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:1:3,3:3-3,3-3:25,8,0,0:3,25:NULL:170.187:366.612,131.36:0,0:0,1.7126e-07,1 +chr1 3257455 . gaagaagaagaagaa . . PASS END=3257469;RU=gaa;PERIOD=3;REF=5;GRID=2,8;STUTTERUP=0.00327135;STUTTERDOWN=0.00916136;STUTTERP=0.889517;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:1.00001:5,5:5-5,5-5:23,11,0,3:5,23:4,3:216.8:366.612,131.36:0,0:0,4.39512e-07,1 +chr1 3263762 . acccacccaccc . . PASS END=3263773;RU=accc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000458929;STUTTERDOWN=0.0018357;STUTTERP=0.987382;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:0.999996:3,3:3-3,3-3:20,15,0,0:3,20:NULL:218.28:366.612,131.36:0,0:0,1.16154e-05,0.999987 +chr1 3266661 . tctctctctctctctctctctctctctctctctctctctctctctc tctctctctctctctctctctctctctctctc,tctctctctctctctctctctctctctctctctc . PASS END=3266706;RU=tc;PERIOD=2;REF=23;GRID=12,21;STUTTERUP=0.0987588;STUTTERDOWN=0.213565;STUTTERP=0.565437;EXPTHRESH=23 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:23:0.859583:16,17:16-18,15-18:6,10,0,5:16,4|17,2:6,1|14,2|15,2:158.259:366.612,131.36:0.702063,0.743564:1,0,0 +chr1 3266707 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=3266746;RU=tg;PERIOD=2;REF=20;GRID=17,26;STUTTERUP=0.0475546;STUTTERDOWN=0.0522177;STUTTERP=0.382835;EXPTHRESH=20 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/1:33:0.271464:20,23:20-23,21-26:3,14,0,15:20,3:6,3|7,3|8,1|10,1|11,1|13,1|15,2|21,2|23,1:261.687:366.612,131.36:0.726627,1.33784:4.26235e-26,2.79685e-05,0.999972 +chr1 3283714 . tgtttgtttgtttgtttgtt . . PASS END=3283733;RU=tgtt;PERIOD=4;REF=5;GRID=2,8;STUTTERUP=0.00152377;STUTTERDOWN=0.0127142;STUTTERP=0.72986;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:0.998014:5,5:5-5,5-5:13,20,0,3:5,13:2,1|3,2:255.744:366.612,131.36:0,0:1.99649e-38,0.00152728,0.99848 +chr1 3284144 . aaccaaccaacc . . PASS END=3284155;RU=aacc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000827569;STUTTERDOWN=0.000413785;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:45:1:3,3:3-3,3-3:27,18,0,0:3,27:NULL:276.757:366.612,131.36:0,0:0,3.40343e-08,1 +chr1 3284442 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg,tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=3284483;RU=tg;PERIOD=2;REF=21;GRID=17,28;STUTTERUP=0.0745925;STUTTERDOWN=0.180569;STUTTERP=0.608323;EXPTHRESH=21 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:47:0.804412:22,23:21-22,21-25:14,13,0,17:21,6|22,8:5,1|6,2|7,1|8,1|9,1|10,1|11,1|12,1|15,1|17,2|18,1|21,2|22,1|23,1:336.16:366.612,131.36:0.484441,1.48323:2.93572e-42,1.0899e-08,1 +chr1 3284513 . tgaatgaatgaatgaatgaatgaa tgaatgaatgaatgaatgaatgaatgaa . PASS END=3284536;RU=tgaa;PERIOD=4;REF=6;GRID=3,10;STUTTERUP=0.00383499;STUTTERDOWN=0.021685;STUTTERP=0.768338;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/1:37:0.999928:6,7:6-7,7-7:29,8,0,0:6,7|7,22:NULL:208.743:366.612,131.36:0.382696,0:0,2.17331e-12,1 +chr1 3286188 . catcatcatcat . . PASS END=3286199;RU=cat;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000408851;STUTTERDOWN=0.00197402;STUTTERP=0.984306;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:47:1:4,4:4-4,4-4:28,16,0,3:4,28:3,3:276.88:366.612,131.36:0,0:0,1.38019e-08,1 +chr1 3287342 . tctcctctcctctcctctcctctcctctcctctcctctcctctcctctcctctcctctcctctcctctcctctcctctcctctcctctcctctcctctcc tctcctctcctctcctctcctctcctctcctctcctctcc . PASS END=3287441;RU=tctcc;PERIOD=5;REF=20;GRID=1,11;STUTTERUP=0.0698385;STUTTERDOWN=0.166848;STUTTERP=0.858892;EXPTHRESH=20 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:6:0.0428838:8,8:1-8,1-8:0,3,0,3:NULL:7,1|8,2:47.3284:366.612,131.36:1.99367,1.99367:1,0,0 +chr1 3287445 . tccccctccccctccccctccccc tccccctccccctccccctccccctccccc . PASS END=3287468;RU=tccccc;PERIOD=6;REF=4;GRID=2,8;STUTTERUP=0.00875454;STUTTERDOWN=0.00716118;STUTTERP=0.895621;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:6:0.557197:5,5:5-5,5-5:4,2,0,0:5,4:NULL:34.0361:366.612,131.36:0.29703,0.29703:5.92393e-13,0.157841,0.842234 +chr1 3287528 . ctttctttctttctttctttctttctttctttctttctttctttctttctttcttt ctttctttctttctttctttctttcttt,ctttctttctttctttctttctttctttctttctttctttctttctttctttctttcttt . PASS END=3287583;RU=cttt;PERIOD=4;REF=14;GRID=3,17;STUTTERUP=0.0383965;STUTTERDOWN=0.0306392;STUTTERP=0.415684;EXPTHRESH=14 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:10:0.0290867:7,15:3-14,6-15:0,6,0,2:NULL:4,1|14,1:69.6104:366.612,131.36:3.94079,3.01377:6.41645e-08,0.806418,0.193633 +chr1 3298789 . aaaacaaaacaaaacaaaac aaaacaaaacaaaacaaaacaaaacaaaacaaaac . PASS END=3298808;RU=aaaac;PERIOD=5;REF=4;GRID=4,10;STUTTERUP=0.00104589;STUTTERDOWN=0.0200292;STUTTERP=0.427088;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:31:0.999963:7,7:7-7,7-7:18,11,0,2:7,18:4,1|5,1:193.51:366.612,131.36:0,0:0,0,1 +chr1 3308941 . aaaataaaataaaataaaataaaataaaat aaaat . PASS END=3308970;RU=aaaat;PERIOD=5;REF=6;GRID=1,103;STUTTERUP=0.00152719;STUTTERDOWN=0.00869896;STUTTERP=0.599176;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP .:.:.:.:.:.:.:.:.:.:.:. +chr1 3309296 . ttctttctttctttctttctttctttctttctttctttctttct ttct,ttctttct . PASS END=3309339;RU=ttct;PERIOD=4;REF=11;GRID=1,103;STUTTERUP=0.00381827;STUTTERDOWN=0.018986;STUTTERP=0.616437;EXPTHRESH=11 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:11:0.0507287:1,2:1-2,1-2:0,11,0,0:NULL:NULL:95.391:366.612,131.36:0.499387,0.494455:0.718816,0.268655,0.0125524 +chr1 3311045 . aagaaaaagaaaaagaaa . . PASS END=3311062;RU=aagaaa;PERIOD=6;REF=3;GRID=1,6;STUTTERUP=0.00125588;STUTTERDOWN=0.00303184;STUTTERP=0.986219;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:25:0.983812:3,3:3-3,3-3:9,16,0,0:3,9:NULL:183.474:366.612,131.36:0,0:2.32816e-26,0.0130668,0.986963 +chr1 3317551 . taaataaataaa . . PASS END=3317562;RU=taaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00151164;STUTTERDOWN=0.00151164;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:11:0.60986:3,3:3-3,3-3:4,7,0,0:3,4:NULL:78.8406:366.612,131.36:0,0:5.51413e-12,0.183566,0.816501 +chr1 3317572 . tatatatatatatatatatatatatatatatatatatatatatatatatatatatata ta . PASS END=3317629;RU=ta;PERIOD=2;REF=29;GRID=1,103;STUTTERUP=0.0773871;STUTTERDOWN=0.161673;STUTTERP=0.676637;EXPTHRESH=29 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:10:0.00216521:1,1:1-26,1-26:0,10,0,0:NULL:NULL:89.3505:366.612,131.36:6.01366,6.01366:0.64016,0.333863,0.0260525 +chr1 3317629 . agagagagagagagagagagagagagagagagagag agagagagagagagagagagagagagagagagag . PASS END=3317664;RU=ag;PERIOD=2;REF=18;GRID=1,20;STUTTERUP=0.0415197;STUTTERDOWN=0.0292732;STUTTERP=0.739384;EXPTHRESH=18 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:10:0.0145036:17,17:8-20,8-20:0,7,0,3:NULL:8,1|10,1|17,1:89.8084:366.612,131.36:4.75419,4.75419:0.228232,0.664371,0.107496 +chr1 3318469 . ttttgttttgttttg . . PASS END=3318483;RU=ttttg;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000441185;STUTTERDOWN=0.00176472;STUTTERP=0.987382;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:45:1:3,3:2-3,2-3:23,21,0,0:3,23:NULL:290.045:366.612,131.36:0.253975,0.253975:0,9.8791e-07,1 +chr1 3319830 . ttgttgttgttgttgttgttg . . PASS END=3319850;RU=ttg;PERIOD=3;REF=7;GRID=4,10;STUTTERUP=0.00255882;STUTTERDOWN=0.00671547;STUTTERP=0.89929;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:25:0.999884:7,7:7-7,7-7:17,8,0,0:7,17:NULL:143.581:366.612,131.36:0,0:5.60519e-45,7.1866e-05,0.999932 +chr1 3325716 . ctctctctctctctctctctctctctct ctctctctctctctctctctctct,ctctctctctctctctctctctctct . PASS END=3325743;RU=ct;PERIOD=2;REF=14;GRID=1,15;STUTTERUP=0.0772068;STUTTERDOWN=0.10279;STUTTERP=0.767651;EXPTHRESH=14 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:15:0.0305249:12,13:1-15,1-15:0,12,0,3:NULL:4,1|7,1|12,1:134.041:366.612,131.36:4.67388,4.71352:0.51569,0.449359,0.0350738 +chr1 3327145 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=3327194;RU=tg;PERIOD=2;REF=25;GRID=18,24;STUTTERUP=0.0809455;STUTTERDOWN=0.172131;STUTTERP=0.818327;EXPTHRESH=25 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:24:0.453927:21,21:21-22,21-22:3,11,0,10:21,3:4,2|8,1|12,1|13,1|17,1|18,2|20,2:196.883:366.612,131.36:0.294378,0.294378:1,0,0 +chr1 3327251 . tatctatctatctatctatctatctatctatctatctatc tatctatctatctatctatctatctatctatctatctatctatctatctatctatc . PASS END=3327290;RU=tatc;PERIOD=4;REF=10;GRID=10,17;STUTTERUP=0.0135188;STUTTERDOWN=0.0320195;STUTTERP=0.505109;EXPTHRESH=10 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:32:0.950032:14,14:13-14,13-14:8,11,0,12:14,8:7,3|8,2|9,2|10,2|11,1|12,1|13,1:223.195:366.612,131.36:0.44763,0.44763:0,0,1 +chr1 3339592 . gagagagagagagagagaga gagagagagagagaga . PASS END=3339611;RU=ga;PERIOD=2;REF=10;GRID=7,13;STUTTERUP=0.0125928;STUTTERDOWN=0.064145;STUTTERP=0.836699;EXPTHRESH=10 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:9:0.0383828:8,8:8-10,8-10:0,8,0,0:NULL:NULL:75.7368:366.612,131.36:0.957892,0.957892:0.256004,0.503285,0.24073 +chr1 3339980 . tgtttgtttgtttgtttgtttgtttgtttgtt tgtttgtttgtttgtttgtttgtttgtttgtttgtt . PASS END=3340011;RU=tgtt;PERIOD=4;REF=8;GRID=6,12;STUTTERUP=0.00130532;STUTTERDOWN=0.0222601;STUTTERP=0.826033;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:37:0.999475:9,9:9-9,9-9:14,12,0,11:9,14:3,3|4,1|5,1|6,1|7,1|8,4:249.953:366.612,131.36:0,0:0,2.18235e-05,0.999979 +chr1 3340203 . tttgtttgtttgtttgtttgtttg tttgtttgtttgtttgtttg . PASS END=3340226;RU=tttg;PERIOD=4;REF=6;GRID=2,8;STUTTERUP=0.00424621;STUTTERDOWN=0.00300459;STUTTERP=0.975927;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:27:0.995765:5,5:5-5,5-5:12,15,0,0:5,12:NULL:185.688:366.612,131.36:0,0:0.998877,0.00112576,2.65565e-31 +chr1 3342039 . catgcatgcatg . . PASS END=3342050;RU=catg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000504598;STUTTERDOWN=0.000504598;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:11:0.75824:3,3:3-3,3-3:5,6,0,0:3,5:NULL:72.7852:366.612,131.36:0,0:3.67506e-17,0.125749,0.874349 +chr1 3342663 . ataaataaataa . . PASS END=3342674;RU=ataa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.0128218;STUTTERDOWN=0.00090919;STUTTERP=0.978618;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:30:1.00001:3,3:3-3,3-3:22,8,0,0:3,22:NULL:160.015:366.612,131.36:0,0:7.63848e-42,1.64445e-06,1 +chr1 3355412 . atgtatgtatgt . . PASS END=3355423;RU=atgt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000301259;STUTTERDOWN=0.00241004;STUTTERP=0.966669;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:54:1:3,3:3-3,3-3:30,24,0,0:3,30:NULL:332.388:366.612,131.36:0,0:0,1.13867e-08,1 +chr1 3357227 . ttatttatttat . . PASS END=3357238;RU=ttat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000482204;STUTTERDOWN=0.00137748;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:46:1:3,3:3-3,3-3:30,13,0,3:3,30:2,3:259.516:366.612,131.36:0,0:0,2.25091e-09,1 +chr1 3360114 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=3360159;RU=tg;PERIOD=2;REF=23;GRID=22,29;STUTTERUP=0.0803032;STUTTERDOWN=0.246049;STUTTERP=0.762402;EXPTHRESH=23 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:23:0.156806:26,26:22-26,22-26:2,11,0,9:26,2:4,1|5,1|7,1|11,1|12,1|15,1|18,2|19,1:183.118:366.612,131.36:1.29813,1.29813:1.00743e-06,0.171728,0.828341 +chr1 3361293 . ctctctctctctctctctctctctctctctctctctctctctctctctctctctct ctctctctctctctctctctctctctctctctct,ctctctctctctctctctctctctctctctctctct . PASS END=3361348;RU=ct;PERIOD=2;REF=28;GRID=12,21;STUTTERUP=0.0758785;STUTTERDOWN=0.200261;STUTTERP=0.426432;EXPTHRESH=28 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:33:0.988165:17,18:15-17,15-18:8,21,0,3:17,5|18,3:5,1|6,1|11,1:254.984:366.612,131.36:0.447192,0.872412:1,0,0 +chr1 3361348 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg,tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=3361393;RU=tg;PERIOD=2;REF=23;GRID=20,38;STUTTERUP=0.0332141;STUTTERDOWN=0.0865772;STUTTERP=0.449826;EXPTHRESH=23 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:41:0.332648:30,35:23-30,23-36:4,20,0,16:30,4:7,1|11,1|12,1|14,1|17,1|18,1|19,1|20,3|22,1|24,1|25,1|28,1|31,1|35,1:338.187:366.612,131.36:2.4871,3.85048:0,1.165e-10,1 +chr1 3365708 . tttctttctttc tttc . PASS END=3365719;RU=tttc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00668737;STUTTERDOWN=0.000453605;STUTTERP=0.528564;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/0:31:0.31096:1,3:1-1,1-6:11,17,0,3:1,11:2,1|3,2:222.859:366.612,131.36:0,0.849641:6.25475e-16,1,1.78175e-41 +chr1 3365944 . tgtgtgtgtgtg . . PASS END=3365955;RU=tg;PERIOD=2;REF=6;GRID=3,9;STUTTERUP=0.0013209;STUTTERDOWN=0.00680117;STUTTERP=0.946135;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:0.999788:6,6:6-6,6-6:15,12,0,4:6,15:5,4:193.16:366.612,131.36:0,0:5.1848e-44,8.18518e-05,0.999918 +chr1 3386948 . tctttctttctt . . PASS END=3386959;RU=tctt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000487174;STUTTERDOWN=0.00278335;STUTTERP=0.969616;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:0.997909:3,3:3-3,3-3:12,17,0,0:3,12:NULL:198.545:366.612,131.36:0,0:4.33761e-40,0.00135655,0.998648 +chr1 3388595 . acttcacttcacttc . . PASS END=3388609;RU=acttc;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000443338;STUTTERDOWN=0.00214053;STUTTERP=0.984306;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:43:1:3,3:3-3,3-3:25,15,0,3:3,25:2,3:260.848:366.612,131.36:0,0:0,1.35613e-07,1 +chr1 3390191 . tctctctctctctctctctctctctc tctctctctc . PASS END=3390216;RU=tc;PERIOD=2;REF=13;GRID=1,16;STUTTERUP=0.0243252;STUTTERDOWN=0.127296;STUTTERP=0.500139;EXPTHRESH=13 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/0:34:0.999474:5,13:3-13,13-13:23,9,0,0:3,2|5,3|13,18:NULL:203.98:366.612,131.36:1.7577,0:1.83634e-33,1,1.91746e-09 +chr1 3393075 . acacacacacacac . . PASS END=3393088;RU=ac;PERIOD=2;REF=7;GRID=4,10;STUTTERUP=0.00784269;STUTTERDOWN=0.0167073;STUTTERP=0.916704;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:47:1:7,7:7-7,7-7:24,15,0,8:7,24:5,4|6,4:291.55:366.612,131.36:0,0:0,2.26844e-07,1 +chr1 3395163 . aagaaagaaaga . . PASS END=3395174;RU=aaga;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000457664;STUTTERDOWN=0.00130738;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:1:3,3:3-3,3-3:19,16,0,0:3,19:NULL:224.847:366.612,131.36:0,0:0,9.82503e-06,0.999993 +chr1 3403481 . tatatatatatatatata tatatatatatatatatatatatatatatatatatatata . PASS END=3403498;RU=ta;PERIOD=2;REF=9;GRID=16,23;STUTTERUP=0.059321;STUTTERDOWN=0.118218;STUTTERP=0.733479;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:12:0.165483:20,20:16-20,16-20:2,9,0,0:20,2:NULL:99.2001:366.612,131.36:1.26066,1.26066:0,0,1 +chr1 3403725 . accaccaccacc . . PASS END=3403736;RU=acc;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00199994;STUTTERDOWN=0.000828438;STUTTERP=0.986219;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:45:1:4,4:4-4,4-4:27,18,0,0:4,27:NULL:262.147:366.612,131.36:0,0:0,9.58616e-08,1 +chr1 3405593 . tatttatttatt . . PASS END=3405604;RU=tatt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000411735;STUTTERDOWN=0.00117618;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:1:3,3:3-3,3-3:22,15,0,2:3,22:2,2:234.717:366.612,131.36:0,0:0,6.5924e-07,1 +chr1 3405717 . aacaacaacaac . . PASS END=3405728;RU=aac;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000841823;STUTTERDOWN=0.00480956;STUTTERP=0.975403;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:49:1:4,4:4-4,4-4:23,24,0,2:4,23:3,2:320.549:366.612,131.36:0,0:0,4.37449e-07,1 +chr1 3407095 . aaaataaaataaaat . . PASS END=3407109;RU=aaaat;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000927953;STUTTERDOWN=0.00224019;STUTTERP=0.843423;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:30:1:3,3:3-3,3-3:26,4,0,0:3,26:NULL:140.173:366.612,131.36:0,0:0,7.06878e-08,1 +chr1 3408522 . gaaagaaagaaagaaagaaagaaagaaagaaagaaagaaa gaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaa . PASS END=3408561;RU=gaaa;PERIOD=4;REF=10;GRID=11,17;STUTTERUP=0.0084664;STUTTERDOWN=0.0376003;STUTTERP=0.815956;EXPTHRESH=10 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:29:0.65855:14,14:12-14,12-14:5,16,0,8:14,5:5,2|6,1|7,1|8,1|12,2|13,1:242.678:366.612,131.36:0.581383,0.581383:0,0,1 +chr1 3408702 . acacacacacacacacacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacacacac . PASS END=3408745;RU=ac;PERIOD=2;REF=22;GRID=17,25;STUTTERUP=0.0592482;STUTTERDOWN=0.192428;STUTTERP=0.768282;EXPTHRESH=22 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:32:0.744024:21,21:20-22,20-22:9,10,0,12:20,2|21,7:8,1|9,1|10,2|11,1|12,3|15,1|17,1|18,1|19,1:231.355:366.612,131.36:0.579863,0.579863:0.970769,0.0292858,4.61147e-07 +chr1 3412976 . acacacacacacacacacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacacacacacacac,acacacacacacacacacacacacacacacacacacacacacacacacacacacac . PASS END=3413019;RU=ac;PERIOD=2;REF=22;GRID=14,31;STUTTERUP=0.0553659;STUTTERDOWN=0.164174;STUTTERP=0.648952;EXPTHRESH=22 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:47:0.266334:24,28:22-25,17-31:9,24,0,12:22,2|24,7:4,1|7,1|10,1|12,1|15,2|17,1|21,1|23,2|25,1|28,1:373.177:366.612,131.36:1.01145,3.92624:1.80908e-41,2.66864e-13,1 +chr1 3413022 . tctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctc tc . PASS END=3413083;RU=tc;PERIOD=2;REF=31;GRID=1,103;STUTTERUP=0.0346077;STUTTERDOWN=0.27439;STUTTERP=0.500589;EXPTHRESH=31 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:28:0.026846:1,1:1-6,1-6:0,28,0,0:NULL:NULL:246.2:366.612,131.36:1.43779,1.43779:0.994656,0.00535392,5.58523e-07 +chr1 3413143 . acacacacacacacacacacacacacacacacacacacacacac acacacacacacacacacacacacac . PASS END=3413186;RU=ac;PERIOD=2;REF=22;GRID=10,16;STUTTERUP=0.0710666;STUTTERDOWN=0.154162;STUTTERP=0.730776;EXPTHRESH=22 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:32:0.98753:13,13:13-13,13-13:10,20,0,2:13,10:8,1|13,1:243.265:366.612,131.36:0,0:1,0,0 +chr1 3415813 . taaataaataaa . . PASS END=3415824;RU=taaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000421834;STUTTERDOWN=0.000843666;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:0.999965:3,3:2-3,2-3:18,12,0,0:3,18:NULL:174.415:366.612,131.36:0.431574,0.431574:0,3.20106e-05,0.999971 +chr1 3418452 . atgtatgtatgt . . PASS END=3418463;RU=atgt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000751777;STUTTERDOWN=0.000751777;STUTTERP=0.976453;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:59:1:3,3:3-3,3-3:39,18,0,2:3,39:2,2:334.767:366.612,131.36:0,0:0,9.76423e-12,1 +chr1 3419362 . cctacctaccta . . PASS END=3419373;RU=ccta;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000598088;STUTTERDOWN=0.000299045;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:56:1:3,3:3-3,3-3:35,18,0,3:3,35:2,3:320.414:366.612,131.36:0,0:0,9.58282e-11,1 +chr1 3427014 . tatctatctatc . . PASS END=3427025;RU=tatc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000393286;STUTTERDOWN=0.000393286;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:0.999856:3,3:3-3,3-3:16,23,0,0:3,16:NULL:269.899:366.612,131.36:0,0:0,0.000120938,0.99988 +chr1 3437788 . aaacaaacaaac . . PASS END=3437799;RU=aaac;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000372825;STUTTERDOWN=0.000372825;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:54:1:3,3:3-3,3-3:37,17,0,0:3,37:NULL:298.755:366.612,131.36:0,0:0,8.48512e-11,1 +chr1 3440889 . aataaataaata . . PASS END=3440900;RU=aata;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000461193;STUTTERDOWN=0.000922384;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:42:1:3,3:3-3,3-3:32,10,0,0:3,32:NULL:214.287:366.612,131.36:0,0:0,1.03455e-09,1 +chr1 3442170 . ccaccaccaccacca ccaccaccacca . PASS END=3442184;RU=cca;PERIOD=3;REF=5;GRID=1,7;STUTTERUP=0.00332599;STUTTERDOWN=0.0217084;STUTTERP=0.845158;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:29:0.188092:4,4:1-4,1-4:2,26,0,0:4,2:NULL:236.847:366.612,131.36:0.944183,0.944183:0.8773,0.122763,3.51555e-05 +chr1 3444468 . aaggaaggaaggaagg . . PASS END=3444483;RU=aagg;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000889786;STUTTERDOWN=0.00823807;STUTTERP=0.982814;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:43:1:4,4:4-4,4-4:21,22,0,0:4,21:NULL:283.756:366.612,131.36:0,0:0,6.78867e-06,0.999994 +chr1 3452271 . tttgtttgtttg . . PASS END=3452282;RU=tttg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000953693;STUTTERDOWN=0.000436602;STUTTERP=0.998593;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:30:0.999857:3,3:3-3,3-3:16,14,0,0:3,16:NULL:192.804:366.612,131.36:0,0:0,0.000103879,0.999896 +chr1 3452589 . ttttgtttttgtttttgtttttgt . . PASS END=3452612;RU=ttttgt;PERIOD=6;REF=4;GRID=1,7;STUTTERUP=0.00374144;STUTTERDOWN=0.00240103;STUTTERP=0.887868;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:18:0.466473:4,4:1-4,1-4:4,14,0,0:4,4:NULL:151.644:366.612,131.36:0.948533,0.948533:2.53305e-10,0.412736,0.587339 +chr1 3459217 . atctatctatctatctatctatctatctatctatctatctatctatctatctatct atctatctatctatctatctatctatctatctatctatctatctatctatct . PASS END=3459272;RU=atct;PERIOD=4;REF=14;GRID=9,16;STUTTERUP=0.00832165;STUTTERDOWN=0.0488789;STUTTERP=0.62654;EXPTHRESH=14 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:62:1:13,13:13-13,13-13:20,22,0,19:13,20:2,1|4,3|5,1|6,2|7,3|9,3|10,1|11,3|12,2:426.507:366.612,131.36:0,0:1,2.32162e-06,3.05588e-32 +chr1 3460396 . gggacgggacgggac . . PASS END=3460410;RU=gggac;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000542374;STUTTERDOWN=0.00108475;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:11:0.469102:3,3:1-3,1-3:3,8,0,0:3,3:NULL:84.2472:366.612,131.36:0.472766,0.472766:9.34441e-11,0.268776,0.731226 +chr1 3462940 . gtttgtttgtttgtttgtttgttt gtttgtttgtttgtttgtttgtttgtttgtttgtttgttt . PASS END=3462963;RU=gttt;PERIOD=4;REF=6;GRID=7,13;STUTTERUP=0.00157257;STUTTERDOWN=0.0219004;STUTTERP=0.668589;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:32:0.997688:10,10:10-10,10-10:12,12,0,8:10,12:2,1|3,2|5,1|6,3|8,1:219.73:366.612,131.36:0,0:0,0,1 +chr1 3470981 . cacacacacacacacacacacaca ca,cacacacacacaca . PASS END=3471004;RU=ca;PERIOD=2;REF=12;GRID=1,103;STUTTERUP=0.0460676;STUTTERDOWN=0.09684;STUTTERP=0.798549;EXPTHRESH=12 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:7:0.00609839:1,7:1-15,1-15:0,7,0,0:NULL:NULL:66.3926:366.612,131.36:4.33019,4.14174:0.229482,0.554589,0.215959 +chr1 3478864 . acacacacacacacacac acacacacacacacacacac . PASS END=3478881;RU=ac;PERIOD=2;REF=9;GRID=7,13;STUTTERUP=0.0157105;STUTTERDOWN=0.0254115;STUTTERP=0.920365;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:26:0.995329:10,10:10-10,10-10:11,13,0,2:10,11:4,1|9,1:180.777:366.612,131.36:0,0:4.37525e-40,0.0012587,0.998747 +chr1 3481278 . tttgtttgtttgtttg . . PASS END=3481293;RU=tttg;PERIOD=4;REF=4;GRID=1,8;STUTTERUP=0.00140596;STUTTERDOWN=0.00401633;STUTTERP=0.859019;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:0.999981:4,4:4-5,4-5:19,15,0,0:4,19:NULL:218.731:366.612,131.36:0.334882,0.334882:0,3.05595e-05,0.999971 +chr1 3483580 . acacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacac . PASS END=3483607;RU=ac;PERIOD=2;REF=14;GRID=2,23;STUTTERUP=0.0425282;STUTTERDOWN=0.151968;STUTTERP=0.78595;EXPTHRESH=14 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:50:0.919819:19,19:5-20,5-20:18,23,0,8:18,2|19,14|20,2:5,1|6,1|9,1|10,1|14,1|17,2|19,1:371.263:366.612,131.36:6.99379,6.99379:0,3.84008e-05,0.999963 +chr1 3487177 . ccatccatccat . . PASS END=3487188;RU=ccat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000409015;STUTTERDOWN=0.000818029;STUTTERP=0.73234;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:48:1:3,3:3-3,3-3:26,22,0,0:3,26:NULL:300.483:366.612,131.36:0,0:0,8.36725e-08,1 +chr1 3487959 . ctctctctctctctctctctctctctctct ctctctctctctctctctct,ctctctctctctctctctctctct . PASS END=3487988;RU=ct;PERIOD=2;REF=15;GRID=6,15;STUTTERUP=0.104431;STUTTERDOWN=0.195331;STUTTERP=0.52832;EXPTHRESH=15 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:34:0.918849:10,12:9-12,12-12:14,17,0,3:9,2|10,3|12,9:8,1|9,1|10,1:257.849:366.612,131.36:1.08161,0:1,3.86238e-06,1.11061e-21 +chr1 3487988 . tatatatatatatatatatatatatatatata tatatatatatatatatata,tatatatatatatatatatata . PASS END=3488019;RU=ta;PERIOD=2;REF=16;GRID=7,17;STUTTERUP=0.0979901;STUTTERDOWN=0.179445;STUTTERP=0.461288;EXPTHRESH=16 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:23:0.758499:10,11:10-14,10-14:4,18,0,0:10,2|11,2:NULL:187.38:366.612,131.36:1.91717,1.5352:0.993196,0.00682201,1.22632e-09 +chr1 3490427 . gcgcgcgcgcgcgc gcgcgcgcgcgc . PASS END=3490440;RU=gc;PERIOD=2;REF=7;GRID=2,9;STUTTERUP=0.0467905;STUTTERDOWN=0.0260242;STUTTERP=0.884536;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:46:1:6,6:6-6,6-6:25,20,0,0:6,25:NULL:282.87:366.612,131.36:0.0990099,0.0990099:1,1.37667e-07,2.66303e-41 +chr1 3491872 . cacacacacaca cacacacacacacaca . PASS END=3491883;RU=ca;PERIOD=2;REF=6;GRID=4,11;STUTTERUP=0.00726883;STUTTERDOWN=0.0179302;STUTTERP=0.801966;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:18:0.227788:8,8:7-8,7-8:2,15,0,0:8,2:NULL:141.248:366.612,131.36:0.59948,0.59948:2.72633e-08,0.258838,0.741169 +chr1 3494930 . cattcattcattcattcattcatt . . PASS END=3494953;RU=catt;PERIOD=4;REF=6;GRID=3,9;STUTTERUP=0.00258592;STUTTERDOWN=0.011252;STUTTERP=0.847136;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:26:0.997386:6,6:6-6,6-6:12,9,0,5:6,12:3,2|4,2|5,1:167.591:366.612,131.36:0,0:3.95949e-32,0.00131093,0.998694 +chr1 3496471 . ttcttttcttttctt . . PASS END=3496485;RU=ttctt;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000409884;STUTTERDOWN=0.00327903;STUTTERP=0.826703;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:42:1:3,3:3-3,3-3:24,18,0,0:3,24:NULL:260.674:366.612,131.36:0,0:0,5.47066e-07,1 +chr1 3496603 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt,gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=3496632;RU=gt;PERIOD=2;REF=15;GRID=15,30;STUTTERUP=0.0563837;STUTTERDOWN=0.188778;STUTTERP=0.746556;EXPTHRESH=15 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:54:0.283637:22,29:22-22,21-29:15,11,0,25:21,4|22,11:5,1|8,1|9,1|11,1|12,1|13,2|14,1|15,2|16,4|17,4|18,2|19,1|20,2|21,1|27,1:382.349:366.612,131.36:0,3.54444:0,0,1 +chr1 3499569 . acccacccaccc acccacccacccacccaccc . PASS END=3499580;RU=accc;PERIOD=4;REF=3;GRID=1,103;STUTTERUP=0.00280305;STUTTERDOWN=0.00280305;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/1:3:0.00263713:3,5:1-15,1-15:0,3,0,0:NULL:NULL:27.7607:366.612,131.36:5.93652,5.79452:0.00457848,0.154971,0.840537 +chr1 3507557 . acagacagacagacagacag . . PASS END=3507576;RU=acag;PERIOD=4;REF=5;GRID=1,8;STUTTERUP=0.00239654;STUTTERDOWN=0.0084492;STUTTERP=0.999;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:17:0.99109:5,5:4-5,4-5:11,5,0,0:5,11:NULL:87.6499:366.612,131.36:0.437216,0.437216:3.1104e-29,0.00586497,0.99415 +chr1 3507759 . aacaacaacaac . . PASS END=3507770;RU=aac;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000966337;STUTTERDOWN=0.00138024;STUTTERP=0.959079;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:18:0.999806:4,4:4-4,4-4:16,2,0,0:4,16:NULL:81.2805:366.612,131.36:0,0:0,0.000112515,0.999888 +chr1 3509243 . acacacacacacacacacacacacacacacacacacacacacacacac . . PASS END=3509290;RU=ac;PERIOD=2;REF=24;GRID=20,28;STUTTERUP=0.0861986;STUTTERDOWN=0.223676;STUTTERP=0.74265;EXPTHRESH=24 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:52:0.901943:24,24:23-25,23-25:20,17,0,15:23,4|24,13|25,3:8,1|11,1|14,2|15,1|17,2|18,1|19,2|21,2|22,1|23,2:377.082:366.612,131.36:0.474835,0.474835:3.69924e-13,0.0100262,0.989998 +chr1 3509605 . aaacaaaacaaaaca . . PASS END=3509619;RU=aaaca;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000507752;STUTTERDOWN=0.000507752;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:23:0.999867:3,3:3-3,3-3:16,7,0,0:3,16:NULL:126.671:366.612,131.36:0,0:0,6.98466e-05,0.999933 +chr1 3510223 . aaataaataaat . . PASS END=3510234;RU=aaat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000838686;STUTTERDOWN=0.000419343;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:1:3,3:3-3,3-3:20,9,0,0:3,20:NULL:164.508:366.612,131.36:0,0:0,6.1897e-06,0.999995 +chr1 3518996 . tattattattattattattattattattattattattat tattattattattattattattattattattattat . PASS END=3519034;RU=tat;PERIOD=3;REF=13;GRID=7,15;STUTTERUP=0.0224958;STUTTERDOWN=0.0597962;STUTTERP=0.763058;EXPTHRESH=13 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:31:0.996552:12,12:10-12,10-12:12,10,0,8:12,12:3,1|4,1|7,2|10,3|11,1:200.993:366.612,131.36:0.647134,0.647134:0.998178,0.0018276,7.66627e-17 +chr1 3519121 . actcactcactc . . PASS END=3519132;RU=actc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000525944;STUTTERDOWN=0.000525944;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:1:3,3:3-3,3-3:24,14,0,0:3,24:NULL:219.554:366.612,131.36:0,0:0,7.08751e-07,1 +chr1 3523067 . taataataataataataataataataa taa . PASS END=3523093;RU=taa;PERIOD=3;REF=9;GRID=1,103;STUTTERUP=0.0166377;STUTTERDOWN=0.0550678;STUTTERP=0.748038;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:13:0.039164:1,1:1-5,1-5:0,13,0,0:NULL:NULL:123.852:366.612,131.36:1.14834,1.14834:0.581722,0.376272,0.0421281 +chr1 3527389 . catccatccatc . . PASS END=3527400;RU=catc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000317331;STUTTERDOWN=0.000317331;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:41:1:3,3:3-3,3-3:28,13,0,0:3,28:NULL:230.582:366.612,131.36:0,0:0,1.79127e-08,1 +chr1 3529807 . aaataaataaataaataaataaataaataaataaataaataaat aaataaataaataaataaataaataaataaataaat . PASS END=3529850;RU=aaat;PERIOD=4;REF=11;GRID=6,12;STUTTERUP=0.00833984;STUTTERDOWN=0.0395613;STUTTERP=0.617415;EXPTHRESH=11 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:37:0.999979:9,9:9-9,9-9:18,11,0,8:9,18:3,1|4,1|5,1|6,2|8,3:233.364:366.612,131.36:0,0:0.999993,1.06837e-05,6.47422e-38 +chr1 3530404 . tattattattattattattattattattattattattattat tattattattattattattattattattattattattattattattattat . PASS END=3530445;RU=tat;PERIOD=3;REF=14;GRID=14,20;STUTTERUP=0.0440597;STUTTERDOWN=0.0953786;STUTTERP=0.695533;EXPTHRESH=14 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:28:0.901029:17,17:17-17,17-17:7,11,0,10:17,7:4,1|7,2|8,1|12,2|13,1|15,2|16,1:203.867:366.612,131.36:0,0:0,0,1 +chr1 3537894 . gtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=3537913;RU=gt;PERIOD=2;REF=10;GRID=10,18;STUTTERUP=0.0300493;STUTTERDOWN=0.0711799;STUTTERP=0.849458;EXPTHRESH=10 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:18:0.385014:15,15:13-15,13-15:3,9,0,5:15,3:5,1|7,1|12,2|14,1:137.424:366.612,131.36:0.921165,0.921165:0,0,1 +chr1 3540990 . tgttgttgttgttgt . . PASS END=3541004;RU=tgt;PERIOD=3;REF=5;GRID=2,8;STUTTERUP=0.000835438;STUTTERDOWN=0.0037081;STUTTERP=0.923971;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:34:0.999861:5,5:5-5,5-5:16,16,0,2:5,16:4,2:226.904:366.612,131.36:0,0:0,7.16376e-05,0.999932 +chr1 3541012 . ttgttttttgttttttgtttt ttgttttttgtttt . PASS END=3541032;RU=ttgtttt;PERIOD=7;REF=3;GRID=1,5;STUTTERUP=0.000647751;STUTTERDOWN=0.00125997;STUTTERP=0.919256;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:26:0.999509:2,2:2-2,2-2:13,13,0,0:2,13:NULL:172.491:366.612,131.36:0,0:0.999758,0.000244667,2.76786e-40 +chr1 3554787 . gtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgt . PASS END=3554802;RU=gt;PERIOD=2;REF=8;GRID=6,13;STUTTERUP=0.017316;STUTTERDOWN=0.0591694;STUTTERP=0.845891;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:38:0.999986:9,9:9-9,9-9:18,12,0,7:9,18:6,1|7,2|8,4:237.054:366.612,131.36:0.139319,0.139319:0,5.68972e-07,1 +chr1 3555544 . cacacacacacacacacacacacacacacacacacacacacacacacaca cacacacacacacacacacacacacacacacacacacacaca,cacacacacacacacacacacacacacacacacacacacacacaca . PASS END=3555593;RU=ca;PERIOD=2;REF=25;GRID=17,26;STUTTERUP=0.110246;STUTTERDOWN=0.182914;STUTTERP=0.71216;EXPTHRESH=25 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:44:0.362242:21,23:21-21,22-24:8,16,0,19:21,8:5,1|6,1|8,1|10,1|11,1|12,4|13,2|15,3|19,2|22,2|23,1:343.558:366.612,131.36:0.0990099,0.615138:0.636692,0.363356,8.41314e-18 +chr1 3559181 . tctctctctctctctctctctctctctctctctctc tctctctctctctctc . PASS END=3559216;RU=tc;PERIOD=2;REF=18;GRID=5,11;STUTTERUP=0.0518966;STUTTERDOWN=0.27713;STUTTERP=0.521235;EXPTHRESH=18 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:22:0.539656:8,8:6-8,6-8:5,17,0,0:8,5:NULL:177.717:366.612,131.36:0.472766,0.472766:1,0,0 +chr1 3559217 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtg,tgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=3559264;RU=tg;PERIOD=2;REF=24;GRID=5,27;STUTTERUP=0.0501477;STUTTERDOWN=0.180113;STUTTERP=0.456531;EXPTHRESH=24 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:20:0.831844:8,13:8-24,11-24:7,10,0,2:8,3|11,2|13,2:6,1|7,1:146.703:366.612,131.36:6.53897,4.86742:1,2.25946e-06,4.52011e-29 +chr1 3559288 . tctctctctctc . . PASS END=3559299;RU=tc;PERIOD=2;REF=6;GRID=3,9;STUTTERUP=0.00378301;STUTTERDOWN=0.0101577;STUTTERP=0.89291;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:30:0.999953:6,6:6-6,6-6:18,12,0,0:6,18:NULL:183.101:366.612,131.36:0,0:1.68156e-44,5.04122e-05,0.999949 +chr1 3560915 . aaacaaacaaacaaacaaac . . PASS END=3560934;RU=aaac;PERIOD=4;REF=5;GRID=2,8;STUTTERUP=0.000660344;STUTTERDOWN=0.00820806;STUTTERP=0.836875;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:0.999839:5,5:5-5,5-5:15,19,0,4:5,15:3,1|4,3:259.872:366.612,131.36:0,0:0,8.33776e-05,0.999918 +chr1 3567195 . ctctctctctctctctctctctctctctctctctctctctctctctctct . . PASS END=3567244;RU=ct;PERIOD=2;REF=25;GRID=19,28;STUTTERUP=0.0450026;STUTTERDOWN=0.267509;STUTTERP=0.606704;EXPTHRESH=25 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:25:0.815539:25,25:22-25,22-25:9,6,0,9:24,2|25,7:4,1|5,1|10,1|11,2|13,1|16,1|17,1|22,1:170.884:366.612,131.36:1.1105,1.1105:3.3225e-09,0.143123,0.85696 +chr1 3568471 . gatggatggatg . . PASS END=3568482;RU=gatg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000426466;STUTTERDOWN=0.000426466;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:0.999924:3,3:3-3,3-3:16,15,0,2:3,16:2,2:214.124:366.612,131.36:0,0:0,4.05373e-05,0.999963 +chr1 3569699 . gaggaggaggag . . PASS END=3569710;RU=gag;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.0003356;STUTTERDOWN=0.00648139;STUTTERP=0.935725;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:44:1:4,4:4-4,4-4:23,21,0,0:4,23:NULL:284.952:366.612,131.36:0,0:0,1.6216e-06,1 +chr1 3570098 . caaaacaaaacaaaa . . PASS END=3570112;RU=caaaa;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000418169;STUTTERDOWN=0.00167266;STUTTERP=0.844424;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:1:3,3:3-3,3-3:28,9,0,0:3,28:NULL:194.924:366.612,131.36:0,0:0,2.27263e-08,1 +chr1 3570893 . atatcatatcatatatatcatatcatatatatcatatcatat . . PASS END=3570934;RU=atatcatatcatat;PERIOD=14;REF=3;GRID=1,6;STUTTERUP=0.05;STUTTERDOWN=0.05;STUTTERP=0.9;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:20:0.984638:3,3:3-3,3-3:10,10,0,0:3,10:NULL:133.018:366.612,131.36:0,0:1.3946e-12,0.0121244,0.9879 +chr1 3574648 . cacacacacacacacacacacaca caca,cacacacacacacaca . PASS END=3574671;RU=ca;PERIOD=2;REF=12;GRID=1,15;STUTTERUP=0.0680636;STUTTERDOWN=0.0809374;STUTTERP=0.494471;EXPTHRESH=12 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:41:0.986214:2,8:1-12,3-12:4,32,0,2:2,2|8,2:5,1|7,1:334.309:366.612,131.36:1.82748,2.18962:0.999941,6.0901e-05,4.05663e-13 +chr1 3575668 . cacacacacacacacacacacacacacacacacacacacacacaca cacacacacacacacacacacacacaca,cacacacacacacacacacacacacacacacacacacacacaca . PASS END=3575713;RU=ca;PERIOD=2;REF=23;GRID=9,27;STUTTERUP=0.046231;STUTTERDOWN=0.203514;STUTTERP=0.736352;EXPTHRESH=23 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:32:0.111384:14,22:12-24,22-24:2,20,0,6:22,2:7,2|8,1|9,1|13,1|17,1:240.982:366.612,131.36:5.29045,0.837205:0.887813,0.108392,0.00390201 +chr1 3576109 . atagatagatagatagatagatagatagatagatagatagatag atagatagatagatag,atagatagatagatagatag . PASS END=3576152;RU=atag;PERIOD=4;REF=11;GRID=1,8;STUTTERUP=0.066753;STUTTERDOWN=0.0376956;STUTTERP=0.692851;EXPTHRESH=11 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:36:0.997672:4,5:4-4,4-5:15,21,0,0:4,10|5,5:NULL:273.219:366.612,131.36:0,0.390807:1,0,0 +chr1 3576169 . taaataaataaataaataaataaa taaataaataaa . PASS END=3576192;RU=taaa;PERIOD=4;REF=6;GRID=1,7;STUTTERUP=0.00100381;STUTTERDOWN=0.0107728;STUTTERP=0.82588;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:46:0.629186:3,3:3-4,3-4:21,24,0,0:3,19|4,2:NULL:322.466:366.612,131.36:0.491073,0.491073:1,1.28293e-06,0 +chr1 3576190 . aaacaaacaaac aaac . PASS END=3576201;RU=aaac;PERIOD=4;REF=3;GRID=1,103;STUTTERUP=0.0288874;STUTTERDOWN=0.000955549;STUTTERP=0.342766;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:20:0.0705051:1,1:1-2,1-2:0,20,0,0:NULL:NULL:187.471:366.612,131.36:0.572034,0.572034:0.267009,0.523725,0.209271 +chr1 3576505 . tagtagtagtagtagtagtagtagtag tagtag . PASS END=3576531;RU=tag;PERIOD=3;REF=9;GRID=1,11;STUTTERUP=0.0366576;STUTTERDOWN=0.0557535;STUTTERP=0.537562;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:13:0.325152:2,2:2-8,2-8:3,9,0,0:2,3:NULL:89.3921:366.612,131.36:2.97837,2.97837:0.857414,0.14267,5.98554e-12 +chr1 3576606 . agaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaaga agaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaaga,agaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaaga . PASS END=3576674;RU=aga;PERIOD=3;REF=23;GRID=1,40;STUTTERUP=0.0384268;STUTTERDOWN=0.16673;STUTTERP=0.583553;EXPTHRESH=23 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:18:0.0196081:28,39:12-39,15-40:0,6,0,12:NULL:6,1|8,1|12,4|14,1|18,1|25,2|28,1|37,1:148.215:366.612,131.36:8.12156,7.60409:7.34188e-30,0.228657,0.771374 +chr1 3577214 . caatcaatcaat . . PASS END=3577225;RU=caat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000511496;STUTTERDOWN=0.00102299;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:25:0.999312:3,3:3-3,3-3:14,11,0,0:3,14:NULL:155.142:366.612,131.36:0,0:0,0.000428151,0.999575 +chr1 3581254 . caaacaaacaaacaaacaaa caaacaaacaaacaaacaaacaaacaaacaaacaaa . PASS END=3581273;RU=caaa;PERIOD=4;REF=5;GRID=5,12;STUTTERUP=0.000670145;STUTTERDOWN=0.029915;STUTTERP=0.513678;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:17:0.924424:9,9:8-9,8-9:8,8,0,0:9,8:NULL:113.429:366.612,131.36:0.442564,0.442564:0,0,1 +chr1 3585710 . acacacacacacacacacacacacacacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacac . PASS END=3585763;RU=ac;PERIOD=2;REF=27;GRID=16,22;STUTTERUP=0.0414012;STUTTERDOWN=0.136671;STUTTERP=0.713564;EXPTHRESH=27 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:25:0.988159:19,19:19-19,19-19:11,14,0,0:19,11:NULL:180.75:366.612,131.36:0,0:1,0,0 +chr1 3588411 . acacacacacacacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacac . PASS END=3588450;RU=ac;PERIOD=2;REF=20;GRID=13,23;STUTTERUP=0.0676992;STUTTERDOWN=0.218202;STUTTERP=0.757708;EXPTHRESH=20 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/0:42:0.404092:18,20:17-18,16-20:14,12,0,16:16,3|17,2|18,9:4,1|5,5|7,1|12,3|13,1|14,2|17,2|20,1:318.935:366.612,131.36:0.275098,1.43157:0.000363908,0.999637,5.75798e-15 +chr1 3589857 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=3589900;RU=tg;PERIOD=2;REF=22;GRID=15,24;STUTTERUP=0.0584723;STUTTERDOWN=0.245225;STUTTERP=0.679892;EXPTHRESH=22 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:29:0.94442:20,20:19-21,19-21:9,10,0,7:20,9:4,1|5,2|7,1|8,2|19,1:191.577:366.612,131.36:0.417958,0.417958:0.984787,0.0152459,6.41648e-11 +chr1 3590265 . atatatatatatat atatat . PASS END=3590278;RU=at;PERIOD=2;REF=7;GRID=1,6;STUTTERUP=0.0181376;STUTTERDOWN=0.0153278;STUTTERP=0.839137;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:32:0.999755:3,3:1-3,1-3:15,16,0,0:3,15:NULL:213.737:366.612,131.36:0.851255,0.851255:1,0,0 +chr1 3593993 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtg . PASS END=3594042;RU=tg;PERIOD=2;REF=25;GRID=1,103;STUTTERUP=0.0777332;STUTTERDOWN=0.209519;STUTTERP=0.75135;EXPTHRESH=25 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:4:0.00116688:2,2:2-12,2-12:0,4,0,0:NULL:NULL:34.3347:366.612,131.36:2.8056,2.8056:0.296546,0.547881,0.155608 +chr1 3594304 . tttgttttgttttgt tttgttttgttttgttttgt . PASS END=3594318;RU=tttgt;PERIOD=5;REF=3;GRID=1,7;STUTTERUP=0.000561683;STUTTERDOWN=0.0276302;STUTTERP=0.9392;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:41:0.999784:4,4:4-4,4-4:15,21,0,5:4,15:2,1|3,4:300.965:366.612,131.36:0,0:0,2.69095e-05,0.999972 +chr1 3595528 . tttgtttgtttgtttgtttg tttgtttgtttgtttgtttgtttg . PASS END=3595547;RU=tttg;PERIOD=4;REF=5;GRID=3,9;STUTTERUP=0.00125573;STUTTERDOWN=0.0320814;STUTTERP=0.836502;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:35:0.999943:6,6:6-6,6-6:17,12,0,6:6,17:2,1|3,2|5,3:219.837:366.612,131.36:0,0:0,7.38434e-06,0.999994 +chr1 3597713 . ccacccacccac . . PASS END=3597724;RU=ccac;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000313438;STUTTERDOWN=0.000313438;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:53:1:3,3:3-3,3-3:26,27,0,0:3,26:NULL:356.282:366.612,131.36:0,0:0,1.9024e-07,1 +chr1 3598374 . agagagagagagag ag . PASS END=3598387;RU=ag;PERIOD=2;REF=7;GRID=1,6;STUTTERUP=0.00203362;STUTTERDOWN=0.00768944;STUTTERP=0.808763;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:14:0.0669496:1,1:1-3,1-3:0,13,0,0:NULL:NULL:121.25:366.612,131.36:0.913899,0.913899:1,0,0 +chr1 3599536 . atatatatatatatatatatatatatatatatatatatatat atatatatatatatatatatatatatatat . PASS END=3599577;RU=at;PERIOD=2;REF=21;GRID=9,19;STUTTERUP=0.093049;STUTTERDOWN=0.32341;STUTTERP=0.632066;EXPTHRESH=21 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:10:0.123078:15,15:12-16,12-16:2,6,0,0:15,2:NULL:67.6077:366.612,131.36:1.89137,1.89137:1,0,0 +chr1 3599896 . aaacaaacaaac . . PASS END=3599907;RU=aaac;PERIOD=4;REF=3;GRID=1,7;STUTTERUP=0.00143892;STUTTERDOWN=0.00402765;STUTTERP=0.812178;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:22:0.998658:3,3:3-4,3-4:13,8,0,0:3,13:NULL:122.393:366.612,131.36:0.46122,0.46122:2.46323e-38,0.000685506,0.999317 +chr1 3600086 . acaaacaaacaaacaaacaa . . PASS END=3600105;RU=acaa;PERIOD=4;REF=5;GRID=2,8;STUTTERUP=0.00139117;STUTTERDOWN=0.00828982;STUTTERP=0.952254;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:1.00001:5,5:5-5,5-5:20,13,0,6:5,20:4,6:238.826:366.612,131.36:0,0:0,2.78696e-06,1 +chr1 3608018 . ttgtttgtttgt . . PASS END=3608029;RU=ttgt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000747498;STUTTERDOWN=0.00298996;STUTTERP=0.91856;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:45:1:3,3:3-3,3-3:27,13,0,5:3,27:2,4|3,1:267.245:366.612,131.36:0,0:0,1.50003e-08,1 +chr1 3608156 . tttgtttgtttgtttg . . PASS END=3608171;RU=tttg;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000628587;STUTTERDOWN=0.00278999;STUTTERP=0.923971;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:42:1:4,4:4-4,4-4:25,15,0,2:4,25:2,1|3,1:249.862:366.612,131.36:0,0:0,3.34792e-07,1 +chr1 3610003 . cacacacacacacacacacacacacacacacacacacacacaca cacacacacacacacacacacacacacacacacacacacacacaca . PASS END=3610046;RU=ca;PERIOD=2;REF=22;GRID=19,27;STUTTERUP=0.074968;STUTTERDOWN=0.192074;STUTTERP=0.743036;EXPTHRESH=22 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:43:0.646453:23,23:22-24,22-24:14,12,0,16:22,4|23,10:5,1|6,2|7,2|9,2|15,2|16,1|17,2|20,3|22,1:307.269:366.612,131.36:0.451337,0.451337:1.95176e-26,0.000370915,0.99963 +chr1 3612774 . aaagaaagaaagaaag . . PASS END=3612789;RU=aaag;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000569052;STUTTERDOWN=0.00245771;STUTTERP=0.982238;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:12:0.210875:4,4:1-4,1-4:2,10,0,0:4,2:NULL:94.1995:366.612,131.36:1.38593,1.38593:2.8758e-07,0.546696,0.453414 +chr1 3613442 . ctgctgctgctg . . PASS END=3613453;RU=ctg;PERIOD=3;REF=4;GRID=1,8;STUTTERUP=0.00302199;STUTTERDOWN=0.00277806;STUTTERP=0.960013;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:51:0.999998:4,4:4-5,4-5:20,30,0,0:4,20:NULL:345.283:366.612,131.36:0.236383,0.236383:0,1.51018e-05,0.999986 +chr1 3630160 . aattaattaatt . . PASS END=3630171;RU=aatt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000403122;STUTTERDOWN=0.00230314;STUTTERP=0.829224;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:0.999879:3,3:3-3,3-3:16,13,0,0:3,16:NULL:181.582:366.612,131.36:0,0:0,8.50016e-05,0.999917 +chr1 3631051 . attaattaatta . . PASS END=3631062;RU=atta;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000423872;STUTTERDOWN=0.00169547;STUTTERP=0.987382;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:40:0.998978:3,3:3-3,3-3:15,25,0,0:3,15:NULL:289.134:366.612,131.36:0,0:0,0.000866248,0.999135 +chr1 3638662 . tgtttgtttgtttgtttgtttgtttgtttgtt tgtttgtttgtttgtttgtttgtt . PASS END=3638693;RU=tgtt;PERIOD=4;REF=8;GRID=3,9;STUTTERUP=0.00275826;STUTTERDOWN=0.00967935;STUTTERP=0.928272;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:46:0.999957:6,6:6-6,6-6:17,25,0,4:6,17:3,2|5,2:331.039:366.612,131.36:0,0:0.999995,5.32595e-06,0 +chr1 3639042 . aagaaagaaaga . . PASS END=3639053;RU=aaga;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00025326;STUTTERDOWN=0.00266031;STUTTERP=0.977258;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:41:1:3,3:3-3,3-3:25,13,0,3:3,25:2,3:236.707:366.612,131.36:0,0:0,5.6034e-08,1 +chr1 3649526 . acacacacacacacacacacacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacacacac . PASS END=3649573;RU=ac;PERIOD=2;REF=24;GRID=17,24;STUTTERUP=0.0644857;STUTTERDOWN=0.185753;STUTTERP=0.694178;EXPTHRESH=24 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:43:0.837773:21,21:20-21,20-21:6,20,0,16:21,6:5,1|6,1|7,2|12,2|13,2|14,2|15,2|16,1|19,2|20,1:340.528:366.612,131.36:0.298675,0.298675:0.986037,0.0139951,1.83348e-12 +chr1 3650739 . acacacacacacacacacacacacacacacacacacacacacac acacacacacacacacacacacacacacac . PASS END=3650782;RU=ac;PERIOD=2;REF=22;GRID=8,20;STUTTERUP=0.0611239;STUTTERDOWN=0.178323;STUTTERP=0.806531;EXPTHRESH=22 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:37:0.998517:15,15:11-15,11-15:20,10,0,5:14,3|15,17:9,4|10,1:222.223:366.612,131.36:1.16277,1.16277:1,0,0 +chr1 3651177 . aaggaaggaagg . . PASS END=3651188;RU=aagg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00048145;STUTTERDOWN=0.00137533;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:1.00001:3,3:3-3,3-3:22,14,0,0:3,22:NULL:219.182:366.612,131.36:0,0:0,2.11714e-06,1 +chr1 3652162 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . . PASS END=3652195;RU=gt;PERIOD=2;REF=17;GRID=13,20;STUTTERUP=0.0504054;STUTTERDOWN=0.195233;STUTTERP=0.843023;EXPTHRESH=17 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:42:0.916268:17,17:16-17,16-17:16,21,0,5:16,4|17,12:8,1|9,1|12,1|14,2:316.434:366.612,131.36:0.382696,0.382696:1.15124e-12,0.0835824,0.916516 +chr1 3652198 . atgtatgtatgt . . PASS END=3652209;RU=atgt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00105794;STUTTERDOWN=0.00211587;STUTTERP=0.866591;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:1.00001:3,3:3-3,3-3:21,18,0,0:3,21:NULL:252.979:366.612,131.36:0,0:0,2.25692e-06,1 +chr1 3652267 . atttatttattt . . PASS END=3652278;RU=attt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000492615;STUTTERDOWN=0.000985229;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:1:3,3:3-3,3-3:20,15,0,0:3,20:NULL:221.678:366.612,131.36:0,0:0,5.64366e-06,0.999995 +chr1 3653461 . gtgggtgggtgg . . PASS END=3653472;RU=gtgg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000315695;STUTTERDOWN=0.000901827;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:56:1:3,3:3-3,3-3:29,27,0,0:3,29:NULL:360.913:366.612,131.36:0,0:0,5.32789e-08,1 +chr1 3655005 . ataaataaataaataaataaataa . . PASS END=3655028;RU=ataa;PERIOD=4;REF=6;GRID=3,9;STUTTERUP=0.00152414;STUTTERDOWN=0.0206083;STUTTERP=0.609317;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:28:0.999914:6,6:6-6,6-6:17,11,0,0:6,17:NULL:169.944:366.612,131.36:0,0:0,6.7504e-05,0.999933 +chr1 3658217 . acacacacacacacacacacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacacacacacacacacacacac . PASS END=3658262;RU=ac;PERIOD=2;REF=23;GRID=24,31;STUTTERUP=0.0860209;STUTTERDOWN=0.225533;STUTTERP=0.723308;EXPTHRESH=23 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:29:0.402513:28,28:27-28,27-28:6,11,0,12:27,2|28,4:6,3|9,1|10,1|17,1|18,1|22,1|23,1|24,2|27,1:222.141:366.612,131.36:0.478946,0.478946:0,0,1 +chr1 3658997 . taaaataaaataaaa . . PASS END=3659011;RU=taaaa;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000538105;STUTTERDOWN=0.00107621;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:41:1:3,3:3-3,3-3:26,15,0,0:3,26:NULL:243.445:366.612,131.36:0,0:0,2.70447e-07,1 +chr1 3659687 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=3659732;RU=gt;PERIOD=2;REF=23;GRID=14,26;STUTTERUP=0.0870599;STUTTERDOWN=0.245611;STUTTERP=0.626272;EXPTHRESH=23 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:44:0.525084:21,21:17-23,17-23:16,12,0,14:19,2|20,4|21,10:8,4|9,1|10,2|12,1|13,2|14,2|16,1|19,1:310.77:366.612,131.36:0.992275,0.992275:0.999879,0.000123886,3.17682e-17 +chr1 3660735 . tgttttgttttgttttgttttgttt . . PASS END=3660759;RU=tgttt;PERIOD=5;REF=5;GRID=2,8;STUTTERUP=0.000496825;STUTTERDOWN=0.00521879;STUTTERP=0.772892;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:42:0.998797:5,5:5-5,5-5:12,21,0,9:5,12:3,6|4,2|5,1:312.548:366.612,131.36:0,0:0,0.000756779,0.999248 +chr1 3661144 . tgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtg . PASS END=3661161;RU=tg;PERIOD=2;REF=9;GRID=7,14;STUTTERUP=0.0321866;STUTTERDOWN=0.0691135;STUTTERP=0.815158;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:63:1:11,11:11-11,11-11:36,20,0,7:10,3|11,33:4,1|5,2|6,1|7,1|9,1|10,1:390.389:366.612,131.36:0,0:0,4.32167e-11,1 +chr1 3667713 . aacaaacaaaca . . PASS END=3667724;RU=aaca;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000418808;STUTTERDOWN=0.000418808;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:41:1:3,3:3-3,3-3:28,13,0,0:3,28:NULL:231.239:366.612,131.36:0,0:0,4.28522e-08,1 +chr1 3671145 . gcagcagcagcagca . . PASS END=3671159;RU=gca;PERIOD=3;REF=5;GRID=1,8;STUTTERUP=0.000834133;STUTTERDOWN=0.0207365;STUTTERP=0.962165;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:61:1:5,5:5-5,5-5:33,28,0,0:4,2|5,31:NULL:397.821:366.612,131.36:0.0990099,0.0990099:0,8.92102e-07,1 +chr1 3671658 . gccgccgccgccgcc . . PASS END=3671672;RU=gcc;PERIOD=3;REF=5;GRID=2,8;STUTTERUP=0.000497454;STUTTERDOWN=0.0113683;STUTTERP=0.977178;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:44:1:5,5:5-5,5-5:23,21,0,0:5,23:NULL:285.729:366.612,131.36:0,0:0,1.51329e-06,1 +chr1 3672852 . caccaccaccac cac . PASS END=3672863;RU=cac;PERIOD=3;REF=4;GRID=1,6;STUTTERUP=0.00288448;STUTTERDOWN=0.00411999;STUTTERP=0.892226;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:16:0.0545822:1,1:1-3,1-3:0,14,0,0:NULL:NULL:125.243:366.612,131.36:0.623212,0.623212:0.349383,0.488596,0.162064 +chr1 3673065 . cttccttccttccttccttccttccttccttccttccttccttccttccttccttccttc cttccttccttccttccttccttccttccttccttccttccttccttccttccttccttccttccttccttc . PASS END=3673124;RU=cttc;PERIOD=4;REF=15;GRID=14,21;STUTTERUP=0.0118864;STUTTERDOWN=0.0365896;STUTTERP=0.883304;EXPTHRESH=15 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:20:0.48575:18,18:17-18,17-18:3,10,0,6:18,3:2,1|5,1|7,1|8,1|12,1|17,1:156.234:366.612,131.36:0.478946,0.478946:2.14036e-22,0.0868164,0.91328 +chr1 3673125 . ctctctctctctctctctctctctctctctctctctctctctctctctct ctctctctctctctctctctctctctctctctctct . PASS END=3673174;RU=ct;PERIOD=2;REF=25;GRID=12,22;STUTTERUP=0.122141;STUTTERDOWN=0.207698;STUTTERP=0.630706;EXPTHRESH=25 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:15:0.109:18,18:15-19,15-19:2,10,0,0:18,2:NULL:106.067:366.612,131.36:1.60555,1.60555:1,0,0 +chr1 3677305 . agagagagagag . . PASS END=3677316;RU=ag;PERIOD=2;REF=6;GRID=3,9;STUTTERUP=0.00386973;STUTTERDOWN=0.016144;STUTTERP=0.894884;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:43:1:6,6:6-6,6-6:23,20,0,0:6,23:NULL:282.976:366.612,131.36:0,0:0,1.29706e-06,1 +chr1 3679100 . tttgtttgtttgtttgtttg tttgtttgtttgtttg . PASS END=3679119;RU=tttg;PERIOD=4;REF=5;GRID=1,7;STUTTERUP=0.00288072;STUTTERDOWN=0.00528299;STUTTERP=0.995075;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:34:0.999952:4,4:4-4,4-4:17,14,0,3:4,17:2,1|3,2:216.889:366.612,131.36:0,0:0.999971,3.05182e-05,8.95878e-40 +chr1 3680409 . ttttgttttgttttg . . PASS END=3680423;RU=ttttg;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000864016;STUTTERDOWN=0.00123409;STUTTERP=0.820218;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:23:0.999047:3,3:3-3,3-3:13,10,0,0:3,13:NULL:144.587:366.612,131.36:0,0:2.22554e-41,0.000601739,0.999401 +chr1 3681094 . tctatctatcta . . PASS END=3681105;RU=tcta;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00124243;STUTTERDOWN=0.00209992;STUTTERP=0.825421;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:24:0.999866:3,3:3-3,3-3:16,8,0,0:3,16:NULL:135.989:366.612,131.36:0,0:0,8.57214e-05,0.999917 +chr1 3686501 . tatatatatatatatatatatatatatatatatatata ta . PASS END=3686538;RU=ta;PERIOD=2;REF=19;GRID=1,103;STUTTERUP=0.0783833;STUTTERDOWN=0.095077;STUTTERP=0.543491;EXPTHRESH=19 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:23:0.0184747:1,1:1-4,1-4:0,23,0,0:NULL:NULL:207.554:366.612,131.36:0.993953,0.993953:0.873247,0.124515,0.00234243 +chr1 3688514 . aaacaaacaaacaaac . . PASS END=3688529;RU=aaac;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.00053694;STUTTERDOWN=0.00363006;STUTTERP=0.958596;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:32:0.999971:4,4:4-4,4-4:17,13,0,2:4,17:3,2:208.339:366.612,131.36:0,0:0,2.13281e-05,0.999979 +chr1 3689585 . gtgggtgggtgggtgg . . PASS END=3689600;RU=gtgg;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.00196138;STUTTERDOWN=0.0142472;STUTTERP=0.961421;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:0.846048:4,4:2-4,2-4:6,25,0,2:4,6:2,1|3,1:254.143:366.612,131.36:0.485452,0.485452:1.57694e-16,0.0988066,0.901298 +chr1 3693848 . tctctgtctctgtctctg . . PASS END=3693865;RU=tctctg;PERIOD=6;REF=3;GRID=1,6;STUTTERUP=0.000485417;STUTTERDOWN=0.000485417;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:1:3,3:3-3,3-3:23,13,0,2:3,23:2,2:224.771:366.612,131.36:0,0:0,4.71796e-07,1 +chr1 3693870 . tgtgtgtgtgtgtg . . PASS END=3693883;RU=tg;PERIOD=2;REF=7;GRID=4,10;STUTTERUP=0.014767;STUTTERDOWN=0.0324668;STUTTERP=0.958778;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:32:1:7,7:7-7,7-7:20,10,0,2:7,20:4,1|6,1:186.249:366.612,131.36:0,0:6.01707e-37,5.85978e-06,0.999995 +chr1 3695906 . ttttattttatttta ttttattttattttatttta . PASS END=3695920;RU=tttta;PERIOD=5;REF=3;GRID=1,7;STUTTERUP=0.00131961;STUTTERDOWN=0.003791;STUTTERP=0.954564;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:21:0.977606:4,4:4-4,4-4:9,10,0,2:4,9:3,2:143.282:366.612,131.36:0,0:0,0.00535545,0.994656 +chr1 3699904 . ctttctttcttt . . PASS END=3699915;RU=cttt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000484865;STUTTERDOWN=0.000969728;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:26:0.997682:3,3:3-3,3-3:13,13,0,0:3,13:NULL:177.632:366.612,131.36:0,0:3.50325e-43,0.00138937,0.998617 +chr1 3700824 . catcatcatcat . . PASS END=3700835;RU=cat;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00132044;STUTTERDOWN=0.00156249;STUTTERP=0.968308;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:49:1:4,4:4-4,4-4:24,21,0,4:4,24:3,4:317.857:366.612,131.36:0,0:0,3.12785e-07,1 +chr1 3702280 . aaataaataaat . . PASS END=3702291;RU=aaat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000416118;STUTTERDOWN=0.000416118;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:41:1:3,3:3-3,3-3:24,15,0,2:3,24:2,2:246.834:366.612,131.36:0,0:0,6.36609e-07,1 +chr1 3702293 . aaataaaataaaata . . PASS END=3702307;RU=aaata;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000446824;STUTTERDOWN=0.00255282;STUTTERP=0.829224;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:1:3,3:3-3,3-3:23,15,0,0:3,23:NULL:226.913:366.612,131.36:0,0:0,1.69776e-06,1 +chr1 3708462 . gagagagagagaga gagagagaga . PASS END=3708475;RU=ga;PERIOD=2;REF=7;GRID=1,103;STUTTERUP=0.0184615;STUTTERDOWN=0.0747875;STUTTERP=0.736072;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:9:0.00667709:5,5:1-6,1-6:0,9,0,0:NULL:NULL:84.5076:366.612,131.36:1.98272,1.98272:0.147395,0.516524,0.336216 +chr1 3712175 . acacacacacacacacacacacacacac acacacacacacacac . PASS END=3712202;RU=ac;PERIOD=2;REF=14;GRID=4,14;STUTTERUP=0.0609384;STUTTERDOWN=0.143072;STUTTERP=0.601638;EXPTHRESH=14 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:28:0.723808:8,8:7-11,7-11:5,16,0,4:8,5:6,2|7,1|8,1:197.448:366.612,131.36:1.37592,1.37592:0.976772,0.0232742,1.39106e-16 +chr1 3712203 . gagagagagagagagagagagagagagagagagagagagagagagagagagagagaga gagagagagagagagagagagagagagagagagagagagagagagagagagagagagaga,gagagagagagagagagagagagagagagagagagagagagagagagagagagagagagagaga . PASS END=3712260;RU=ga;PERIOD=2;REF=29;GRID=30,36;STUTTERUP=0.067653;STUTTERDOWN=0.296493;STUTTERP=0.526901;EXPTHRESH=29 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:20:0.0579816:30,32:30-33,30-33:0,12,0,7:NULL:5,1|7,1|8,3|11,1|15,1:169.773:366.612,131.36:1.06793,1.04894:0,0,1 +chr1 3719601 . agagagagagagagagagagagagagagagagagagagagagag agagagagagagagagagagagagagagagagagagagagagagagagagagagagagag,agagagagagagagagagagagagagagagagagagagagagagagagagagagagagagagagag . PASS END=3719644;RU=ag;PERIOD=2;REF=22;GRID=7,33;STUTTERUP=0.0537652;STUTTERDOWN=0.345397;STUTTERP=0.595215;EXPTHRESH=22 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:19:0.0347453:30,33:10-32,10-32:0,9,0,8:NULL:13,1|14,1|19,1|20,1|22,1|26,1|28,1|30,1:149.785:366.612,131.36:9.11023,9.18537:1.2421e-29,0.214365,0.785679 +chr1 3719848 . ccagccagccag . . PASS END=3719859;RU=ccag;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000431242;STUTTERDOWN=0.000431242;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:1.00001:3,3:3-3,3-3:22,13,0,2:3,22:2,2:216.479:366.612,131.36:0,0:0,8.62623e-07,1 +chr1 3720011 . gtggtggtggtg . . PASS END=3720022;RU=gtg;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000655763;STUTTERDOWN=0.00660445;STUTTERP=0.943295;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:40:1:4,4:4-4,4-4:25,15,0,0:4,25:NULL:234.32:366.612,131.36:0,0:0,2.50935e-07,1 +chr1 3722193 . caccaccaccac . . PASS END=3722204;RU=cac;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000355931;STUTTERDOWN=0.0031596;STUTTERP=0.981068;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:0.999986:4,4:4-4,4-4:19,20,0,0:4,19:NULL:255.587:366.612,131.36:0,0:0,2.0731e-05,0.999979 +chr1 3724786 . ctctctctctctctctctctctctctctctctctctctctctctctctct ctctctctctctctct . PASS END=3724835;RU=ct;PERIOD=2;REF=25;GRID=4,11;STUTTERUP=0.0663429;STUTTERDOWN=0.212648;STUTTERP=0.545762;EXPTHRESH=25 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:17:0.920241:8,8:7-8,7-8:11,6,0,0:7,2|8,9:NULL:107.946:366.612,131.36:0.311527,0.311527:1,0,0 +chr1 3724835 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtg . PASS END=3724868;RU=tg;PERIOD=2;REF=17;GRID=3,22;STUTTERUP=0.0322588;STUTTERDOWN=0.0494013;STUTTERP=0.359657;EXPTHRESH=17 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:25:0.704735:7,7:6-19,6-19:14,10,0,0:6,2|7,12:NULL:156.457:366.612,131.36:5.39532,5.39532:0.999773,0.000228516,0 +chr1 3726870 . cttccttccttccttccttccttccttccttccttc cttccttccttccttccttccttc,cttccttccttccttccttccttccttc . PASS END=3726905;RU=cttc;PERIOD=4;REF=9;GRID=3,12;STUTTERUP=0.0183605;STUTTERDOWN=0.0214238;STUTTERP=0.625593;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:13:0.995342:6,7:6-9,7-9:6,5,0,0:6,2|7,4:NULL:80.5326:366.612,131.36:1.26508,0.526896:0.999614,0.000386882,3.11278e-14 +chr1 3727052 . ccacccacccac . . PASS END=3727063;RU=ccac;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000446525;STUTTERDOWN=0.000893049;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:22:0.999387:3,3:3-3,3-3:14,8,0,0:3,14:NULL:130.249:366.612,131.36:0,0:0,0.000337427,0.999666 +chr1 3727955 . cacacacacaca cacacacaca . PASS END=3727966;RU=ca;PERIOD=2;REF=6;GRID=2,9;STUTTERUP=0.00912454;STUTTERDOWN=0.0207046;STUTTERP=0.855109;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:13:0.523675:5,5:5-6,5-6:4,8,0,0:5,4:NULL:88.9008:366.612,131.36:0.605662,0.605662:0.794176,0.205873,4.81081e-08 +chr1 3730566 . atatatatatatatatatatatatatatatatatatatatatat atatatatatatatatatatatatatatatatatatatatatatat . PASS END=3730609;RU=at;PERIOD=2;REF=22;GRID=23,30;STUTTERUP=0.142812;STUTTERDOWN=0.286698;STUTTERP=0.744772;EXPTHRESH=22 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:5:0.0242636:23,23:23-27,23-27:0,3,0,0:NULL:NULL:27.3808:366.612,131.36:1.10572,1.10572:0,0,1 +chr1 3730917 . aaaataaaataaaat . . PASS END=3730931;RU=aaaat;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000513367;STUTTERDOWN=0.000513367;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:22:0.99712:3,3:3-3,3-3:12,10,0,0:3,12:NULL:138.177:366.612,131.36:0,0:1.15463e-39,0.0017405,0.998262 +chr1 3732771 . acaaacaaacaaacaa . . PASS END=3732786;RU=acaa;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000595544;STUTTERDOWN=0.00287542;STUTTERP=0.846811;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:1:4,4:4-4,4-4:20,9,0,0:4,20:NULL:159.888:366.612,131.36:0,0:0,6.7041e-06,0.999994 +chr1 3733827 . tttgtttgtttgtttgtttg tttgtttgtttgtttgtttgtttg . PASS END=3733846;RU=tttg;PERIOD=4;REF=5;GRID=3,9;STUTTERUP=0.00103174;STUTTERDOWN=0.0111813;STUTTERP=0.673858;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:34:0.999765:6,6:6-6,6-6:15,13,0,6:6,15:3,2|4,1|5,3:218.421:366.612,131.36:0,0:0,2.32535e-05,0.999979 +chr1 3733847 . ttttgtttttgtttttgt . . PASS END=3733864;RU=ttttgt;PERIOD=6;REF=3;GRID=1,6;STUTTERUP=0.00127488;STUTTERDOWN=0.000892577;STUTTERP=0.959079;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:22:0.999818:3,3:3-3,3-3:16,6,0,0:3,16:NULL:117.606:366.612,131.36:0,0:0,0.000105411,0.999895 +chr1 3742835 . acatacatacat . . PASS END=3742846;RU=acat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000441534;STUTTERDOWN=0.000441534;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:32:1:3,3:3-3,3-3:24,8,0,0:3,24:NULL:167.131:366.612,131.36:0,0:0,2.71881e-07,1 +chr1 3744407 . ggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaa ggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaa . PASS END=3744462;RU=ggaa;PERIOD=4;REF=14;GRID=8,14;STUTTERUP=0.00719006;STUTTERDOWN=0.0495383;STUTTERP=0.70657;EXPTHRESH=14 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:20:0.993983:11,11:11-11,11-11:11,3,0,6:11,11:3,1|5,1|7,2|8,1|9,1:116.828:366.612,131.36:0,0:0.999066,0.000937214,5.358e-29 +chr1 3745050 . agagagagagagagagagagagagagagagagagagagagagagagagagagag agagag . PASS END=3745103;RU=ag;PERIOD=2;REF=27;GRID=1,103;STUTTERUP=0.105781;STUTTERDOWN=0.167931;STUTTERP=0.512132;EXPTHRESH=27 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:11:0.00833439:3,3:2-5,2-5:0,11,0,0:NULL:NULL:95.702:366.612,131.36:0.85137,0.85137:0.805952,0.189878,0.00422831 +chr1 3752086 . gtgtgtgtgtgt . . PASS END=3752097;RU=gt;PERIOD=2;REF=6;GRID=3,9;STUTTERUP=0.00395385;STUTTERDOWN=0.00790769;STUTTERP=0.938587;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:23:0.999816:6,6:6-6,6-6:16,7,0,0:6,16:NULL:130.022:366.612,131.36:0,0:2.15979e-39,0.000115849,0.999887 +chr1 3758404 . aaacaaaacaaaacaaaacaaaacaaaacaaaacaaaacaaaaca aaacaaaacaaaacaaaacaaaacaaaacaaaaca . PASS END=3758448;RU=aaaca;PERIOD=5;REF=9;GRID=4,10;STUTTERUP=0.00359685;STUTTERDOWN=0.0163248;STUTTERP=0.704299;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:25:0.996019:7,7:7-7,7-7:11,11,0,3:7,11:3,1|5,1|6,1:166.028:366.612,131.36:0,0:0.998838,0.00116594,1.13138e-28 +chr1 3765019 . atttatttattt . . PASS END=3765030;RU=attt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00211091;STUTTERDOWN=0.00249785;STUTTERP=0.968308;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:34:0.999994:3,3:3-3,3-3:19,15,0,0:3,19:NULL:207.901:366.612,131.36:0,0:0,1.32469e-05,0.999987 +chr1 3766121 . acccacccaccc . . PASS END=3766132;RU=accc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000954404;STUTTERDOWN=0.000954404;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:22:0.963733:3,3:3-3,3-3:7,15,0,0:3,7:NULL:162.987:366.612,131.36:0,0:4.39709e-22,0.0207749,0.979265 +chr1 3774612 . acacacacacacacacacacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacac . PASS END=3774657;RU=ac;PERIOD=2;REF=23;GRID=15,22;STUTTERUP=0.08077;STUTTERDOWN=0.178769;STUTTERP=0.71277;EXPTHRESH=23 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:32:0.861539:19,19:18-19,18-19:13,9,0,10:18,3|19,10:7,2|10,1|13,1|14,2|15,2|17,1|18,1:225.995:366.612,131.36:0.35561,0.35561:1,0,0 +chr1 3779502 . ttttgtttttgtttttgt . . PASS END=3779519;RU=ttttgt;PERIOD=6;REF=3;GRID=1,6;STUTTERUP=0.000644395;STUTTERDOWN=0.00257755;STUTTERP=0.844424;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:18:0.978872:3,3:3-3,3-3:9,9,0,0:3,9:NULL:117.204:366.612,131.36:0,0:9.67506e-30,0.0137041,0.986326 +chr1 3784264 . tttatttattta . . PASS END=3784275;RU=ttta;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000871778;STUTTERDOWN=0.00043589;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:40:1:3,3:3-3,3-3:28,12,0,0:3,28:NULL:224.825:366.612,131.36:0,0:0,3.24046e-08,1 +chr1 3785257 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt,gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=3785292;RU=gt;PERIOD=2;REF=18;GRID=18,28;STUTTERUP=0.0652788;STUTTERDOWN=0.225124;STUTTERP=0.603761;EXPTHRESH=18 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:42:0.796789:23,24:21-25,24-25:10,9,0,20:23,4|24,6:4,2|5,2|6,1|9,1|10,2|11,2|15,1|16,2|17,1|18,4|22,1|23,1:290.161:366.612,131.36:0.845709,0.242928:0,0,1 +chr1 3786174 . tttatttattta . . PASS END=3786185;RU=ttta;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00054978;STUTTERDOWN=0.00109956;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:1.00001:3,3:3-3,3-3:21,10,0,0:3,21:NULL:169.623:366.612,131.36:0,0:0,2.02586e-06,1 +chr1 3786490 . taaataaataaa . . PASS END=3786501;RU=taaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00042374;STUTTERDOWN=0.000847479;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:28:1:3,3:3-3,3-3:23,5,0,0:3,23:NULL:139.261:366.612,131.36:0,0:0,4.1567e-07,1 +chr1 3788152 . catacatacata . . PASS END=3788163;RU=cata;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00126102;STUTTERDOWN=0.000882872;STUTTERP=0.959079;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:0.999885:3,3:3-3,3-3:16,19,0,0:3,16:NULL:237.894:366.612,131.36:0,0:0,8.15691e-05,0.999919 +chr1 3788588 . ctctctccctctctccctctctccctctctccctctctcc . . PASS END=3788627;RU=ctctctcc;PERIOD=8;REF=5;GRID=2,8;STUTTERUP=0.00216587;STUTTERDOWN=0.00618526;STUTTERP=0.494965;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:16:0.645137:5,5:2-5,2-5:5,11,0,0:5,5:NULL:123.911:366.612,131.36:0.675883,0.675883:1.07449e-14,0.312121,0.68789 +chr1 3789797 . aataaataaata . . PASS END=3789808;RU=aata;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000451688;STUTTERDOWN=0.0030537;STUTTERP=0.833561;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:20:0.998953:3,3:3-3,3-3:14,6,0,0:3,14:NULL:115.25:366.612,131.36:0,0:0,0.000634039,0.99937 +chr1 3805050 . ttggttggttgg ttggttgg . PASS END=3805061;RU=ttgg;PERIOD=4;REF=3;GRID=1,103;STUTTERUP=0.000913979;STUTTERDOWN=0.00182796;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:19:0.0810857:2,2:1-3,1-3:0,19,0,0:NULL:NULL:190.732:366.612,131.36:0.651813,0.651813:0.251698,0.520872,0.227449 +chr1 3805151 . ctgcctctgcctctgcctctgcct ctgcct,ctgcctctgcct . PASS END=3805174;RU=ctgcct;PERIOD=6;REF=4;GRID=1,103;STUTTERUP=0.00106247;STUTTERDOWN=0.00212494;STUTTERP=0.999;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:19:0.268599:1,2:1-2,1-2:0,19,0,0:NULL:NULL:189.234:366.612,131.36:0.573574,0.493065:0.660386,0.313909,0.0257531 +chr1 3805421 . acccacccaccc . . PASS END=3805432;RU=accc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00153233;STUTTERDOWN=0.00153233;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:8:0.45434:3,3:2-3,2-3:3,5,0,0:3,3:NULL:53.6259:366.612,131.36:0.222277,0.222277:2.34056e-09,0.235506,0.764519 +chr1 3808366 . ttgtttgtttgt . . PASS END=3808377;RU=ttgt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000586378;STUTTERDOWN=0.00137115;STUTTERP=0.925218;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:43:0.999908:3,3:3-3,3-3:17,26,0,0:3,17:NULL:306.492:366.612,131.36:0,0:0,7.48206e-05,0.999926 +chr1 3820046 . atacatacatac . . PASS END=3820057;RU=atac;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000410736;STUTTERDOWN=0.00117332;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:46:1:3,3:3-3,3-3:24,19,0,3:3,24:2,3:284.425:366.612,131.36:0,0:0,2.20899e-07,1 +chr1 3820489 . gaagagaagagaagagaagagaagagaagagaagagaagagaagagaagagaagagaagagaaga gaaga . PASS END=3820553;RU=gaaga;PERIOD=5;REF=13;GRID=1,103;STUTTERUP=0.00995908;STUTTERDOWN=0.0366633;STUTTERP=0.945177;EXPTHRESH=13 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:12:0.0470469:1,1:1-3,1-3:0,12,0,0:NULL:NULL:107.696:366.612,131.36:0.738802,0.738802:0.881235,0.117651,0.00121683 +chr1 3821324 . atgaaatgaaatgaa . . PASS END=3821338;RU=atgaa;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000493451;STUTTERDOWN=0.00333604;STUTTERP=0.958596;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:1:3,3:3-3,3-3:24,11,0,0:3,24:NULL:193.08:366.612,131.36:0,0:0,2.98735e-07,1 +chr1 3821877 . aataaataaata . . PASS END=3821888;RU=aata;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000454564;STUTTERDOWN=0.00129852;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:1.00001:3,3:3-3,3-3:21,14,0,0:3,21:NULL:209.292:366.612,131.36:0,0:0,3.26394e-06,1 +chr1 3824596 . gggtgggtgggt . . PASS END=3824607;RU=gggt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00190864;STUTTERDOWN=0.00190864;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:8:0.270275:3,3:3-5,3-5:2,6,0,0:3,2:NULL:60.4922:366.612,131.36:0.557805,0.557805:1.71077e-06,0.273652,0.726351 +chr1 3830973 . tggctggctggc . . PASS END=3830984;RU=tggc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000337274;STUTTERDOWN=0.00134908;STUTTERP=0.987382;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:0.999344:3,3:3-3,3-3:14,25,0,0:3,14:NULL:289.904:366.612,131.36:0,0:0,0.000518182,0.999484 +chr1 3835805 . acacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacacacac . PASS END=3835830;RU=ac;PERIOD=2;REF=13;GRID=16,27;STUTTERUP=0.0382248;STUTTERDOWN=0.170497;STUTTERP=0.663461;EXPTHRESH=13 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:55:0.524651:21,21:19-24,19-24:16,17,0,20:19,3|20,2|21,9|22,2:4,1|5,1|7,1|10,3|12,1|14,3|16,3|17,1|18,4|19,1|20,1:410.769:366.612,131.36:1.4981,1.4981:0,0,1 +chr1 3838836 . ttgtttgtttgtttgtttgt ttgt . PASS END=3838855;RU=ttgt;PERIOD=4;REF=5;GRID=1,103;STUTTERUP=0.00165173;STUTTERDOWN=0.00662251;STUTTERP=0.733842;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:19:0.0611499:1,1:1-3,1-3:0,19,0,0:NULL:NULL:176.361:366.612,131.36:0.763982,0.763982:0.495318,0.428118,0.0766308 +chr1 3842935 . gtttgtttgtttgttt gtttgtttgttt . PASS END=3842950;RU=gttt;PERIOD=4;REF=4;GRID=1,6;STUTTERUP=0.000995991;STUTTERDOWN=0.00240444;STUTTERP=0.986219;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:16:0.103226:3,3:1-4,1-4:0,13,0,3:NULL:2,2|3,1:139.412:366.612,131.36:0.668152,0.668152:0.265285,0.537828,0.196891 +chr1 3846941 . acccacccaccc . . PASS END=3846952;RU=accc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00106197;STUTTERDOWN=0.00212394;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:15:0.964559:3,3:3-3,3-3:8,7,0,0:3,8:NULL:90.4399:366.612,131.36:0,0:1.77949e-24,0.014786,0.985246 +chr1 3856577 . cttgcttgcttgcttgcttgcttg cttgcttgcttgcttgcttgcttgcttg . PASS END=3856600;RU=cttg;PERIOD=4;REF=6;GRID=4,10;STUTTERUP=0.000567554;STUTTERDOWN=0.0160459;STUTTERP=0.768856;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:44:0.999866:7,7:7-7,7-7:16,22,0,6:7,16:3,2|4,1|6,3:304.611:366.612,131.36:0,0:0,1.80724e-05,0.999985 +chr1 3858322 . ggagggagggag . . PASS END=3858333;RU=ggag;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000909189;STUTTERDOWN=0.00153669;STUTTERP=0.825421;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:56:1:3,3:3-3,3-3:42,12,0,2:3,42:2,2:287.409:366.612,131.36:0,0:0,6.46565e-13,1 +chr1 3859194 . ttgttgttgttgttgttg ttgttgttgttgttg . PASS END=3859211;RU=ttg;PERIOD=3;REF=6;GRID=2,8;STUTTERUP=0.00337508;STUTTERDOWN=0.005239;STUTTERP=0.979853;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:69:1:5,5:5-5,5-5:41,24,0,4:5,41:3,2|4,2:410.296:366.612,131.36:0,0:1,2.43332e-12,0 +chr1 3863716 . aataacaataacaataac . . PASS END=3863733;RU=aataac;PERIOD=6;REF=3;GRID=1,6;STUTTERUP=0.000404591;STUTTERDOWN=0.00424994;STUTTERP=0.977258;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:1:3,3:3-3,3-3:23,12,0,0:3,23:NULL:208.152:366.612,131.36:0,0:0,1.27778e-06,1 +chr1 3869461 . aaaacaaaacaaaacaaaacaaaac aaaac . PASS END=3869485;RU=aaaac;PERIOD=5;REF=5;GRID=1,103;STUTTERUP=0.00159032;STUTTERDOWN=0.0072501;STUTTERP=0.685601;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:7:0.0233967:1,1:1-2,1-2:0,7,0,0:NULL:NULL:61.8713:366.612,131.36:0.379868,0.379868:0.2013,0.56247,0.236278 +chr1 3870192 . taaataaataaa . . PASS END=3870203;RU=taaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000401398;STUTTERDOWN=0.000401398;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:34:0.999475:3,3:3-3,3-3:14,20,0,0:3,14:NULL:237.66:366.612,131.36:0,0:0,0.000336171,0.999667 +chr1 3870234 . aaaataaaataaaat aaaataaaat . PASS END=3870248;RU=aaaat;PERIOD=5;REF=3;GRID=1,5;STUTTERUP=0.00101145;STUTTERDOWN=0.00203637;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:34:0.999274:2,2:2-2,2-2:13,21,0,0:2,13:NULL:246.786:366.612,131.36:0,0:0.999607,0.000394087,3.85503e-36 +chr1 3886751 . tagatagatagatagatagatagatagatagatagatagataga . . PASS END=3886794;RU=taga;PERIOD=4;REF=11;GRID=7,14;STUTTERUP=0.00412781;STUTTERDOWN=0.0358799;STUTTERP=0.532454;EXPTHRESH=11 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:27:0.99542:11,11:10-11,10-11:12,14,0,0:11,12:NULL:180.536:366.612,131.36:0.36513,0.36513:5.1308e-32,0.00375858,0.996254 +chr1 3896272 . acccacccaccc . . PASS END=3896283;RU=accc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00120161;STUTTERDOWN=0.00120161;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:9:0.683871:3,3:2-3,2-3:5,4,0,0:3,5:NULL:58.6488:366.612,131.36:0.169767,0.169767:5.75032e-15,0.148271,0.851811 +chr1 3898788 . taaataaataaa . . PASS END=3898799;RU=taaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00096639;STUTTERDOWN=0.000483196;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:1:3,3:3-3,3-3:20,17,0,0:3,20:NULL:236.45:366.612,131.36:0,0:0,4.53293e-06,0.999995 +chr1 3898809 . ataataataata . . PASS END=3898820;RU=ata;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00229077;STUTTERDOWN=0.00774359;STUTTERP=0.839312;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:0.999304:4,4:4-4,4-4:14,19,0,0:4,14:NULL:234.002:366.612,131.36:0,0:6.90189e-39,0.000574116,0.99943 +chr1 3902855 . aaacaaacaaacaaacaaacaaacaaac aaacaaacaaacaaacaaacaaac . PASS END=3902882;RU=aaac;PERIOD=4;REF=7;GRID=2,9;STUTTERUP=0.000970568;STUTTERDOWN=0.0155918;STUTTERP=0.89844;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:31:0.972597:6,6:5-6,5-6:19,10,0,2:5,2|6,17:5,2:191.553:366.612,131.36:0.398507,0.398507:0.999994,8.10062e-06,9.10738e-35 +chr1 3908575 . tgttttgttttgttt . . PASS END=3908589;RU=tgttt;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000507833;STUTTERDOWN=0.000507833;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:42:1:3,3:3-3,3-3:23,19,0,0:3,23:NULL:261.146:366.612,131.36:0,0:0,8.71967e-07,1 +chr1 3911778 . acagacagacag . . PASS END=3911789;RU=acag;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000437546;STUTTERDOWN=0.000437546;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:34:1.00001:3,3:3-3,3-3:20,14,0,0:3,20:NULL:202.137:366.612,131.36:0,0:0,3.67449e-06,1 +chr1 3913472 . ccccacccccacccccac . . PASS END=3913489;RU=ccccac;PERIOD=6;REF=3;GRID=1,6;STUTTERUP=0.00115298;STUTTERDOWN=0.00115298;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:24:0.994325:3,3:3-3,3-3:11,13,0,0:3,11:NULL:168.599:366.612,131.36:0,0:6.82753e-33,0.00376458,0.996247 +chr1 3917711 . gagagagagagagagagagagagagagagagagagaga gagagagagagagagagagagagagagagagagagagagagagagaga . PASS END=3917748;RU=ga;PERIOD=2;REF=19;GRID=16,27;STUTTERUP=0.0486501;STUTTERDOWN=0.153035;STUTTERP=0.455664;EXPTHRESH=19 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/1:18:0.889114:19,24:19-23,22-24:7,5,0,5:19,3|23,2|24,2:5,1|7,1|12,1|13,1|15,1:123.646:366.612,131.36:1.71576,0.657801:3.79657e-12,5.74102e-05,0.999942 +chr1 3919065 . tttgtttgtttg . . PASS END=3919076;RU=tttg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000509177;STUTTERDOWN=0.000509177;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:30:0.999992:3,3:3-3,3-3:19,11,0,0:3,19:NULL:175.122:366.612,131.36:0,0:0,1.60593e-05,0.999986 +chr1 3919745 . tattttattttattttattttattttattttattttattttattttattt tattttattttattttattttattttattt . PASS END=3919794;RU=tattt;PERIOD=5;REF=10;GRID=3,9;STUTTERUP=0.00356018;STUTTERDOWN=0.0225335;STUTTERP=0.58555;EXPTHRESH=10 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:26:0.940197:6,6:6-6,6-6:8,16,0,2:6,8:4,1|5,1:200.349:366.612,131.36:0.417958,0.417958:1,0,0 +chr1 3923978 . tatatatatatatata tatatatatatatatata . PASS END=3923993;RU=ta;PERIOD=2;REF=8;GRID=4,13;STUTTERUP=0.0434726;STUTTERDOWN=0.062748;STUTTERP=0.827258;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:15:0.926104:9,9:7-10,7-10:8,4,0,0:9,8:NULL:67.4941:366.612,131.36:0.929323,0.929323:6.6815e-18,0.0350496,0.965016 +chr1 3924698 . gagaggagaggagaggagaggagaggagaggagaggagaggagag . . PASS END=3924742;RU=gagag;PERIOD=5;REF=9;GRID=1,12;STUTTERUP=0.00125572;STUTTERDOWN=0.00787339;STUTTERP=0.40745;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:20:0.0643016:9,9:6-11,6-11:0,11,0,9:NULL:2,1|3,1|6,3|7,2|8,1|9,1:165.574:366.612,131.36:1.57311,1.57311:5.08532e-09,0.495721,0.504304 +chr1 3924854 . ctgctgctgctg . . PASS END=3924865;RU=ctg;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00132724;STUTTERDOWN=0.000464615;STUTTERP=0.941457;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:0.999785:4,4:4-4,4-4:16,13,0,0:4,16:NULL:184.539:366.612,131.36:0,0:0,0.000136256,0.999865 +chr1 3925698 . agagagagagag . . PASS END=3925709;RU=ag;PERIOD=2;REF=6;GRID=3,9;STUTTERUP=0.00385452;STUTTERDOWN=0.0157458;STUTTERP=0.859983;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:40:1:6,6:6-6,6-6:31,7,0,2:6,31:5,2:208.134:366.612,131.36:0,0:0,2.33183e-09,1 +chr1 3929285 . acacacacacacacacacacacacacac acacacacacacacacacacac . PASS END=3929312;RU=ac;PERIOD=2;REF=14;GRID=7,14;STUTTERUP=0.0362455;STUTTERDOWN=0.103585;STUTTERP=0.827874;EXPTHRESH=14 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:40:0.99692:11,11:10-11,10-11:12,20,0,7:11,12:4,1|6,2|8,3|10,1:289.866:366.612,131.36:0.169767,0.169767:0.999713,0.000288637,6.51961e-32 +chr1 3932876 . aaaacaaaacaaaac . . PASS END=3932890;RU=aaaac;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000493338;STUTTERDOWN=0.00281857;STUTTERP=0.829224;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:27:0.99924:3,3:3-3,3-3:13,14,0,0:3,13:NULL:182.319:366.612,131.36:0,0:1.54143e-44,0.000526743,0.999476 +chr1 3936576 . aacaaacaaaca . . PASS END=3936587;RU=aaca;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000475583;STUTTERDOWN=0.000475583;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:1:3,3:3-3,3-3:23,16,0,0:3,23:NULL:233.798:366.612,131.36:0,0:0,1.09396e-06,1 +chr1 3943923 . atatatatatat . . PASS END=3943934;RU=at;PERIOD=2;REF=6;GRID=3,9;STUTTERUP=0.0164126;STUTTERDOWN=0.00786812;STUTTERP=0.927079;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:0.996744:6,6:6-6,6-6:12,17,0,0:6,12:NULL:198.475:366.612,131.36:0,0:2.90152e-22,0.00225795,0.997746 +chr1 3945858 . agaaagaaagaa . . PASS END=3945869;RU=agaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000423707;STUTTERDOWN=0.00121038;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:24:0.994776:3,3:3-3,3-3:11,13,0,0:3,11:NULL:164.432:366.612,131.36:0,0:9.3349e-38,0.00312694,0.996882 +chr1 3949566 . acacacacacac acacacacacacacacacacacacacacac . PASS END=3949577;RU=ac;PERIOD=2;REF=6;GRID=2,18;STUTTERUP=0.00456059;STUTTERDOWN=0.0194308;STUTTERP=0.969441;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:23:0.0905103:15,15:3-15,3-15:4,18,0,0:15,4:NULL:186.702:366.612,131.36:4.19547,4.19547:0,0.533203,0.466901 +chr1 3952215 . aaacaaacaaacaaac . . PASS END=3952230;RU=aaac;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000818113;STUTTERDOWN=0.00757449;STUTTERP=0.945127;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:40:0.999761:4,4:3-4,3-4:15,20,0,4:4,15:2,2|3,2:270.441:366.612,131.36:0.345543,0.345543:0,0.000148609,0.999856 +chr1 3952974 . agacagacagac . . PASS END=3952985;RU=agac;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000380921;STUTTERDOWN=0.00338144;STUTTERP=0.981068;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:30:1.00001:3,3:3-3,3-3:21,9,0,0:3,21:NULL:167.283:366.612,131.36:0,0:0,2.12211e-06,1 +chr1 3955861 . taaataaataaa . . PASS END=3955872;RU=taaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000258842;STUTTERDOWN=0.000739416;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:1:3,3:3-3,3-3:24,15,0,0:3,24:NULL:231.683:366.612,131.36:0,0:0,2.6316e-07,1 +chr1 3956922 . taataataataa . . PASS END=3956933;RU=taa;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000787668;STUTTERDOWN=0.00349607;STUTTERP=0.854468;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:0.999886:4,4:4-4,4-4:17,18,0,0:4,17:NULL:230.649:366.612,131.36:0,0:0,8.15416e-05,0.999919 +chr1 3960762 . tgatgatgatga . . PASS END=3960773;RU=tga;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00031737;STUTTERDOWN=0.00181322;STUTTERP=0.969616;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:51:1:4,4:4-4,4-4:29,20,0,2:4,29:3,2:305.791:366.612,131.36:0,0:0,7.27355e-09,1 +chr1 3967310 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt,gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=3967353;RU=gt;PERIOD=2;REF=22;GRID=9,28;STUTTERUP=0.0768704;STUTTERDOWN=0.203614;STUTTERP=0.749454;EXPTHRESH=22 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:24:0.306429:21,25:21-21,12-25:13,0,0,9:21,11|22,2:7,1|8,1|9,1|12,1|14,1|15,1|19,1|20,1|25,1:145.172:366.612,131.36:0.139319,4.93443:7.43147e-05,0.999921,4.24387e-06 +chr1 3969294 . caaacaaacaaacaaa . . PASS END=3969309;RU=caaa;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000403486;STUTTERDOWN=0.00161393;STUTTERP=0.706087;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:1:4,4:4-4,4-4:20,14,0,2:4,20:3,2:225.215:366.612,131.36:0,0:0,6.4141e-06,0.999995 +chr1 3972539 . ttatttatttatttatttat ttatttatttatttatttatttat . PASS END=3972558;RU=ttat;PERIOD=4;REF=5;GRID=3,9;STUTTERUP=0.000554228;STUTTERDOWN=0.0115761;STUTTERP=0.824699;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:39:1.00001:6,6:6-6,6-6:20,14,0,5:6,20:3,1|4,1|5,3:241.788:366.612,131.36:0,0:0,6.07488e-07,1 +chr1 3985823 . cacacacacaca ca . PASS END=3985834;RU=ca;PERIOD=2;REF=6;GRID=1,103;STUTTERUP=0.0069316;STUTTERDOWN=0.00377011;STUTTERP=0.851496;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP .:.:.:.:.:.:.:.:.:.:.:. +chr1 3992697 . gcagaggcagaggcagag . . PASS END=3992714;RU=gcagag;PERIOD=6;REF=3;GRID=1,6;STUTTERUP=0.000490148;STUTTERDOWN=0.00331371;STUTTERP=0.770853;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:48:1:3,3:3-3,3-3:25,21,0,2:3,25:2,2:304.686:366.612,131.36:0,0:0,1.71221e-07,1 +chr1 3996489 . acacacacacacacacacacacac acacacacacacac . PASS END=3996512;RU=ac;PERIOD=2;REF=12;GRID=4,10;STUTTERUP=0.0222731;STUTTERDOWN=0.0464693;STUTTERP=0.860889;EXPTHRESH=12 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:27:1:7,7:7-7,7-7:20,7,0,0:7,20:NULL:142.446:366.612,131.36:0,0:1,0,0 +chr1 3997264 . ttattattatta . . PASS END=3997275;RU=tta;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00103925;STUTTERDOWN=0.00207848;STUTTERP=0.999;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:26:0.99985:4,4:4-4,4-4:16,10,0,0:4,16:NULL:155.95:366.612,131.36:0,0:0,0.00010225,0.999902 +chr1 3997282 . tttatttattta . . PASS END=3997293;RU=ttta;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000503071;STUTTERDOWN=0.000503071;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:1:3,3:3-3,3-3:20,9,0,0:3,20:NULL:163.036:366.612,131.36:0,0:0,4.92314e-06,0.999995 +chr1 4000875 . atatatatatatatatatatatatatatatatatatatatatatat atatatatatatatat . PASS END=4000920;RU=at;PERIOD=2;REF=23;GRID=5,11;STUTTERUP=0.0959297;STUTTERDOWN=0.0931465;STUTTERP=0.753373;EXPTHRESH=23 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:5:0.405946:8,8:8-8,8-8:3,2,0,0:8,3:NULL:33.0948:366.612,131.36:0,0:1,0,0 +chr1 4008030 . acacacacacacacacacacacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacacacac . PASS END=4008077;RU=ac;PERIOD=2;REF=24;GRID=16,26;STUTTERUP=0.0786509;STUTTERDOWN=0.246639;STUTTERP=0.733579;EXPTHRESH=24 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:43:0.39318:21,21:19-23,19-23:10,17,0,14:19,2|21,6|22,2:5,1|6,1|8,2|10,1|11,1|12,1|15,1|18,2|19,1|20,3:320.681:366.612,131.36:1.12445,1.12445:0.997836,0.00217262,4.18948e-16 +chr1 4008365 . aagaaagaaaga . . PASS END=4008376;RU=aaga;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000440086;STUTTERDOWN=0.00297526;STUTTERP=0.958596;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:44:1:3,3:3-3,3-3:24,20,0,0:3,24:NULL:269.288:366.612,131.36:0,0:0,3.01382e-07,1 +chr1 4012417 . aaagaaagaaag . . PASS END=4012428;RU=aaag;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000560157;STUTTERDOWN=0.00160016;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:0.999412:3,3:3-3,3-3:14,19,0,0:3,14:NULL:232.822:366.612,131.36:0,0:0,0.000418171,0.999583 +chr1 4014539 . aaaacaaaacaaaacaaaacaaaac . . PASS END=4014563;RU=aaaac;PERIOD=5;REF=5;GRID=2,8;STUTTERUP=0.00108646;STUTTERDOWN=0.00620723;STUTTERP=0.834179;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:0.999984:5,5:5-5,5-5:17,15,0,3:5,17:2,1|3,1|4,1:234.113:366.612,131.36:0,0:0,2.31096e-05,0.999979 +chr1 4019418 . tatttatttatt . . PASS END=4019429;RU=tatt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000363537;STUTTERDOWN=0.000727074;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:52:1:3,3:3-3,3-3:29,20,0,3:3,29:2,3:324.942:366.612,131.36:0,0:0,5.3575e-09,1 +chr1 4036362 . ctggagctggagctggag . . PASS END=4036379;RU=ctggag;PERIOD=6;REF=3;GRID=1,6;STUTTERUP=0.000410436;STUTTERDOWN=0.00198167;STUTTERP=0.984306;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:40:1:3,3:3-3,3-3:24,16,0,0:3,24:NULL:241.53:366.612,131.36:0,0:0,5.28407e-07,1 +chr1 4039989 . ttgttgttgttgttg . . PASS END=4040003;RU=ttg;PERIOD=3;REF=5;GRID=2,8;STUTTERUP=0.00115365;STUTTERDOWN=0.0084842;STUTTERP=0.899993;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:32:0.999953:5,5:5-5,5-5:17,11,0,4:5,17:4,3|5,1:198.973:366.612,131.36:0,0:0,1.54565e-05,0.999986 +chr1 4042319 . cttcttcttctt . . PASS END=4042330;RU=ctt;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00110383;STUTTERDOWN=0.00110383;STUTTERP=0.976453;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:34:0.999908:4,4:4-4,4-4:17,17,0,0:4,17:NULL:225.388:366.612,131.36:0,0:0,5.97355e-05,0.999941 +chr1 4043396 . agaaaagaaaagaaa . . PASS END=4043410;RU=agaaa;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.00326879;STUTTERDOWN=0.00973918;STUTTERP=0.86134;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:17:0.986364:3,3:3-3,3-3:9,8,0,0:3,9:NULL:111.117:366.612,131.36:0,0:1.46513e-23,0.00742272,0.992595 +chr1 4043458 . gagagagagagagagagagagagagagagagagagagagagagagagagagagagagagagaga gagagagagagagagagagagagagagagagagagagagagagagaga . PASS END=4043521;RU=ga;PERIOD=2;REF=32;GRID=1,35;STUTTERUP=0.100867;STUTTERDOWN=0.210392;STUTTERP=0.711888;EXPTHRESH=32 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/0:16:0.0474443:24,32:12-34,14-34:0,8,0,8:NULL:6,1|11,1|12,1|17,1|22,1|24,2|32,1:139.366:366.612,131.36:5.90214,4.69152:1.60462e-07,0.855372,0.144712 +chr1 4048648 . gagtgagtgagt . . PASS END=4048659;RU=gagt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000270379;STUTTERDOWN=0.000772375;STUTTERP=0.761601;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:58:1:3,3:3-3,3-3:33,25,0,0:3,33:NULL:358.07:366.612,131.36:0,0:0,1.58187e-09,1 +chr1 4048769 . aattaattaattaattaattaatt . . PASS END=4048792;RU=aatt;PERIOD=4;REF=6;GRID=3,9;STUTTERUP=0.00491462;STUTTERDOWN=0.0111518;STUTTERP=0.647305;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:42:1:6,6:6-6,6-6:21,19,0,2:6,21:3,1|4,1:279.964:366.612,131.36:0,0:0,5.16892e-06,0.999995 +chr1 4049279 . aaacaaacaaacaaac . . PASS END=4049294;RU=aaac;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.00102469;STUTTERDOWN=0.00785962;STUTTERP=0.902352;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:44:1:4,4:4-4,4-4:18,19,0,7:4,18:3,7:299.67:366.612,131.36:0,0:0,8.99795e-06,0.999994 +chr1 4055341 . attattattattattattattattattattattatt . . PASS END=4055376;RU=att;PERIOD=3;REF=12;GRID=8,16;STUTTERUP=0.0402773;STUTTERDOWN=0.0504836;STUTTERP=0.638379;EXPTHRESH=12 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:0.999969:12,12:12-12,12-12:18,10,0,6:12,18:7,2|10,3|11,1:213.116:366.612,131.36:0.14072,0.14072:3.86333e-28,2.54812e-05,0.999978 +chr1 4056452 . ctctctctctctctctctctctctctctctctctctctctctctctctctctct . . PASS END=4056505;RU=ct;PERIOD=2;REF=27;GRID=23,33;STUTTERUP=0.0734002;STUTTERDOWN=0.0908386;STUTTERP=0.41233;EXPTHRESH=27 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:28:0.17784:27,27:26-30,26-30:2,15,0,8:27,2:7,1|12,1|14,1|17,3|22,1|25,1:218.029:366.612,131.36:1.68439,1.68439:0.00145928,0.39155,0.607056 +chr1 4060377 . aaacaaacaaacaaacaaac aaacaaacaaacaaacaaacaaac . PASS END=4060396;RU=aaac;PERIOD=4;REF=5;GRID=3,9;STUTTERUP=0.00153541;STUTTERDOWN=0.0369929;STUTTERP=0.942635;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:28:0.997495:6,6:6-6,6-6:12,10,0,6:6,12:4,3|5,2|6,1:184.752:366.612,131.36:0,0:0,0.000218626,0.999782 +chr1 4063131 . cacacacacacaca . . PASS END=4063144;RU=ca;PERIOD=2;REF=7;GRID=4,11;STUTTERUP=0.00825451;STUTTERDOWN=0.0158286;STUTTERP=0.956293;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:43:1.00001:7,7:7-8,7-8:20,17,0,5:7,20:5,2|6,3:266.987:366.612,131.36:0.195027,0.195027:2.77177e-42,2.99005e-06,1 +chr1 4065627 . aaaacaaaacaaaacaaaacaaaacaaaacaaaac aaaacaaaacaaaacaaaacaaaac . PASS END=4065661;RU=aaaac;PERIOD=5;REF=7;GRID=2,8;STUTTERUP=0.00272264;STUTTERDOWN=0.00551261;STUTTERP=0.479839;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:33:1.00001:5,5:5-5,5-5:21,8,0,4:5,21:3,2|4,2:183.106:366.612,131.36:0,0:1,1.37486e-06,0 +chr1 4065673 . aaacaaacaaacaaac . . PASS END=4065688;RU=aaac;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.0021097;STUTTERDOWN=0.00775762;STUTTERP=0.794654;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:34:1.00001:4,4:4-4,4-4:20,12,0,2:4,20:3,2:202.169:366.612,131.36:0,0:0,2.97336e-06,1 +chr1 4069662 . attaattaattaattaattaatta . . PASS END=4069685;RU=atta;PERIOD=4;REF=6;GRID=3,9;STUTTERUP=0.00183532;STUTTERDOWN=0.012408;STUTTERP=0.685328;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:16:0.999628:6,6:6-6,6-6:15,1,0,0:6,15:NULL:68.9845:366.612,131.36:0,0:6.72623e-44,0.000183829,0.999819 +chr1 4070485 . atatatatatatat . . PASS END=4070498;RU=at;PERIOD=2;REF=7;GRID=4,11;STUTTERUP=0.0739675;STUTTERDOWN=0.00903731;STUTTERP=0.940801;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:30:0.915977:7,7:7-8,7-8:16,14,0,0:7,13|8,3:NULL:199.227:366.612,131.36:0.398507,0.398507:8.33491e-19,0.000217094,0.999787 +chr1 4070608 . gttagttagtta . . PASS END=4070619;RU=gtta;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000424171;STUTTERDOWN=0.00204799;STUTTERP=0.984306;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:1:3,3:3-3,3-3:25,12,0,0:3,25:NULL:210.416:366.612,131.36:0,0:0,1.74971e-07,1 +chr1 4086252 . acacacacacacacacacacacacacacacacac acacacacacacacacacacacacac . PASS END=4086285;RU=ac;PERIOD=2;REF=17;GRID=9,16;STUTTERUP=0.0470122;STUTTERDOWN=0.15894;STUTTERP=0.824678;EXPTHRESH=17 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:53:0.99982:13,13:13-13,13-13:24,18,0,11:12,3|13,21:6,1|7,1|8,2|9,1|10,2|11,2|12,2:360.267:366.612,131.36:0.139319,0.139319:1,0,0 +chr1 4088150 . gtttgtttgtttgtttgttt gtttgtttgtttgtttgtttgttt . PASS END=4088169;RU=gttt;PERIOD=4;REF=5;GRID=3,9;STUTTERUP=0.00181352;STUTTERDOWN=0.0277813;STUTTERP=0.89825;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:32:0.994246:6,6:6-6,6-6:11,14,0,7:6,11:2,1|3,3|4,1|5,2:226.958:366.612,131.36:0,0:0,0.000958557,0.999044 +chr1 4090397 . cacacacacacacacacacacacacacacacacacacacacacaca cacacacacacacacacacacacacacacacacacacacacacacacacaca,cacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacaca . PASS END=4090442;RU=ca;PERIOD=2;REF=23;GRID=22,37;STUTTERUP=0.0860981;STUTTERDOWN=0.247032;STUTTERP=0.692283;EXPTHRESH=23 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:41:0.269344:26,34:26-27,26-37:6,17,0,17:26,4|27,2:6,1|7,1|9,2|10,1|12,1|13,1|14,2|15,1|17,1|18,1|19,1|25,3|34,1:335.572:366.612,131.36:0.478127,3.78591:2.61917e-41,8.59452e-08,1 +chr1 4091063 . acaacaacaacaaca . . PASS END=4091077;RU=aca;PERIOD=3;REF=5;GRID=2,8;STUTTERUP=0.00124064;STUTTERDOWN=0.0112606;STUTTERP=0.969795;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:26:0.999691:5,5:5-5,5-5:15,11,0,0:5,15:NULL:159.729:366.612,131.36:0,0:2.66247e-44,0.000197065,0.999804 +chr1 4095201 . aaggaaggaagg . . PASS END=4095212;RU=aagg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000494935;STUTTERDOWN=0.000494935;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:47:1:3,3:3-3,3-3:24,19,0,4:3,24:2,4:291.104:366.612,131.36:0,0:0,1.63943e-07,1 +chr1 4095413 . tttgtttgtttgtttg . . PASS END=4095428;RU=tttg;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.00125113;STUTTERDOWN=0.00845848;STUTTERP=0.873383;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:1:4,4:4-4,4-4:24,11,0,2:4,24:3,2:208.474:366.612,131.36:0,0:0,2.60547e-07,1 +chr1 4100799 . attttattttattttattttattttatttt attttattttattttattttatttt . PASS END=4100828;RU=atttt;PERIOD=5;REF=6;GRID=1,9;STUTTERUP=0.00485827;STUTTERDOWN=0.0138363;STUTTERP=0.712876;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:41:1:5,5:5-5,5-5:28,11,0,0:5,28:NULL:216.446:366.612,131.36:0.314035,0.314035:1,1.76026e-08,0 +chr1 4101417 . tgttgttgttgttgt . . PASS END=4101431;RU=tgt;PERIOD=3;REF=5;GRID=2,9;STUTTERUP=0.00216375;STUTTERDOWN=0.00795638;STUTTERP=0.999;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:28:0.999503:5,5:5-6,5-6:14,10,0,3:5,14:3,1|4,2:168.403:366.612,131.36:0.390807,0.390807:1.25007e-37,0.000219022,0.999782 +chr1 4107366 . tatatatatata tatatata . PASS END=4107377;RU=ta;PERIOD=2;REF=6;GRID=1,7;STUTTERUP=0.0168537;STUTTERDOWN=0.0130229;STUTTERP=0.955941;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:26:0.999018:4,4:4-4,4-4:14,12,0,0:4,14:NULL:169.247:366.612,131.36:0,0:0.999828,0.000172148,0 +chr1 4112131 . gctgctgctgct . . PASS END=4112142;RU=gct;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000390745;STUTTERDOWN=0.00111622;STUTTERP=0.941457;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:41:1:4,4:4-4,4-4:23,16,0,2:4,23:3,2:252.469:366.612,131.36:0,0:0,5.36964e-07,1 +chr1 4114636 . ctatctatctat . . PASS END=4114647;RU=ctat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000456353;STUTTERDOWN=0.00182539;STUTTERP=0.987382;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:1.00001:3,3:3-3,3-3:20,14,0,4:3,20:2,4:231.282:366.612,131.36:0,0:0,3.55721e-06,1 +chr1 4116064 . ctctctctctct ctctctctct . PASS END=4116075;RU=ct;PERIOD=2;REF=6;GRID=2,8;STUTTERUP=0.00483596;STUTTERDOWN=0.00722064;STUTTERP=0.916513;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:41:1:5,5:5-5,5-5:29,12,0,0:5,29:NULL:225.742:366.612,131.36:0,0:1,1.27345e-08,0 +chr1 4119174 . aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag . PASS END=4119245;RU=aaag;PERIOD=4;REF=18;GRID=14,21;STUTTERUP=0.0110182;STUTTERDOWN=0.085105;STUTTERP=0.58206;EXPTHRESH=18 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:11:0.0352826:14,14:14-18,14-18:0,9,0,0:NULL:NULL:85.5332:366.612,131.36:0.91647,0.91647:0.411079,0.463977,0.125045 +chr1 4121252 . tgtctgtctgtc . . PASS END=4121263;RU=tgtc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000428796;STUTTERDOWN=0.000428796;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:1.00001:3,3:3-3,3-3:21,15,0,0:3,21:NULL:215.764:366.612,131.36:0,0:0,3.36844e-06,1 +chr1 4122075 . aaataaataaat . . PASS END=4122086;RU=aaat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000815444;STUTTERDOWN=0.000815444;STUTTERP=0.976453;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:34:0.999747:3,3:3-3,3-3:15,19,0,0:3,15:NULL:238.814:366.612,131.36:0,0:0,0.000190552,0.999811 +chr1 4122666 . atctatctatct . . PASS END=4122677;RU=atct;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000510646;STUTTERDOWN=0.00102129;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:0.999583:3,3:3-3,3-3:15,18,0,2:3,15:2,2:240.054:366.612,131.36:0,0:0,0.000271211,0.999729 +chr1 4123576 . aaacaaacaaacaaacaaacaaac aaacaaacaaacaaacaaac . PASS END=4123599;RU=aaac;PERIOD=4;REF=6;GRID=2,8;STUTTERUP=0.00134467;STUTTERDOWN=0.00318417;STUTTERP=0.955472;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:42:1.00001:5,5:5-5,5-5:22,14,0,6:5,22:2,1|3,2|4,3:254.229:366.612,131.36:0,0:1,1.48473e-06,0 +chr1 4123957 . tctctctctctctc tctctctctctc . PASS END=4123970;RU=tc;PERIOD=2;REF=7;GRID=2,16;STUTTERUP=0.0503848;STUTTERDOWN=0.0265773;STUTTERP=0.894275;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:31:1.00002:6,6:6-13,6-13:20,9,0,0:6,20:NULL:164.174:366.612,131.36:3.50358,3.50358:0.999993,1.07436e-05,6.70284e-33 +chr1 4129715 . ctttctttcttt . . PASS END=4129726;RU=cttt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00052019;STUTTERDOWN=0.00148599;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:26:0.997594:3,3:3-3,3-3:12,14,0,0:3,12:NULL:170.303:366.612,131.36:0,0:2.21629e-40,0.00131315,0.998693 +chr1 4129886 . gtttgtttgtttgtttgtttgtttgttt gtttgtttgtttgtttgtttgttt . PASS END=4129913;RU=gttt;PERIOD=4;REF=7;GRID=3,9;STUTTERUP=0.00244029;STUTTERDOWN=0.0101521;STUTTERP=0.766429;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:22:0.997906:6,6:6-6,6-6:12,7,0,3:6,12:5,3:135.019:366.612,131.36:0,0:0.998541,0.00146427,3.03668e-26 +chr1 4129930 . ttgttgttgttg . . PASS END=4129941;RU=ttg;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000458787;STUTTERDOWN=0.00131059;STUTTERP=0.941457;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:0.99999:4,4:4-4,4-4:18,9,0,2:4,18:3,2:165.39:366.612,131.36:0,0:0,1.34504e-05,0.999987 +chr1 4140418 . tttgtttgtttg . . PASS END=4140429;RU=tttg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000571827;STUTTERDOWN=0.000571827;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:32:1:3,3:3-3,3-3:20,12,0,0:3,20:NULL:188.772:366.612,131.36:0,0:0,5.09731e-06,0.999995 +chr1 4140449 . tttggtttggtttgg . . PASS END=4140463;RU=tttgg;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.00053549;STUTTERDOWN=0.00258547;STUTTERP=0.841787;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:1:3,3:3-3,3-3:20,9,0,0:3,20:NULL:161.345:366.612,131.36:0,0:0,6.67801e-06,0.999994 +chr1 4142498 . cagcagcagcagcagcagcagcagcagcagcagcagcagcagcagcagcagcagcagcagcagcagcagcagcagcag cagcagcagcagcagcagcagcagcagcagcagcagcagcagcagcagcagcagcagcagcagcagcagcagcagcagcag . PASS END=4142575;RU=cag;PERIOD=3;REF=26;GRID=23,31;STUTTERUP=0.0227309;STUTTERDOWN=0.1805;STUTTERP=0.815821;EXPTHRESH=26 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:40:0.105745:27,27:26-28,26-28:0,20,0,17:NULL:6,1|8,1|14,1|15,1|16,1|17,2|18,1|19,2|20,1|21,1|22,1|23,1|25,1|27,2:318.949:366.612,131.36:0.964013,0.964013:3.46523e-16,0.372634,0.627414 +chr1 4144308 . ttgttgttgttgttgttgttgttgttg ttgttgttgttgttgttgttgttgttgttg . PASS END=4144334;RU=ttg;PERIOD=3;REF=9;GRID=5,14;STUTTERUP=0.00861617;STUTTERDOWN=0.0367425;STUTTERP=0.854453;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:30:0.999524:10,10:8-11,8-11:15,11,0,2:10,15:6,1|9,1:179.861:366.612,131.36:0.743036,0.743036:0,0.000188528,0.999812 +chr1 4144510 . ttgttttgttttgttttgtt ttgttttgttttgttttgttttgtt,ttgttttgttttgttttgttttgttttgttttgttttgtt . PASS END=4144529;RU=ttgtt;PERIOD=5;REF=4;GRID=2,11;STUTTERUP=0.0020631;STUTTERDOWN=0.00687951;STUTTERP=0.838559;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:20:1:5,8:5-5,8-8:13,7,0,0:5,7|8,6:NULL:126.229:366.612,131.36:0,0.29703:0,4.58966e-24,1 +chr1 4148898 . tttattttattttat . . PASS END=4148912;RU=tttat;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000566945;STUTTERDOWN=0.000566945;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:1:3,3:3-3,3-3:20,9,0,0:3,20:NULL:160.419:366.612,131.36:0,0:0,6.91862e-06,0.999994 +chr1 4153288 . tttgtttgtttgtttgtttg . . PASS END=4153307;RU=tttg;PERIOD=4;REF=5;GRID=2,8;STUTTERUP=0.000452883;STUTTERDOWN=0.0146621;STUTTERP=0.912854;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:26:0.789864:5,5:5-5,5-5:5,19,0,2:5,5:3,2:210.391:366.612,131.36:0.19802,0.19802:1.59991e-17,0.15992,0.840154 +chr1 4163090 . attattattatt . . PASS END=4163101;RU=att;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000903661;STUTTERDOWN=0.00129072;STUTTERP=0.959079;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:0.999898:4,4:4-4,4-4:16,17,0,3:4,16:3,3:235.259:366.612,131.36:0,0:0,4.16304e-05,0.999962 +chr1 4168643 . tttatttattta . . PASS END=4168654;RU=ttta;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000372254;STUTTERDOWN=0.00106339;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:46:1:3,3:3-3,3-3:35,11,0,0:3,35:NULL:240.263:366.612,131.36:0,0:0,1.01644e-10,1 +chr1 4173459 . atttatttatttattt . . PASS END=4173474;RU=attt;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000848211;STUTTERDOWN=0.00242303;STUTTERP=0.828472;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:40:1:4,4:4-4,4-4:21,17,0,2:4,21:3,2:258.487:366.612,131.36:0,0:0,4.15327e-06,0.999995 +chr1 4185941 . tttgtttgtttg tttgtttgtttgtttg . PASS END=4185952;RU=tttg;PERIOD=4;REF=3;GRID=1,7;STUTTERUP=0.000594202;STUTTERDOWN=0.00464922;STUTTERP=0.95893;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:19:0.984525:4,4:4-4,4-4:9,7,0,3:4,9:2,1|3,2:127.34:366.612,131.36:0,0:0,0.0021856,0.997821 +chr1 4186148 . taaataaataaa . . PASS END=4186159;RU=taaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000496975;STUTTERDOWN=0.000496975;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:22:0.96708:3,3:3-3,3-3:8,14,0,0:3,8:NULL:160.325:366.612,131.36:0,0:3.57923e-27,0.0206187,0.979424 +chr1 4195196 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtg . PASS END=4195231;RU=tg;PERIOD=2;REF=18;GRID=5,11;STUTTERUP=0.0452665;STUTTERDOWN=0.106027;STUTTERP=0.744911;EXPTHRESH=18 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:40:0.998545:8,8:8-8,8-8:13,16,0,11:8,13:4,1|5,4|6,2|7,4:285.784:366.612,131.36:0,0:1,0,0 +chr1 4196255 . tttgtttgtttg . . PASS END=4196266;RU=tttg;PERIOD=4;REF=3;GRID=1,7;STUTTERUP=0.00227911;STUTTERDOWN=0.00319736;STUTTERP=0.725994;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:54:1:3,3:2-3,2-3:29,23,0,0:3,29:NULL:332.851:366.612,131.36:0.19802,0.19802:0,1.48593e-08,1 +chr1 4199614 . aattaattaatt . . PASS END=4199625;RU=aatt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000573776;STUTTERDOWN=0.00229508;STUTTERP=0.987382;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:24:0.998573:3,3:3-3,3-3:13,11,0,0:3,13:NULL:150.683:366.612,131.36:0,0:2.36679e-42,0.000925454,0.99908 +chr1 4201150 . taaataaataaa . . PASS END=4201161;RU=taaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000438681;STUTTERDOWN=0.0017547;STUTTERP=0.987382;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:1:3,3:3-3,3-3:24,11,0,0:3,24:NULL:197.664:366.612,131.36:0,0:0,3.7601e-07,1 +chr1 4201564 . aaacaaacaaac . . PASS END=4201575;RU=aaac;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000429752;STUTTERDOWN=0.00207494;STUTTERP=0.984306;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:53:1:3,3:3-3,3-3:29,24,0,0:3,29:NULL:333.733:366.612,131.36:0,0:0,2.26288e-08,1 +chr1 4202537 . aaataaataaat . . PASS END=4202548;RU=aaat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000460793;STUTTERDOWN=0.000460793;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:0.999995:3,3:3-3,3-3:19,16,0,0:3,19:NULL:222.381:366.612,131.36:0,0:0,1.16407e-05,0.999987 +chr1 4208149 . aacaaacaaaca . . PASS END=4208160;RU=aaca;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000557608;STUTTERDOWN=0.00159288;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:24:0.999617:3,3:3-3,3-3:15,9,0,0:3,15:NULL:142.19:366.612,131.36:0,0:0,0.000186105,0.999818 +chr1 4212306 . aaacaaacaaacaaacaaacaaacaaac aaacaaacaaacaaacaaac . PASS END=4212333;RU=aaac;PERIOD=4;REF=7;GRID=2,8;STUTTERUP=0.00375097;STUTTERDOWN=0.0102727;STUTTERP=0.656556;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:41:0.999851:5,5:5-5,5-5:16,21,0,4:5,16:2,1|3,1|4,2:287.361:366.612,131.36:0,0:0.999971,3.26505e-05,6.16571e-44 +chr1 4215533 . atacatacatacatacatacatacatacatacatac atacatacatacatacatacatacatacatacatacatac . PASS END=4215568;RU=atac;PERIOD=4;REF=9;GRID=6,13;STUTTERUP=0.0128141;STUTTERDOWN=0.0365744;STUTTERP=0.831695;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:49:0.995602:10,10:9-10,9-10:11,19,0,18:10,11:2,1|3,2|4,4|5,2|6,4|7,2|8,2|9,1:355.453:366.612,131.36:0.323567,0.323567:1.31864e-37,0.00111544,0.99889 +chr1 4216566 . tgggtgggtggg . . PASS END=4216577;RU=tggg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000339948;STUTTERDOWN=0.000339948;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:57:1:3,3:3-3,3-3:35,22,0,0:3,35:NULL:332.45:366.612,131.36:0,0:0,2.70489e-10,1 +chr1 4219533 . acccacccaccc . . PASS END=4219544;RU=accc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00146466;STUTTERDOWN=0.00146466;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:17:0.935437:3,3:3-3,3-3:7,10,0,0:3,7:NULL:119.381:366.612,131.36:0,0:1.49863e-20,0.0345989,0.965464 +chr1 4222234 . tgatgatgatga . . PASS END=4222245;RU=tga;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00106909;STUTTERDOWN=0.0025809;STUTTERP=0.843423;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:27:0.999847:4,4:4-4,4-4:16,11,0,0:4,16:NULL:165.48:366.612,131.36:0,0:0,0.000104117,0.999896 +chr1 4239423 . aaacaaacaaacaaacaaac . . PASS END=4239442;RU=aaac;PERIOD=4;REF=5;GRID=2,8;STUTTERUP=0.0011724;STUTTERDOWN=0.00431108;STUTTERP=0.744;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:46:1:5,5:5-5,5-5:26,16,0,4:5,26:2,1|3,2|4,1:279.305:366.612,131.36:0,0:0,6.7303e-08,1 +chr1 4243137 . tctgtctgtctg . . PASS END=4243148;RU=tctg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000421204;STUTTERDOWN=0.000421204;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:1.00001:3,3:3-3,3-3:22,12,0,3:3,22:2,3:213.688:366.612,131.36:0,0:0,5.45651e-07,1 +chr1 4243659 . ttgttgttgttgttg . . PASS END=4243673;RU=ttg;PERIOD=3;REF=5;GRID=2,8;STUTTERUP=0.0020479;STUTTERDOWN=0.00527217;STUTTERP=0.859673;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:54:1:5,5:5-5,5-5:31,21,0,2:5,31:4,2:327.119:366.612,131.36:0,0:0,1.94798e-09,1 +chr1 4244758 . aacaacaacaac . . PASS END=4244769;RU=aac;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000775026;STUTTERDOWN=0.003742;STUTTERP=0.990181;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:50:1:4,4:4-4,4-4:31,16,0,3:4,31:3,3:293.809:366.612,131.36:0,0:0,2.75083e-09,1 +chr1 4247940 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtg . PASS END=4247969;RU=tg;PERIOD=2;REF=15;GRID=7,14;STUTTERUP=0.0435054;STUTTERDOWN=0.135367;STUTTERP=0.786163;EXPTHRESH=15 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:43:1:11,11:11-11,11-11:31,6,0,6:10,3|11,28:7,2|8,2|10,1|11,1:236.495:366.612,131.36:0,0:1,0,0 +chr1 4261751 . aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag aaagaaagaaagaaagaaagaaagaaagaaag . PASS END=4261794;RU=aaag;PERIOD=4;REF=11;GRID=5,13;STUTTERUP=0.0112396;STUTTERDOWN=0.0351751;STUTTERP=0.562066;EXPTHRESH=11 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:25:0.487749:8,8:6-10,6-10:4,20,0,0:8,4:NULL:198.192:366.612,131.36:1.16916,1.16916:0.958826,0.0412442,5.35052e-12 +chr1 4269351 . aaataaataaat . . PASS END=4269362;RU=aaat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000381551;STUTTERDOWN=0.0021799;STUTTERP=0.969616;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:49:1:3,3:3-3,3-3:26,21,0,2:3,26:2,2:320.916:366.612,131.36:0,0:0,8.01632e-08,1 +chr1 4275434 . cacacacacacacacacacacacacacacacacacacacacacacacaca cacacacacacacacacacacacacacacacacacacaca,cacacacacacacacacacacacacacacacacacacacaca . PASS END=4275483;RU=ca;PERIOD=2;REF=25;GRID=16,25;STUTTERUP=0.0779137;STUTTERDOWN=0.197762;STUTTERP=0.691292;EXPTHRESH=25 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:52:0.684601:20,21:19-22,19-22:10,18,0,23:19,3|20,3|21,4:7,1|8,3|10,1|11,3|12,1|13,2|14,1|15,2|16,2|17,1|18,1|19,4|20,1:401.399:366.612,131.36:0.840244,0.766416:0.999986,1.54866e-05,5.87923e-25 +chr1 4275539 . ataataataata . . PASS END=4275550;RU=ata;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00395296;STUTTERDOWN=0.00197648;STUTTERP=0.973121;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:0.999984:4,4:4-4,4-4:19,10,0,0:4,19:NULL:165.443:366.612,131.36:0,0:0,2.29498e-05,0.999979 +chr1 4281780 . caaacaaacaaa . . PASS END=4281791;RU=caaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000329096;STUTTERDOWN=0.000658192;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:49:1:3,3:3-3,3-3:31,18,0,0:3,31:NULL:290.686:366.612,131.36:0,0:0,3.08009e-09,1 +chr1 4285029 . gaagggaagggaagggaagggaagggaagggaagggaagggaagggaagggaagggaagggaagggaagggaagggaagggaagg . . PASS END=4285113;RU=gaagg;PERIOD=5;REF=17;GRID=1,20;STUTTERUP=0.0111677;STUTTERDOWN=0.0254699;STUTTERP=0.999;EXPTHRESH=17 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:0.0829037:17,17:5-20,5-20:0,19,0,17:NULL:4,2|5,2|6,1|7,1|10,1|12,2|14,4|15,2|17,2:296.393:366.612,131.36:3.15082,3.15082:5.1637e-16,0.546962,0.453146 +chr1 4285247 . gggaaaggggaagaaagggggaaaggggaagaaagggggaaaggggaagaaagg . . PASS END=4285300;RU=gggaaaggggaagaaagg;PERIOD=18;REF=3;GRID=1,6;STUTTERUP=0.05;STUTTERDOWN=0.05;STUTTERP=0.9;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:0.996535:3,3:3-3,3-3:16,21,0,0:3,16:NULL:264.925:366.612,131.36:0.278639,0.278639:3.66962e-18,0.00345612,0.996551 +chr1 4285317 . gaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaag gaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaaggaaag . PASS END=4285436;RU=gaaag;PERIOD=5;REF=24;GRID=1,27;STUTTERUP=0.05;STUTTERDOWN=0.05;STUTTERP=0.9;EXPTHRESH=24 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:46:0.0760872:25,25:18-26,18-26:0,20,0,26:NULL:3,1|4,3|5,1|6,2|7,2|9,2|10,2|11,1|13,1|14,2|15,1|16,1|17,1|19,1|22,1|23,3|24,1:368.821:366.612,131.36:2.10326,2.10326:4.20639e-09,0.458576,0.541533 +chr1 4287727 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . . PASS END=4287770;RU=tg;PERIOD=2;REF=22;GRID=17,26;STUTTERUP=0.0575563;STUTTERDOWN=0.312207;STUTTERP=0.70461;EXPTHRESH=22 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:40:0.704682:22,22:21-23,21-23:10,14,0,14:21,4|22,6:5,1|7,2|11,1|12,2|13,1|15,2|19,3|20,1|22,1:291.615:366.612,131.36:0.558156,0.558156:2.0267e-13,0.266838,0.733165 +chr1 4288691 . tatatatatata tatatatatatatata . PASS END=4288702;RU=ta;PERIOD=2;REF=6;GRID=5,12;STUTTERUP=0.0471256;STUTTERDOWN=0.0610014;STUTTERP=0.797625;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:9:0.697637:8,8:8-9,8-9:5,3,0,0:8,5:NULL:50.136:366.612,131.36:0.452422,0.452422:1.82103e-14,0.0505904,0.949488 +chr1 4290243 . gatagatagatagatagatagatagatagatagatagatagatagatagatagatagata gatagatagatagatagatagatagatagatagatagatagatagatagatagatagatagata . PASS END=4290302;RU=gata;PERIOD=4;REF=15;GRID=8,19;STUTTERUP=0.0238884;STUTTERDOWN=0.109105;STUTTERP=0.667283;EXPTHRESH=15 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:41:0.889527:16,16:11-16,11-16:7,18,0,14:16,7:2,1|4,1|5,2|6,1|7,2|8,1|11,3|12,1|15,2:307.69:366.612,131.36:2.34317,2.34317:7.37063e-31,0.0402759,0.959793 +chr1 4290307 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=4290346;RU=tg;PERIOD=2;REF=20;GRID=15,22;STUTTERUP=0.0396844;STUTTERDOWN=0.218338;STUTTERP=0.544459;EXPTHRESH=20 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:34:0.535683:19,19:18-19,18-19:10,17,0,7:18,3|19,7:7,1|10,1|11,1|13,1|16,1|17,1|18,1:269.431:366.612,131.36:0.498011,0.498011:0.980544,0.0194926,2.83766e-07 +chr1 4292154 . tgtgtgtgtgtgtg . . PASS END=4292167;RU=tg;PERIOD=2;REF=7;GRID=3,10;STUTTERUP=0.0105091;STUTTERDOWN=0.0351527;STUTTERP=0.951022;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:53:0.999993:7,7:7-7,7-7:28,19,0,6:6,2|7,26:4,1|5,2|6,3:336.129:366.612,131.36:0,0:0,1.02349e-05,0.999993 +chr1 4293061 . atttatttattt . . PASS END=4293072;RU=attt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000458532;STUTTERDOWN=0.00130986;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:44:1.00001:3,3:3-3,3-3:21,20,0,3:3,21:2,3:284.62:366.612,131.36:0,0:0,1.84527e-06,1 +chr1 4297521 . aaataaataaat . . PASS END=4297532;RU=aaat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000426173;STUTTERDOWN=0.00170467;STUTTERP=0.987382;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:41:1:3,3:2-3,2-3:24,14,0,2:3,24:2,2:241.549:366.612,131.36:0.21692,0.21692:0,2.96497e-07,1 +chr1 4298525 . agggagggagggagggagggagggagggagggagggaggg agggagggagggagggagggagggagggagggagggagggaggg . PASS END=4298564;RU=aggg;PERIOD=4;REF=10;GRID=7,15;STUTTERUP=0.0478842;STUTTERDOWN=0.0504013;STUTTERP=0.745527;EXPTHRESH=10 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/1:25:0.324771:10,11:10-12,10-12:2,14,0,8:10,2:2,1|6,1|7,1|8,1|9,2|11,2:195.225:366.612,131.36:0.91978,0.752475:2.09996e-18,0.00323195,0.996777 +chr1 4303708 . gtttgtttgttt . . PASS END=4303719;RU=gttt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000441768;STUTTERDOWN=0.00386331;STUTTERP=0.6489;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:26:0.99999:3,3:3-3,3-3:18,8,0,0:3,18:NULL:143.671:366.612,131.36:0,0:0,1.81234e-05,0.999985 +chr1 4304220 . cttccttccttc . . PASS END=4304231;RU=cttc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00036567;STUTTERDOWN=0.000731338;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:1.00001:3,3:3-3,3-3:21,18,0,0:3,21:NULL:244.536:366.612,131.36:0,0:0,2.37142e-06,1 +chr1 4304531 . tttgtttgtttgtttgtttgtttgtttgtttg tttgtttgtttgtttgtttgtttgtttg . PASS END=4304562;RU=tttg;PERIOD=4;REF=8;GRID=2,10;STUTTERUP=0.00320459;STUTTERDOWN=0.0203249;STUTTERP=0.869574;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:54:1.00001:7,7:5-7,5-7:22,22,0,8:7,22:3,2|4,2|5,3|6,1:353.905:366.612,131.36:0.410384,0.410384:1,1.43191e-06,1.3794e-39 +chr1 4305067 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=4305100;RU=tg;PERIOD=2;REF=17;GRID=1,32;STUTTERUP=0.038295;STUTTERDOWN=0.132195;STUTTERP=0.70501;EXPTHRESH=17 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:28:0.0445602:29,29:12-31,12-31:0,14,0,14:NULL:5,3|7,1|8,1|9,1|11,2|16,1|17,1|20,1|27,1|28,1|29,1:235.738:366.612,131.36:4.68217,4.68217:2.11204e-37,0.105213,0.894887 +chr1 4307140 . aataaaataaaataa . . PASS END=4307154;RU=aataa;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000367173;STUTTERDOWN=0.000734346;STUTTERP=0.73234;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:45:1:3,3:3-3,3-3:25,18,0,2:3,25:2,2:272.688:366.612,131.36:0,0:0,9.41783e-08,1 +chr1 4307673 . ttgttgttgttg . . PASS END=4307684;RU=ttg;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000381658;STUTTERDOWN=0.00400904;STUTTERP=0.977258;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:1:4,4:4-4,4-4:23,15,0,0:4,23:NULL:231.194:366.612,131.36:0,0:0,1.69388e-06,1 +chr1 4309252 . tttgtttgtttgtttg . . PASS END=4309267;RU=tttg;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000394118;STUTTERDOWN=0.00266449;STUTTERP=0.712868;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:1.00001:4,4:4-4,4-4:20,16,0,3:4,20:3,3:246.126:366.612,131.36:0,0:0,2.00039e-06,1 +chr1 4312047 . aataataataat aat . PASS END=4312058;RU=aat;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00100522;STUTTERDOWN=0.00242671;STUTTERP=0.843423;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:19:0.0756969:1,1:1-4,1-4:0,18,0,0:NULL:NULL:166.744:366.612,131.36:1.15812,1.15812:0.566582,0.379435,0.0541254 +chr1 4315806 . tttatttattta . . PASS END=4315817;RU=ttta;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00057169;STUTTERDOWN=0.00276025;STUTTERP=0.984306;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:1:3,3:3-3,3-3:18,13,0,0:3,18:NULL:189.952:366.612,131.36:0,0:0,1.03387e-05,0.999993 +chr1 4318869 . tttggtttggtttggtttggtttggtttggtttggtttggtttggtttggtttgg tttggtttggtttggtttggtttggtttggtttgg . PASS END=4318923;RU=tttgg;PERIOD=5;REF=11;GRID=4,10;STUTTERUP=0.00177145;STUTTERDOWN=0.0130415;STUTTERP=0.587385;EXPTHRESH=11 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:24:0.998032:7,7:7-7,7-7:13,11,0,0:7,13:NULL:155.431:366.612,131.36:0,0:1,0,0 +chr1 4328602 . gtgggtgggtgggtgg . . PASS END=4328617;RU=gtgg;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000432692;STUTTERDOWN=0.0034615;STUTTERP=0.966669;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:56:1:4,4:4-4,4-4:27,29,0,0:4,27:NULL:356.43:366.612,131.36:0,0:0,9.63734e-08,1 +chr1 4328704 . ataaataaataa . . PASS END=4328715;RU=ataa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000387123;STUTTERDOWN=0.00110587;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:50:1:3,3:3-3,3-3:36,14,0,0:3,36:NULL:264.255:366.612,131.36:0,0:0,1.35046e-10,1 +chr1 4329272 . tgttttgttttgttttgttt tgttttgttttgttttgttttgttt . PASS END=4329291;RU=tgttt;PERIOD=5;REF=4;GRID=2,8;STUTTERUP=0.000560186;STUTTERDOWN=0.00497274;STUTTERP=0.907264;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:29:0.999961:5,5:5-5,5-5:17,12,0,0:5,17:NULL:178.516:366.612,131.36:0,0:0,3.54679e-05,0.999964 +chr1 4329605 . ggaagggaagggaagggaagggaagggaagggaagggaagggaagggaagggaagggaagggaagggaagggaagggaag ggaagggaagggaagggaag . PASS END=4329684;RU=ggaag;PERIOD=5;REF=16;GRID=1,103;STUTTERUP=0.0273276;STUTTERDOWN=0.0535134;STUTTERP=0.999;EXPTHRESH=16 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:6:0.00451592:4,4:1-5,1-5:0,6,0,0:NULL:NULL:50.7807:366.612,131.36:1.38953,1.38953:0.539407,0.424989,0.0357611 +chr1 4331004 . agagagagagagag agagagagagagagagagagagagagagagagagagagagagag . PASS END=4331017;RU=ag;PERIOD=2;REF=7;GRID=19,27;STUTTERUP=0.013444;STUTTERDOWN=0.0429996;STUTTERP=0.553264;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:13:0.0229887:22,22:21-24,21-24:0,8,0,3:NULL:6,1|8,1|20,1:96.2491:366.612,131.36:1.14911,1.14911:0,0,1 +chr1 4331408 . tattattattattattat tat . PASS END=4331425;RU=tat;PERIOD=3;REF=6;GRID=1,103;STUTTERUP=0.00182447;STUTTERDOWN=0.0165597;STUTTERP=0.803829;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:8:0.0117972:1,1:1-4,1-4:0,8,0,0:NULL:NULL:78.2954:366.612,131.36:1.13848,1.13848:0.184507,0.538962,0.276614 +chr1 4365108 . tctttctttctt . . PASS END=4365119;RU=tctt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000695139;STUTTERDOWN=0.00139026;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:58:1:3,3:3-3,3-3:35,23,0,0:3,35:NULL:349.875:366.612,131.36:0,0:0,2.82414e-10,1 +chr1 4367608 . acacacacacacacacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacacacacacacac . PASS END=4367649;RU=ac;PERIOD=2;REF=21;GRID=15,28;STUTTERUP=0.0669491;STUTTERDOWN=0.261584;STUTTERP=0.680793;EXPTHRESH=21 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/1:55:0.966374:21,24:20-22,24-24:23,17,0,13:20,2|21,6|22,3|23,3|24,9:6,3|9,1|12,1|16,1|18,1|19,3|20,2|21,1:391.52:366.612,131.36:0.456091,0.0990099:4.87875e-38,1.21687e-06,1 +chr1 4368385 . caaacaaacaaacaaa . . PASS END=4368400;RU=caaa;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000447069;STUTTERDOWN=0.00357651;STUTTERP=0.893947;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:0.999479:4,4:4-4,4-4:14,19,0,2:4,14:3,2:242.427:366.612,131.36:0,0:0,0.000338708,0.999666 +chr1 4376870 . aaataaaataaaata . . PASS END=4376884;RU=aaata;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000530333;STUTTERDOWN=0.00151497;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:0.999929:3,3:3-3,3-3:17,12,0,0:3,17:NULL:177.043:366.612,131.36:0,0:0,3.89198e-05,0.999963 +chr1 4380706 . atatactatacatatactatacatatactatac atatactatac . PASS END=4380738;RU=atatactatac;PERIOD=11;REF=3;GRID=1,103;STUTTERUP=0.05;STUTTERDOWN=0.05;STUTTERP=0.9;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:27:0.685505:1,1:1-1,1-1:0,27,0,0:NULL:NULL:261.91:366.612,131.36:0,0:0.856769,0.140636,0.00268363 +chr1 4381338 . ctttctttcttt . . PASS END=4381349;RU=cttt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000400888;STUTTERDOWN=0.00320706;STUTTERP=0.966669;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:22:0.99978:3,3:3-3,3-3:15,7,0,0:3,15:NULL:122.896:366.612,131.36:0,0:0,0.000123774,0.999879 +chr1 4383095 . aaaataaaataaaataaaat aaaat . PASS END=4383114;RU=aaaat;PERIOD=5;REF=4;GRID=1,7;STUTTERUP=0.00070485;STUTTERDOWN=0.00140969;STUTTERP=0.732476;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:8:0.0611241:1,1:1-4,1-4:0,7,0,0:NULL:NULL:62.4723:366.612,131.36:1.40706,1.40706:0.350436,0.489755,0.159858 +chr1 4388234 . ttttgttttgttttgttttgttttgttttgttttg ttttgttttgttttgttttgttttg . PASS END=4388268;RU=ttttg;PERIOD=5;REF=7;GRID=1,8;STUTTERUP=0.00295429;STUTTERDOWN=0.0108811;STUTTERP=0.669225;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:37:0.999706:5,5:4-5,4-5:15,16,0,5:5,15:2,2|3,2|4,1:243.899:366.612,131.36:0.236383,0.236383:0.999948,5.32144e-05,3.01475e-41 +chr1 4389924 . aaacaaacaaac . . PASS END=4389935;RU=aaac;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000538294;STUTTERDOWN=0.000538294;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:1.00001:3,3:3-3,3-3:20,18,0,0:3,20:NULL:238.624:366.612,131.36:0,0:0,3.72101e-06,1 +chr1 4390516 . gagaagagagaagagagaaga gagaaga . PASS END=4390536;RU=gagaaga;PERIOD=7;REF=3;GRID=1,103;STUTTERUP=0.000392904;STUTTERDOWN=0.000701358;STUTTERP=0.983945;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:16:0.112712:1,1:1-2,1-2:0,16,0,0:NULL:NULL:147.878:366.612,131.36:0.491073,0.491073:0.419702,0.473992,0.106424 +chr1 4391542 . taaataaataaa . . PASS END=4391553;RU=taaa;PERIOD=4;REF=3;GRID=1,7;STUTTERUP=0.000781419;STUTTERDOWN=0.00039071;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:0.996426:3,3:3-4,3-4:12,20,0,0:3,12:NULL:236.309:366.612,131.36:0.495841,0.495841:2.13451e-37,0.00220599,0.997799 +chr1 4391556 . aacaacaacaac aacaacaacaacaac . PASS END=4391567;RU=aac;PERIOD=3;REF=4;GRID=1,8;STUTTERUP=0.00144513;STUTTERDOWN=0.0419071;STUTTERP=0.986731;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:36:0.849097:5,5:4-5,4-5:17,19,0,0:4,3|5,14:NULL:257.578:366.612,131.36:0.486863,0.486863:0,7.64905e-05,0.999925 +chr1 4394196 . tttgtttgtttgtttg tttgtttgtttgtttgtttg . PASS END=4394211;RU=tttg;PERIOD=4;REF=4;GRID=2,8;STUTTERUP=0.00062693;STUTTERDOWN=0.00902738;STUTTERP=0.83875;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:30:0.999904:5,5:5-5,5-5:16,11,0,3:5,16:3,1|4,2:192.136:366.612,131.36:0,0:0,2.63456e-05,0.999978 +chr1 4399750 . gaacagaacagaaca . . PASS END=4399764;RU=gaaca;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000398349;STUTTERDOWN=0.000796697;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:1:3,3:3-3,3-3:23,16,0,0:3,23:NULL:241.427:366.612,131.36:0,0:0,1.09336e-06,1 +chr1 4404415 . accaccaccaccacc . . PASS END=4404429;RU=acc;PERIOD=3;REF=5;GRID=2,8;STUTTERUP=0.000978977;STUTTERDOWN=0.00634581;STUTTERP=0.984589;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:43:1:5,5:5-5,5-5:22,17,0,4:5,22:3,1|4,3:280.212:366.612,131.36:0,0:0,2.68116e-07,1 +chr1 4413710 . atagatacatagatacatagatacatagatacatagatacatagatacatagatacatagatacatagatacatagatac . . PASS END=4413789;RU=atagatac;PERIOD=8;REF=10;GRID=5,13;STUTTERUP=0.00200647;STUTTERDOWN=0.00955133;STUTTERP=0.762098;EXPTHRESH=10 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:23:0.166102:10,10:5-10,5-10:2,12,0,8:10,2:2,1|4,4|6,1|7,1|8,1:170.496:366.612,131.36:1.1234,1.1234:5.66557e-06,0.721365,0.27863 +chr1 4416214 . agacagacagac . . PASS END=4416225;RU=agac;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000406938;STUTTERDOWN=0.000813875;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:1:3,3:3-3,3-3:20,13,0,2:3,20:2,2:212.042:366.612,131.36:0,0:0,4.45306e-06,0.999995 +chr1 4417332 . catgcatgcatg . . PASS END=4417343;RU=catg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000401852;STUTTERDOWN=0.000401852;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:34:1:3,3:3-3,3-3:20,14,0,0:3,20:NULL:217.251:366.612,131.36:0,0:0,7.47455e-06,0.999994 +chr1 4423050 . taatttaatttaatt . . PASS END=4423064;RU=taatt;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000649627;STUTTERDOWN=0.000649627;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:21:0.996592:3,3:3-3,3-3:11,10,0,0:3,11:NULL:135.921:366.612,131.36:0,0:4.76551e-36,0.00230319,0.997701 +chr1 4423239 . cacacacacaca cacacacacacaca . PASS END=4423250;RU=ca;PERIOD=2;REF=6;GRID=4,10;STUTTERUP=0.00845594;STUTTERDOWN=0.0222692;STUTTERP=0.930571;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:30:0.999994:7,7:7-7,7-7:19,11,0,0:7,19:NULL:174.886:366.612,131.36:0,0:0,8.04436e-06,0.999994 +chr1 4425083 . ccaccaccaccaccacca cca . PASS END=4425100;RU=cca;PERIOD=3;REF=6;GRID=1,103;STUTTERUP=0.00161387;STUTTERDOWN=0.0166199;STUTTERP=0.902457;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:27:0.108716:1,1:1-1,1-1:0,27,0,0:NULL:NULL:244.089:366.612,131.36:0.139319,0.139319:0.66748,0.30592,0.0266397 +chr1 4426093 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt,gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=4426130;RU=gt;PERIOD=2;REF=19;GRID=24,32;STUTTERUP=0.0702437;STUTTERDOWN=0.221257;STUTTERP=0.713804;EXPTHRESH=19 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:30:0.271415:27,30:27-28,27-32:3,14,0,12:27,3:7,2|8,1|9,1|10,1|14,1|16,1|17,1|23,1|26,2|29,1:245.354:366.612,131.36:0.537761,1.20589:0,0,1 +chr1 4426860 . aaacaaacaaac . . PASS END=4426871;RU=aaac;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000547319;STUTTERDOWN=0.00218925;STUTTERP=0.987382;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:32:0.999805:3,3:3-3,3-3:15,17,0,0:3,15:NULL:216.953:366.612,131.36:0,0:0,8.43516e-05,0.999918 +chr1 4429409 . ccaccaccacca . . PASS END=4429420;RU=cca;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.0018223;STUTTERDOWN=0.00150969;STUTTERP=0.948224;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:47:1:4,4:4-4,4-4:30,17,0,0:4,30:NULL:267.832:366.612,131.36:0,0:0,8.387e-09,1 +chr1 4429719 . gtgtgtgtgtgt gtgtgtgt . PASS END=4429730;RU=gt;PERIOD=2;REF=6;GRID=1,9;STUTTERUP=0.0204545;STUTTERDOWN=0.0788301;STUTTERP=0.775486;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:30:0.990269:4,4:4-6,4-6:11,18,0,0:4,11:NULL:206.913:366.612,131.36:0.863148,0.863148:0.997246,0.00275907,6.92527e-21 +chr1 4429733 . gagagagagagagagagaga gagagagagagagaga . PASS END=4429752;RU=ga;PERIOD=2;REF=10;GRID=4,11;STUTTERUP=0.0524516;STUTTERDOWN=0.104875;STUTTERP=0.774758;EXPTHRESH=10 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:24:0.979729:8,8:8-8,8-8:10,13,0,0:8,10:NULL:160.169:366.612,131.36:0.139319,0.139319:0.99593,0.00407977,1.80434e-17 +chr1 4430764 . atgaatgaatgaatgaatgaatgaatgaatga atgaatgaatgaatgaatgaatgaatgaatgaatga . PASS END=4430795;RU=atga;PERIOD=4;REF=8;GRID=6,12;STUTTERUP=0.00499317;STUTTERDOWN=0.0322486;STUTTERP=0.676232;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:40:0.999375:9,9:9-9,9-9:14,15,0,11:9,14:2,1|3,1|4,1|5,2|6,1|7,1|8,4:274.613:366.612,131.36:0,0:0,2.02402e-05,0.99998 +chr1 4434303 . tatatatatata tatatatatatatatata,tatatatatatatatatatatata . PASS END=4434314;RU=ta;PERIOD=2;REF=6;GRID=6,16;STUTTERUP=0.0686905;STUTTERDOWN=0.0760485;STUTTERP=0.748597;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:26:0.974761:9,12:9-13,12-12:12,13,0,0:9,2|12,10:NULL:177.35:366.612,131.36:1.49377,0:0,0,1 +chr1 4435269 . caatcaatcaat . . PASS END=4435280;RU=caat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000418327;STUTTERDOWN=0.000418327;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:1:3,3:3-3,3-3:23,13,0,2:3,23:2,2:228.273:366.612,131.36:0,0:0,4.80746e-07,1 +chr1 4448845 . ctgcctgcctgc . . PASS END=4448856;RU=ctgc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00041079;STUTTERDOWN=0.00041079;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:43:0.999965:3,3:3-3,3-3:17,22,0,4:3,17:2,4:297.44:366.612,131.36:0,0:0,1.88329e-05,0.999985 +chr1 4449017 . gatagatagatagatagatagatagatagatagatagatagatagatagatagata gatagatagatagatagatagatagatagatagatagatagatagatagatagatagata,gatagatagatagatagatagatagatagatagatagatagatagatagatagatagatagata . PASS END=4449072;RU=gata;PERIOD=4;REF=14;GRID=12,19;STUTTERUP=0.0133916;STUTTERDOWN=0.0687503;STUTTERP=0.643023;EXPTHRESH=14 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:51:0.914811:15,16:15-15,15-16:10,21,0,20:15,8|16,2:2,2|3,1|4,1|5,2|7,2|9,2|10,1|12,3|13,2|14,3|15,1:398.823:366.612,131.36:0,0.491073:0,4.19426e-05,0.999957 +chr1 4450115 . atatatatatat atatatatat . PASS END=4450126;RU=at;PERIOD=2;REF=6;GRID=1,10;STUTTERUP=0.0165115;STUTTERDOWN=0.00936665;STUTTERP=0.920848;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/0:21:1:5,6:4-5,5-7:11,8,0,0:5,5|6,6:NULL:122.639:366.612,131.36:0.342408,0.372309:1.28879e-08,1,4.9555e-08 +chr1 4451210 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=4451261;RU=tg;PERIOD=2;REF=26;GRID=18,31;STUTTERUP=0.0551425;STUTTERDOWN=0.246352;STUTTERP=0.455003;EXPTHRESH=26 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/0:46:0.632992:22,26:22-28,26-28:15,11,0,19:21,2|22,4|24,3|26,6:6,1|8,1|9,1|11,1|12,2|14,1|18,2|19,1|20,1|21,3|22,3|23,1|28,1:360.671:366.612,131.36:2.73257,1.06305:6.07213e-07,0.865972,0.134122 +chr1 4451385 . ttgttttgttttgtt . . PASS END=4451399;RU=ttgtt;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000399667;STUTTERDOWN=0.0022834;STUTTERP=0.969616;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:52:1:3,3:3-3,3-3:21,31,0,0:3,21:NULL:354.695:366.612,131.36:0,0:0,5.06123e-06,0.999995 +chr1 4451409 . tctgtctgtctg . . PASS END=4451420;RU=tctg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000375635;STUTTERDOWN=0.0021461;STUTTERP=0.829224;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:56:1:3,3:3-3,3-3:29,27,0,0:3,29:NULL:353.468:366.612,131.36:0,0:0,2.236e-08,1 +chr1 4453062 . ggagggagggag . . PASS END=4453073;RU=ggag;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000477581;STUTTERDOWN=0.0019103;STUTTERP=0.987382;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:0.998932:3,3:3-3,3-3:14,24,0,0:3,14:NULL:276.614:366.612,131.36:0,0:0,0.000780357,0.999225 +chr1 4454884 . cctgctgcctgctgcctgctgcctgctgcctgctgcctgctgcctgctgcctgctgcctgctgcctgctgcctgctgcctgctgcctgctgcctgctgcctgctgcctgctg cctgctgcctgctgcctgctgcctgctgcctgctgcctgctg . PASS END=4454995;RU=cctgctg;PERIOD=7;REF=16;GRID=3,19;STUTTERUP=0.05;STUTTERDOWN=0.05;STUTTERP=0.9;EXPTHRESH=16 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/0:54:0.777954:6,16:6-13,12-16:6,24,0,18:6,2|10,2|14,2:2,1|3,2|5,4|6,1|7,1|8,1|10,1|11,1|12,3|13,1|16,2:417.147:366.612,131.36:1.93807,1.59992:3.3098e-10,1,1.04847e-27 +chr1 4461472 . gaagggaagggaagggaagg gaagg . PASS END=4461491;RU=gaagg;PERIOD=5;REF=4;GRID=1,103;STUTTERUP=0.00126157;STUTTERDOWN=0.00504735;STUTTERP=0.98755;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:3:0.00377504:1,1:1-5,1-5:0,3,0,0:NULL:NULL:26.5218:366.612,131.36:0.780108,0.780108:0.0267453,0.388297,0.585074 +chr1 4462221 . tgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=4462246;RU=tg;PERIOD=2;REF=13;GRID=22,28;STUTTERUP=0.0354771;STUTTERDOWN=0.163314;STUTTERP=0.721503;EXPTHRESH=13 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:20:0.0549007:24,24:24-26,24-26:0,11,0,8:NULL:4,1|5,1|10,1|13,1|15,1|20,1|24,2:161.879:366.612,131.36:0.592738,0.592738:0,0,1 +chr1 4467043 . ataaataaataa . . PASS END=4467054;RU=ataa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00105998;STUTTERDOWN=0.000529989;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:40:0.999958:3,3:3-3,3-3:17,21,0,2:3,17:2,2:278.905:366.612,131.36:0,0:0,3.44744e-05,0.999965 +chr1 4467845 . ttgtttgtttgtttgt . . PASS END=4467860;RU=ttgt;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000604468;STUTTERDOWN=0.00345349;STUTTERP=0.749285;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:21:0.953266:4,4:4-4,4-4:7,10,0,4:4,7:3,4:149.755:366.612,131.36:0,0:5.79576e-24,0.019206,0.980836 +chr1 4468187 . atcatcatcatc . . PASS END=4468198;RU=atc;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.0012526;STUTTERDOWN=0.00389246;STUTTERP=0.99674;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:1:4,4:4-4,4-4:23,11,0,2:4,23:3,2:207.549:366.612,131.36:0,0:0,5.2263e-07,1 +chr1 4469245 . cacacacacacacacaca . . PASS END=4469262;RU=ca;PERIOD=2;REF=9;GRID=4,13;STUTTERUP=0.0232118;STUTTERDOWN=0.0484182;STUTTERP=0.896028;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:43:1:9,9:9-9,9-9:26,11,0,3:9,26:7,1|8,2:236.579:366.612,131.36:0.19802,0.19802:4.37205e-43,1.08494e-07,1 +chr1 4471019 . agccagccagcc . . PASS END=4471030;RU=agcc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000416678;STUTTERDOWN=0.000416678;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:34:1.00001:3,3:3-3,3-3:20,12,0,2:3,20:2,2:201.95:366.612,131.36:0,0:0,2.25541e-06,1 +chr1 4472443 . tgtgtgtgtgtgtg . . PASS END=4472456;RU=tg;PERIOD=2;REF=7;GRID=4,10;STUTTERUP=0.00489938;STUTTERDOWN=0.00939494;STUTTERP=0.954871;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:0.999899:7,7:7-7,7-7:17,14,0,0:7,17:NULL:202.743:366.612,131.36:0,0:5.0226e-40,6.89604e-05,0.999933 +chr1 4473588 . tttgtttgtttg . . PASS END=4473599;RU=tttg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000387078;STUTTERDOWN=0.00154829;STUTTERP=0.987382;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:46:1:3,3:3-3,3-3:30,16,0,0:3,30:NULL:267.43:366.612,131.36:0,0:0,8.19186e-09,1 +chr1 4475372 . gttggttggttg . . PASS END=4475383;RU=gttg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000867301;STUTTERDOWN=0.00123878;STUTTERP=0.820218;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:50:0.999993:3,3:3-3,3-3:19,31,0,0:3,19:NULL:352.768:366.612,131.36:0,0:0,1.81628e-05,0.999985 +chr1 4475462 . tggttggttggt . . PASS END=4475473;RU=tggt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000565398;STUTTERDOWN=0.00136494;STUTTERP=0.986219;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:45:0.999904:3,3:3-3,3-3:17,28,0,0:3,17:NULL:328.445:366.612,131.36:0,0:0,9.22666e-05,0.99991 +chr1 4476345 . ggaaggaaggaaggaaggaaggaaggaaggaaggaaggaa ggaaggaaggaaggaaggaaggaaggaaggaaggaa . PASS END=4476384;RU=ggaa;PERIOD=4;REF=10;GRID=6,12;STUTTERUP=0.00247157;STUTTERDOWN=0.0268306;STUTTERP=0.593888;EXPTHRESH=10 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:30:0.999495:9,9:9-9,9-9:14,12,0,4:9,14:3,1|8,3:203.82:366.612,131.36:0,0:0.999667,0.000333038,6.32498e-26 +chr1 4476816 . ccctccctccctccct ccctccctccct . PASS END=4476831;RU=ccct;PERIOD=4;REF=4;GRID=1,6;STUTTERUP=0.0364003;STUTTERDOWN=0.0351463;STUTTERP=0.784389;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:24:0.153545:3,3:2-4,2-4:0,21,0,3:NULL:3,3:212.852:366.612,131.36:0.46881,0.46881:0.281163,0.517279,0.201561 +chr1 4477626 . taaataaataaa . . PASS END=4477637;RU=taaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00038974;STUTTERDOWN=0.00155894;STUTTERP=0.627729;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:47:1:3,3:3-3,3-3:27,20,0,0:3,27:NULL:295.899:366.612,131.36:0,0:0,9.2065e-08,1 +chr1 4490091 . aacaacaacaacaacaacaac . . PASS END=4490111;RU=aac;PERIOD=3;REF=7;GRID=4,10;STUTTERUP=0.00236501;STUTTERDOWN=0.0243543;STUTTERP=0.854518;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:22:0.99516:7,7:7-7,7-7:11,8,0,3:7,11:3,1|4,1|6,1:138.756:366.612,131.36:0,0:4.41312e-30,0.00219522,0.997813 +chr1 4491987 . tgctgctgctgc . . PASS END=4491998;RU=tgc;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00100115;STUTTERDOWN=0.00285992;STUTTERP=0.952743;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:0.999887:4,4:4-4,4-4:17,20,0,0:4,17:NULL:250.469:366.612,131.36:0,0:0,8.49653e-05,0.999917 +chr1 4500015 . ataataataata . . PASS END=4500026;RU=ata;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00359539;STUTTERDOWN=0.00595727;STUTTERP=0.966219;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:55:1:4,4:4-4,4-4:27,28,0,0:4,27:NULL:370.374:366.612,131.36:0,0:0,1.39988e-07,1 +chr1 4500558 . acatacatacat . . PASS END=4500569;RU=acat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00327704;STUTTERDOWN=0.00295325;STUTTERP=0.909066;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:49:1:3,3:3-3,3-3:34,14,0,0:3,34:NULL:264.928:366.612,131.36:0.0990099,0.0990099:0,4.35992e-10,1 +chr1 4500614 . aataaataaata . . PASS END=4500625;RU=aata;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00085896;STUTTERDOWN=0.00085896;STUTTERP=0.976453;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:0.999964:3,3:3-3,3-3:18,11,0,0:3,18:NULL:177.338:366.612,131.36:0,0:0,3.26547e-05,0.999971 +chr1 4501653 . gtagtagtagtagta . . PASS END=4501667;RU=gta;PERIOD=3;REF=5;GRID=2,8;STUTTERUP=0.00243425;STUTTERDOWN=0.00895105;STUTTERP=0.999;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:32:1.00001:5,5:5-5,5-5:21,11,0,0:5,21:NULL:187.389:366.612,131.36:0,0:0,3.62527e-06,1 +chr1 4509810 . tgtgtgtgtgtg . . PASS END=4509821;RU=tg;PERIOD=2;REF=6;GRID=3,10;STUTTERUP=0.0154309;STUTTERDOWN=0.0315642;STUTTERP=0.448552;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:63:1.00001:6,6:6-8,6-8:42,19,0,2:6,42:5,1|7,1:373.597:366.612,131.36:0.598989,0.598989:0,1.67446e-12,1 +chr1 4510185 . tatttatttatt . . PASS END=4510196;RU=tatt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000457886;STUTTERDOWN=0.000457886;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:1.00001:3,3:3-3,3-3:22,13,0,2:3,22:2,2:221.005:366.612,131.36:0,0:0,6.7528e-07,1 +chr1 4510496 . gaagaagaagaagaagaa gaagaagaagaagaagaagaagaagaagaagaagaagaagaa . PASS END=4510513;RU=gaa;PERIOD=3;REF=6;GRID=13,19;STUTTERUP=0.00433222;STUTTERDOWN=0.0448472;STUTTERP=0.714643;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:14:0.0382175:14,14:13-17,13-17:0,8,0,5:NULL:8,1|10,1|11,1|14,2:113.132:366.612,131.36:1.00025,1.00025:0,0,1 +chr1 4510513 . aggaggaggaggaggaggaggaggaggagg aggaggaggaggaggaggaggaggaggaggaggagg . PASS END=4510542;RU=agg;PERIOD=3;REF=10;GRID=12,18;STUTTERUP=0.00153084;STUTTERDOWN=0.0246244;STUTTERP=0.64893;EXPTHRESH=10 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:14:0.0515067:12,12:12-15,12-15:0,6,0,7:NULL:4,2|7,2|10,1|11,1|12,1:110.798:366.612,131.36:1.40594,1.40594:0,0,1 +chr1 4512324 . aacaaaacaaaacaa . . PASS END=4512338;RU=aacaa;PERIOD=5;REF=3;GRID=1,7;STUTTERUP=0.000528879;STUTTERDOWN=0.00255354;STUTTERP=0.984306;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:0.998922:3,3:3-4,3-4:14,18,0,3:3,14:2,3:242.475:366.612,131.36:0.452422,0.452422:1.4013e-45,0.000483448,0.999521 +chr1 4514924 . ttggttggttgg . . PASS END=4514935;RU=ttgg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000774532;STUTTERDOWN=0.000387267;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:41:0.999946:3,3:3-3,3-3:16,21,0,4:3,16:2,3|3,1:284.082:366.612,131.36:0,0:0,1.97494e-05,0.99998 +chr1 4515460 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg,tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=4515507;RU=tg;PERIOD=2;REF=24;GRID=21,30;STUTTERUP=0.0804829;STUTTERDOWN=0.269776;STUTTERP=0.625426;EXPTHRESH=24 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:37:0.684135:26,27:25-26,24-27:10,15,0,11:25,2|26,6|27,2:6,1|7,1|8,1|11,1|14,2|16,2|18,1|21,2:281.402:366.612,131.36:0.363246,0.786989:1.3169e-16,0.00404163,0.995968 +chr1 4515925 . gtttgtttgtttgtttgtttgtttgtttgtttgttt gtttgtttgtttgtttgtttgtttgttt . PASS END=4515960;RU=gttt;PERIOD=4;REF=9;GRID=2,10;STUTTERUP=0.00181448;STUTTERDOWN=0.0194892;STUTTERP=0.617196;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:47:1.00001:7,7:5-7,5-7:20,18,0,8:7,20:2,1|4,1|6,6:306.672:366.612,131.36:0.339533,0.339533:1,2.28116e-06,0 +chr1 4517194 . aataaataaataaataaataaataaataaataaataaataaataaata aataaataaataaataaataaataaataaataaataaataaata . PASS END=4517241;RU=aata;PERIOD=4;REF=12;GRID=8,14;STUTTERUP=0.00908953;STUTTERDOWN=0.0358452;STUTTERP=0.6063;EXPTHRESH=12 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:33:0.99183:11,11:11-11,11-11:11,12,0,10:11,11:3,2|4,1|5,1|6,2|7,2|8,2:228.232:366.612,131.36:0,0:0.997852,0.00215301,3.01162e-19 +chr1 4517464 . gtgtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=4517491;RU=gt;PERIOD=2;REF=14;GRID=15,26;STUTTERUP=0.0484085;STUTTERDOWN=0.197359;STUTTERP=0.77133;EXPTHRESH=14 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:43:0.989754:19,19:19-23,19-23:15,14,0,13:18,2|19,13:5,1|6,1|8,1|10,3|12,1|13,2|15,3|16,1:305.876:366.612,131.36:1.53858,1.53858:0,0,1 +chr1 4519236 . ttttgttttgttttg . . PASS END=4519250;RU=ttttg;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000453987;STUTTERDOWN=0.00219195;STUTTERP=0.984306;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:41:0.999986:3,3:3-3,3-3:18,23,0,0:3,18:NULL:280.201:366.612,131.36:0,0:0,2.30958e-05,0.999979 +chr1 4522379 . tttgtttgtttg . . PASS END=4522390;RU=tttg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000548002;STUTTERDOWN=0.000548002;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:14:0.447837:3,3:1-3,1-3:3,11,0,0:3,3:NULL:106.851:366.612,131.36:0.339533,0.339533:1.14479e-10,0.29444,0.705567 +chr1 4527121 . tatatatatatatatata . . PASS END=4527138;RU=ta;PERIOD=2;REF=9;GRID=6,12;STUTTERUP=0.0415341;STUTTERDOWN=0.110609;STUTTERP=0.819609;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:2:0.236118:9,9:9-9,9-9:2,0,0,0:9,2:NULL:8.24721:366.612,131.36:0,0:0.000905115,0.37211,0.627037 +chr1 4527198 . atatatatatatatatatat at . PASS END=4527217;RU=at;PERIOD=2;REF=10;GRID=1,103;STUTTERUP=0.0521401;STUTTERDOWN=0.114174;STUTTERP=0.622257;EXPTHRESH=10 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP .:.:.:.:.:.:.:.:.:.:.:. +chr1 4528748 . cacacacacacacacacacacacacacacacacacacacacacacaca cacacacacacacacacacacacacacacaca . PASS END=4528795;RU=ca;PERIOD=2;REF=24;GRID=8,19;STUTTERUP=0.0605029;STUTTERDOWN=0.194984;STUTTERP=0.691169;EXPTHRESH=24 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:55:0.99964:16,16:11-16,11-16:17,20,0,17:16,17:5,1|7,2|8,3|9,1|10,2|11,2|12,3|14,1|15,2:388.295:366.612,131.36:0.848833,0.848833:1,0,0 +chr1 4529762 . gggtgggtgggt . . PASS END=4529773;RU=gggt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00206071;STUTTERDOWN=0.00102701;STUTTERP=0.730665;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:11:0.870944:3,3:3-3,3-3:6,5,0,0:3,6:NULL:67.1805:366.612,131.36:0,0:2.05362e-17,0.0642545,0.935837 +chr1 4530947 . gagggagggagggagggagggagggagggagggagggagggagggagggagggagggagggagggagggagggagggagggagg gagg . PASS END=4531030;RU=gagg;PERIOD=4;REF=21;GRID=1,103;STUTTERUP=0.05;STUTTERDOWN=0.05;STUTTERP=0.9;EXPTHRESH=21 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP .:.:.:.:.:.:.:.:.:.:.:. +chr1 4533708 . aaacaaacaaac aaac . PASS END=4533719;RU=aaac;PERIOD=4;REF=3;GRID=1,103;STUTTERUP=0.00100243;STUTTERDOWN=0.00200485;STUTTERP=0.73234;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP .:.:.:.:.:.:.:.:.:.:.:. +chr1 4536587 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=4536616;RU=tg;PERIOD=2;REF=15;GRID=20,32;STUTTERUP=0.0449451;STUTTERDOWN=0.179777;STUTTERP=0.743408;EXPTHRESH=15 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:28:0.479008:25,25:23-29,23-29:7,5,0,14:24,2|25,5:6,2|7,3|8,2|10,1|13,1|14,1|19,2|22,1|23,1:190.956:366.612,131.36:2.46314,2.46314:0,0,1 +chr1 4537486 . cccacccaccca . . PASS END=4537497;RU=ccca;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000343366;STUTTERDOWN=0.000343366;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:42:1:3,3:3-3,3-3:30,12,0,0:3,30:NULL:228.608:366.612,131.36:0,0:0,5.14401e-09,1 +chr1 4539497 . aaaacaaaacaaaacaaaac aaaacaaaacaaaacaaaacaaaac . PASS END=4539516;RU=aaaac;PERIOD=5;REF=4;GRID=1,8;STUTTERUP=0.00061026;STUTTERDOWN=0.0141385;STUTTERP=0.979763;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:38:0.999962:5,5:4-5,4-5:18,17,0,2:5,18:2,1|3,1:242.545:366.612,131.36:0.195027,0.195027:0,3.80167e-05,0.999964 +chr1 4540447 . tttattttattttat . . PASS END=4540461;RU=tttat;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000433416;STUTTERDOWN=0.000866831;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:1.00001:3,3:3-3,3-3:21,14,0,0:3,21:NULL:211.578:366.612,131.36:0,0:0,3.02473e-06,1 +chr1 4542382 . aagaaagaaaga . . PASS END=4542393;RU=aaga;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000438164;STUTTERDOWN=0.000876327;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:28:1.00001:3,3:3-3,3-3:22,6,0,0:3,22:NULL:142.975:366.612,131.36:0,0:0,1.05021e-06,1 +chr1 4543194 . ttattattatta . . PASS END=4543205;RU=tta;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.0025152;STUTTERDOWN=0.00425114;STUTTERP=0.883078;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:0.999995:4,4:4-4,4-4:20,13,0,0:4,20:NULL:200.318:366.612,131.36:0,0:0,1.19973e-05,0.999987 +chr1 4544564 . tgtttgtttgtttgtttgtttgtttgtt tgtttgtttgtttgtttgtttgtt . PASS END=4544591;RU=tgtt;PERIOD=4;REF=7;GRID=3,9;STUTTERUP=0.000737087;STUTTERDOWN=0.00816251;STUTTERP=0.615182;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:34:0.99878:6,6:6-6,6-6:13,19,0,2:6,13:3,1|4,1:244.016:366.612,131.36:0,0:0.999628,0.000375309,2.56771e-31 +chr1 4545765 . acacacacacac acacacacacacacac . PASS END=4545776;RU=ac;PERIOD=2;REF=6;GRID=5,11;STUTTERUP=0.0078277;STUTTERDOWN=0.0501471;STUTTERP=0.833825;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:53:1.00001:8,8:8-8,8-8:20,26,0,7:8,20:5,1|6,2|7,4:381.986:366.612,131.36:0,0:0,7.87563e-08,1 +chr1 4547787 . aggaggaggagg . . PASS END=4547798;RU=agg;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000749125;STUTTERDOWN=0.00299647;STUTTERP=0.993276;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:46:1:4,4:4-4,4-4:28,18,0,0:4,28:NULL:285.577:366.612,131.36:0,0:0,7.32086e-08,1 +chr1 4556934 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt gt . PASS END=4556979;RU=gt;PERIOD=2;REF=23;GRID=1,103;STUTTERUP=0.0891309;STUTTERDOWN=0.204859;STUTTERP=0.681573;EXPTHRESH=23 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP .:.:.:.:.:.:.:.:.:.:.:. +chr1 4566916 . gggtgggtgggt . . PASS END=4566927;RU=gggt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00227106;STUTTERDOWN=0.00454205;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:13:0.567369:3,3:2-3,2-3:4,8,0,0:3,4:NULL:85.089:366.612,131.36:0.48221,0.48221:3.09765e-11,0.190045,0.810013 +chr1 4567644 . gtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=4567655;RU=gt;PERIOD=2;REF=6;GRID=1,25;STUTTERUP=0.00435045;STUTTERDOWN=0.0132529;STUTTERP=0.97317;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:12:0.0338735:22,22:19-22,19-22:0,0,0,12:NULL:4,1|6,2|7,1|9,1|14,1|16,1|18,1|19,3|22,1:95.6448:366.612,131.36:1.4827,1.4827:0,0.000460747,0.999544 +chr1 4569841 . ttgtttgtttgt ttgtttgtttgtttgt . PASS END=4569852;RU=ttgt;PERIOD=4;REF=3;GRID=1,7;STUTTERUP=0.000440377;STUTTERDOWN=0.00392306;STUTTERP=0.907196;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:42:1.00001:4,4:4-4,4-4:22,17,0,3:4,22:3,3:260.7:366.612,131.36:0,0:0,3.04953e-07,1 +chr1 4571456 . aaacaaacaaac . . PASS END=4571467;RU=aaac;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000499648;STUTTERDOWN=0.00199857;STUTTERP=0.987382;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:0.999049:3,3:2-3,2-3:13,20,0,2:3,13:2,2:245.581:366.612,131.36:0.469019,0.469019:5.38099e-43,0.000642941,0.999362 +chr1 4578817 . attgcattgcattgc . . PASS END=4578831;RU=attgc;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000409264;STUTTERDOWN=0.00163704;STUTTERP=0.987382;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:1:3,3:3-3,3-3:22,16,0,0:3,22:NULL:233.183:366.612,131.36:0,0:0,1.90477e-06,1 +chr1 4579277 . acacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacac,acacacacacacacacacacacacacacacacacacac . PASS END=4579306;RU=ac;PERIOD=2;REF=15;GRID=15,22;STUTTERUP=0.0488709;STUTTERDOWN=0.158219;STUTTERP=0.81578;EXPTHRESH=15 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:43:0.939866:18,19:18-19,19-19:9,17,0,17:18,4|19,5:4,1|7,1|8,2|9,3|11,1|12,1|13,3|14,3|15,1|18,1:339.652:366.612,131.36:0.442564,0.139319:0,0,1 +chr1 4580702 . atttatttattt attt . PASS END=4580713;RU=attt;PERIOD=4;REF=3;GRID=1,103;STUTTERUP=0.0018222;STUTTERDOWN=0.00260269;STUTTERP=0.959079;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:24:0.125985:1,1:1-2,1-2:0,24,0,0:NULL:NULL:234.882:366.612,131.36:0.499779,0.499779:0.445043,0.463997,0.0911081 +chr1 4581133 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg,tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=4581176;RU=tg;PERIOD=2;REF=22;GRID=20,40;STUTTERUP=0.0559922;STUTTERDOWN=0.231489;STUTTERP=0.699556;EXPTHRESH=22 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:34:0.297711:29,38:28-29,23-39:7,14,0,12:28,3|29,4:4,1|7,1|9,1|16,1|18,3|19,2|23,1|29,1|37,1:263.144:366.612,131.36:0.695188,6.28375:0,6.17484e-08,1 +chr1 4581630 . aattaattaatt . . PASS END=4581641;RU=aatt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00113325;STUTTERDOWN=0.00158681;STUTTERP=0.990318;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:34:1:3,3:3-3,3-3:24,10,0,0:3,24:NULL:187.918:366.612,131.36:0,0:0,3.38291e-07,1 +chr1 4599798 . tttgttttgttttgt . . PASS END=4599812;RU=tttgt;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.00043091;STUTTERDOWN=0.00086182;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:55:0.999999:3,3:3-3,3-3:20,35,0,0:3,20:NULL:397.608:366.612,131.36:0,0:0,1.02541e-05,0.999993 +chr1 4602828 . ctctctctctctctctctctctctctctctctctctctctctctctctctctctctct ctctctctctctctctctctctctctctctctctctctctctctctct,ctctctctctctctctctctctctctctctctctctctctctctctctctctctct . PASS END=4602885;RU=ct;PERIOD=2;REF=29;GRID=1,31;STUTTERUP=0.0668188;STUTTERDOWN=0.275563;STUTTERP=0.678137;EXPTHRESH=29 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:22:0.0249419:24,28:7-29,13-29:0,14,0,8:NULL:9,1|11,2|13,2|16,1|24,1|28,1:190.043:366.612,131.36:6.72884,4.25337:0.29436,0.659006,0.0467059 +chr1 4603083 . cctcccctcccctcc . . PASS END=4603097;RU=cctcc;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000573241;STUTTERDOWN=0.00114648;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:23:0.99967:3,3:3-3,3-3:15,8,0,0:3,15:NULL:131.501:366.612,131.36:0,0:0,0.000205378,0.999796 +chr1 4608057 . gggtgggtgggt . . PASS END=4608068;RU=gggt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00116739;STUTTERDOWN=0.00116739;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:23:0.880045:3,3:3-3,3-3:6,17,0,0:3,6:NULL:173.037:366.612,131.36:0,0:1.75633e-18,0.0713738,0.92872 +chr1 4612833 . tatttatttatt . . PASS END=4612844;RU=tatt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000496323;STUTTERDOWN=0.000496323;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:34:0.999731:3,3:3-3,3-3:15,19,0,0:3,15:NULL:237.486:366.612,131.36:0,0:0,0.000187178,0.999812 +chr1 4613348 . aaataaataaataaat . . PASS END=4613363;RU=aaat;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000979241;STUTTERDOWN=0.00434637;STUTTERP=0.790188;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:46:1:4,4:4-4,4-4:25,18,0,3:4,25:2,1|3,2:288.879:366.612,131.36:0,0:0,1.33209e-07,1 +chr1 4618031 . ctctctctctct . . PASS END=4618042;RU=ct;PERIOD=2;REF=6;GRID=2,9;STUTTERUP=0.00458527;STUTTERDOWN=0.0226354;STUTTERP=0.840938;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:0.999981:6,6:6-6,6-6:18,18,0,2:6,18:5,2:248.094:366.612,131.36:0.139319,0.139319:7.70714e-44,1.47598e-05,0.999987 +chr1 4618737 . gtttgtttgtttgttt . . PASS END=4618752;RU=gttt;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000493438;STUTTERDOWN=0.00333596;STUTTERP=0.958596;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:0.999742:4,4:4-4,4-4:16,11,0,2:4,16:2,1|3,1:178.008:366.612,131.36:0,0:0,0.000134948,0.999865 +chr1 4619846 . accaccaccacc . . PASS END=4619857;RU=acc;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00057382;STUTTERDOWN=0.00277053;STUTTERP=0.984306;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:32:0.999951:4,4:4-4,4-4:17,13,0,2:4,17:3,2:207.956:366.612,131.36:0,0:0,2.92333e-05,0.999971 +chr1 4619861 . tccatccatccatccatccatccatccatccatccatccatcca . . PASS END=4619904;RU=tcca;PERIOD=4;REF=11;GRID=8,14;STUTTERUP=0.0169262;STUTTERDOWN=0.0283993;STUTTERP=0.460539;EXPTHRESH=11 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:0.999879:11,11:11-11,11-11:17,12,0,0:11,17:NULL:190.814:366.612,131.36:0,0:8.87201e-36,8.94935e-05,0.999911 +chr1 4620573 . acacacacacacacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacacacacac . PASS END=4620612;RU=ac;PERIOD=2;REF=20;GRID=18,26;STUTTERUP=0.0775168;STUTTERDOWN=0.221306;STUTTERP=0.713884;EXPTHRESH=20 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:44:0.98897:22,22:22-23,22-23:11,14,0,17:22,11:9,1|10,2|11,1|12,2|13,1|14,1|15,1|16,4|21,4:323.128:366.612,131.36:0.253975,0.253975:0,0.00022719,0.999774 +chr1 4621359 . ttttttcttttttcttttttc . . PASS END=4621379;RU=ttttttc;PERIOD=7;REF=3;GRID=1,6;STUTTERUP=0.000561209;STUTTERDOWN=0.00160317;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:30:0.998551:3,3:3-3,3-3:12,16,0,2:3,12:2,2:211.688:366.612,131.36:0,0:2.06014e-39,0.000943101,0.999059 +chr1 4624755 . aggcagaggcagaggcagaggcag . . PASS END=4624778;RU=aggcag;PERIOD=6;REF=4;GRID=1,7;STUTTERUP=0.000599172;STUTTERDOWN=0.00289293;STUTTERP=0.984306;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:27:0.99884:4,4:4-4,4-4:13,12,0,2:4,13:3,2:181.288:366.612,131.36:0,0:3.82835e-42,0.000638048,0.999363 +chr1 4625336 . gagagagagagagagagagagagagagagagagagagagagagagagaga gagagagagagagagagagagagagagagagagagagagagagagagagagagagaga,gagagagagagagagagagagagagagagagagagagagagagagagagagagagagaga . PASS END=4625385;RU=ga;PERIOD=2;REF=25;GRID=7,33;STUTTERUP=0.0466179;STUTTERDOWN=0.327559;STUTTERP=0.708915;EXPTHRESH=25 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:16:0.30768:29,30:10-30,10-31:3,9,0,3:29,3:13,1|23,1|30,1:126.424:366.612,131.36:8.90044,9.91346:4.7859e-17,0.126138,0.873959 +chr1 4626527 . tttgtttgtttg . . PASS END=4626538;RU=tttg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000499898;STUTTERDOWN=0.00241362;STUTTERP=0.984306;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:0.999129:3,3:3-3,3-3:13,14,0,2:3,13:2,2:191.306:366.612,131.36:0,0:1.38729e-43,0.000304124,0.999697 +chr1 4626573 . ttttgttttgttttgttttg . . PASS END=4626592;RU=ttttg;PERIOD=5;REF=4;GRID=1,7;STUTTERUP=0.00131449;STUTTERDOWN=0.00262897;STUTTERP=0.920482;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:34:1.00001:4,4:4-4,4-4:21,11,0,2:4,21:3,2:196.993:366.612,131.36:0,0:0,1.43994e-06,1 +chr1 4626799 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=4626850;RU=gt;PERIOD=2;REF=26;GRID=22,29;STUTTERUP=0.0780904;STUTTERDOWN=0.284006;STUTTERP=0.573918;EXPTHRESH=26 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/0:43:0.702903:25,26:25-26,23-26:5,23,0,15:25,3|26,2:5,1|6,1|7,1|8,1|9,1|13,1|15,2|17,1|18,2|21,1|22,2|25,1:367.648:366.612,131.36:0.569802,0.727436:0.0451303,0.841871,0.113169 +chr1 4629230 . agagagagagagag . . PASS END=4629243;RU=ag;PERIOD=2;REF=7;GRID=4,10;STUTTERUP=0.0141258;STUTTERDOWN=0.0265234;STUTTERP=0.91491;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:67:1:7,7:7-7,7-7:29,34,0,4:7,29:4,1|5,1|6,2:454.035:366.612,131.36:0,0:0,5.7408e-09,1 +chr1 4629974 . agagagagagagagagagagagagagagagagagagagagagagagagag agagagagagagagagagagagagagagagagagagagagagagag . PASS END=4630023;RU=ag;PERIOD=2;REF=25;GRID=19,28;STUTTERUP=0.0778885;STUTTERDOWN=0.245815;STUTTERP=0.689371;EXPTHRESH=25 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:31:0.870331:23,23:23-25,23-25:10,16,0,3:22,2|23,8:14,1|16,1|19,1:227.158:366.612,131.36:0.767183,0.767183:0.995297,0.00471319,2.52889e-12 +chr1 4631170 . aaggacaaaggacaaaggaca . . PASS END=4631190;RU=aaggaca;PERIOD=7;REF=3;GRID=1,6;STUTTERUP=0.000524753;STUTTERDOWN=0.00253362;STUTTERP=0.841787;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:1:3,3:3-3,3-3:20,14,0,2:3,20:2,2:221.92:366.612,131.36:0,0:0,4.45143e-06,0.999995 +chr1 4637541 . aagagaagagaagagaagagaagagaagagaagagaagagaagagaagagaagagaagagaagagaagagaagagaagag aagagaagagaagagaagagaagagaagagaagagaagagaagagaagagaagagaagagaagagaagagaagag . PASS END=4637620;RU=aagag;PERIOD=5;REF=16;GRID=12,19;STUTTERUP=0.00502339;STUTTERDOWN=0.0302649;STUTTERP=0.544052;EXPTHRESH=16 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/0:57:0.997026:15,16:15-16,15-16:5,29,0,23:15,2|16,3:2,1|3,3|4,1|5,2|6,2|7,3|8,3|9,1|13,1|14,3|15,3:458.031:366.612,131.36:0.298675,0.21692:5.33947e-07,0.997066,0.00294373 +chr1 4637824 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=4637855;RU=tg;PERIOD=2;REF=16;GRID=16,23;STUTTERUP=0.0474924;STUTTERDOWN=0.197873;STUTTERP=0.787747;EXPTHRESH=16 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:33:0.995618:20,20:20-20,20-20:13,8,0,11:20,13:5,1|6,2|7,1|8,1|10,1|14,2|16,1|18,1|19,1:218.423:366.612,131.36:0,0:0,0,1 +chr1 4639717 . atttatttatttattt . . PASS END=4639732;RU=attt;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.00188339;STUTTERDOWN=0.00871876;STUTTERP=0.840356;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:47:1:4,4:4-4,4-4:29,12,0,6:4,29:3,6:267.88:366.612,131.36:0,0:0,5.25643e-09,1 +chr1 4642589 . ctttctttcttt . . PASS END=4642600;RU=cttt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000463934;STUTTERDOWN=0.00132529;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:43:1:3,3:3-3,3-3:24,17,0,2:3,24:2,2:268.451:366.612,131.36:0,0:0,1.27997e-07,1 +chr1 4643335 . aaggaaggaagg . . PASS END=4643346;RU=aagg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000734341;STUTTERDOWN=0.00177278;STUTTERP=0.986219;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:42:1:3,3:3-3,3-3:30,8,0,4:3,30:2,4:221.947:366.612,131.36:0,0:0,1.92521e-09,1 +chr1 4648909 . ttgttttgttttgtt . . PASS END=4648923;RU=ttgtt;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000606214;STUTTERDOWN=0.000606214;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:23:0.459673:3,3:1-3,1-3:3,19,0,0:3,3:NULL:180.672:366.612,131.36:0.508722,0.508722:2.71995e-10,0.425296,0.574792 +chr1 4653049 . tttctttctttc . . PASS END=4653060;RU=tttc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000533676;STUTTERDOWN=0.00257671;STUTTERP=0.984306;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:30:1.00001:3,3:3-3,3-3:21,9,0,0:3,21:NULL:166.14:366.612,131.36:0,0:0,1.51626e-06,1 +chr1 4653751 . aaaacaaaaacaaaaaca . . PASS END=4653768;RU=aaaaca;PERIOD=6;REF=3;GRID=1,6;STUTTERUP=0.000464901;STUTTERDOWN=0.00314303;STUTTERP=0.833561;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:43:0.999993:3,3:1-3,1-3:21,21,0,0:3,21:NULL:274.047:366.612,131.36:0.863148,0.863148:0,1.14986e-05,0.999988 +chr1 4654599 . gttggttggttg gttggttggttggttg . PASS END=4654610;RU=gttg;PERIOD=4;REF=3;GRID=1,7;STUTTERUP=0.00093353;STUTTERDOWN=0.00690438;STUTTERP=0.959935;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:34:0.999927:4,4:3-4,3-4:17,16,0,0:4,17:NULL:216.93:366.612,131.36:0.270063,0.270063:0,3.87117e-05,0.999963 +chr1 4655498 . tgtgtgtgtgtg tgtgtgtgtg . PASS END=4655509;RU=tg;PERIOD=2;REF=6;GRID=1,8;STUTTERUP=0.00743744;STUTTERDOWN=0.00223945;STUTTERP=0.962796;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:42:0.999717:5,5:4-5,4-5:16,25,0,0:5,16:NULL:286.158:366.612,131.36:0.334882,0.334882:0.999949,5.08902e-05,1.00893e-43 +chr1 4661585 . acaacaacaaca . . PASS END=4661596;RU=aca;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000927471;STUTTERDOWN=0.000463736;STUTTERP=0.999;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:1.00001:4,4:4-4,4-4:21,13,0,2:4,21:3,2:219.982:366.612,131.36:0,0:0,3.05948e-06,1 +chr1 4661836 . gtgggtgggtgg . . PASS END=4661847;RU=gtgg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00050805;STUTTERDOWN=0.0010161;STUTTERP=0.597956;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:0.999839:3,3:3-3,3-3:16,13,0,0:3,16:NULL:182.229:366.612,131.36:0,0:0,9.61132e-05,0.999904 +chr1 4663912 . aataaataaataaataaataaataaataaata aataaataaataaataaataaata . PASS END=4663943;RU=aata;PERIOD=4;REF=8;GRID=3,9;STUTTERUP=0.00083796;STUTTERDOWN=0.0123239;STUTTERP=0.740223;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:26:0.997908:6,6:6-6,6-6:13,13,0,0:6,13:NULL:175.356:366.612,131.36:0,0:0.999734,0.000269517,6.86485e-36 +chr1 4664837 . gtttgtttgtttgttt . . PASS END=4664852;RU=gttt;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.00210099;STUTTERDOWN=0.00406776;STUTTERP=0.946048;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:1.00001:4,4:4-4,4-4:21,15,0,2:4,21:2,1|3,1:230.746:366.612,131.36:0,0:0,1.93539e-06,1 +chr1 4666307 . aaacaaacaaacaaacaaac . . PASS END=4666326;RU=aaac;PERIOD=4;REF=5;GRID=2,8;STUTTERUP=0.000424517;STUTTERDOWN=0.0110069;STUTTERP=0.84585;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:44:0.999992:5,5:5-5,5-5:18,21,0,5:5,18:3,1|4,4:300.251:366.612,131.36:0,0:0,1.29769e-05,0.999987 +chr1 4666832 . taaataaataaa . . PASS END=4666843;RU=taaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000449302;STUTTERDOWN=0.00359426;STUTTERP=0.966657;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:1.00001:3,3:3-3,3-3:20,16,0,3:3,20:2,3:241.532:366.612,131.36:0,0:0,2.62971e-06,1 +chr1 4675038 . aaaacaaaacaaaac . . PASS END=4675052;RU=aaaac;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000324747;STUTTERDOWN=0.00156795;STUTTERP=0.984306;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:64:1:3,3:3-3,3-3:38,26,0,0:3,38:NULL:382.892:366.612,131.36:0,0:0,3.33165e-11,1 +chr1 4675154 . ataaataaataa . . PASS END=4675165;RU=ataa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000665905;STUTTERDOWN=0.0013318;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:47:1:3,3:3-3,3-3:19,26,0,2:3,19:2,2:322.023:366.612,131.36:0,0:0,8.43525e-06,0.999994 +chr1 4678790 . agtgagtgagtg . . PASS END=4678801;RU=agtg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000536169;STUTTERDOWN=0.000536169;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:21:0.99837:3,3:3-3,3-3:13,8,0,0:3,13:NULL:127.939:366.612,131.36:0,0:8.82818e-43,0.000853769,0.99915 +chr1 4678965 . acagacagacag . . PASS END=4678976;RU=acag;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000668603;STUTTERDOWN=0.0013372;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:15:0.558221:3,3:2-3,2-3:4,11,0,0:3,4:NULL:114.069:366.612,131.36:0.169767,0.169767:6.68288e-13,0.253675,0.746332 +chr1 4682367 . tgttgttgttgttgttgttgttgt tgttgttgttgttgttgt . PASS END=4682390;RU=tgt;PERIOD=3;REF=8;GRID=3,9;STUTTERUP=0.00261449;STUTTERDOWN=0.0280806;STUTTERP=0.937294;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:28:1:6,6:6-6,6-6:21,7,0,0:6,21:NULL:146.642:366.612,131.36:0,0:1,1.95473e-06,0 +chr1 4686168 . cacacacacacacacacacacacacacacacacacacacaca cacacacacacacacacacacacacacacacacacacacacaca . PASS END=4686209;RU=ca;PERIOD=2;REF=21;GRID=19,27;STUTTERUP=0.0719118;STUTTERDOWN=0.200895;STUTTERP=0.764236;EXPTHRESH=21 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:25:0.187797:22,22:22-24,22-24:2,10,0,11:22,2:5,1|6,1|8,1|10,1|11,1|12,2|14,1|15,2|17,1:189.185:366.612,131.36:0.74264,0.74264:0.00012952,0.20116,0.798757 +chr1 4686524 . atttatttatttatttatttatttatttatttatttattt atttatttatttatttatttatttattt . PASS END=4686563;RU=attt;PERIOD=4;REF=10;GRID=7,13;STUTTERUP=0.00426912;STUTTERDOWN=0.0198741;STUTTERP=0.731258;EXPTHRESH=10 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:29:0.151438:7,7:7-10,7-10:0,28,0,0:NULL:NULL:276.397:366.612,131.36:1.35046,1.35046:0.470992,0.446304,0.0828489 +chr1 4686877 . ctcttgcctcttgcctcttgc ctcttgcctcttgc . PASS END=4686897;RU=ctcttgc;PERIOD=7;REF=3;GRID=1,5;STUTTERUP=0.000942488;STUTTERDOWN=0.0018816;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:22:1.00001:2,2:2-2,2-2:20,2,0,0:2,20:NULL:101.017:366.612,131.36:0,0:0.999994,6.05004e-06,0 +chr1 4686995 . caaccaaccaac . . PASS END=4687006;RU=caac;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000668103;STUTTERDOWN=0.000668103;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:24:0.999964:3,3:3-3,3-3:17,7,0,0:3,17:NULL:133.776:366.612,131.36:0,0:0,2.7351e-05,0.999972 +chr1 4687079 . tttgtttgtttgtttgtttgtttgtttgtttgtttgtttg tttgtttgtttgtttgtttgtttgtttgtttgtttg . PASS END=4687118;RU=tttg;PERIOD=4;REF=10;GRID=6,12;STUTTERUP=0.00418724;STUTTERDOWN=0.0356457;STUTTERP=0.652662;EXPTHRESH=10 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:20:0.97354:9,9:9-9,9-9:9,9,0,2:9,9:4,1|6,1:135.748:366.612,131.36:0,0:0.992191,0.00782769,1.51507e-15 +chr1 4689281 . ccgccgccgccg . . PASS END=4689292;RU=ccg;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000321966;STUTTERDOWN=0.00947125;STUTTERP=0.985489;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:44:1:4,4:4-4,4-4:30,14,0,0:4,30:NULL:244.472:366.612,131.36:0,0:0,7.97427e-09,1 +chr1 4689823 . aaacaaacaaac aaacaaacaaacaaac . PASS END=4689834;RU=aaac;PERIOD=4;REF=3;GRID=1,7;STUTTERUP=0.00050774;STUTTERDOWN=0.0138826;STUTTERP=0.911509;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:22:0.570554:4,4:1-4,1-4:4,18,0,0:4,4:NULL:181.263:366.612,131.36:0.896026,0.896026:5.26906e-18,0.295691,0.704315 +chr1 4697276 . cacacacacacacacacacacaca cacacacacacacacacacacacacacacaca . PASS END=4697299;RU=ca;PERIOD=2;REF=12;GRID=10,20;STUTTERUP=0.0502413;STUTTERDOWN=0.126198;STUTTERP=0.824312;EXPTHRESH=12 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:30:0.99099:16,16:13-16,13-16:12,15,0,0:16,12:NULL:194.439:366.612,131.36:1.26733,1.26733:0,0.00227994,0.997724 +chr1 4697462 . attattattatt . . PASS END=4697473;RU=att;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00136984;STUTTERDOWN=0.000978293;STUTTERP=0.990318;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:55:1:4,4:4-4,4-4:22,30,0,3:4,22:3,3:390.194:366.612,131.36:0,0:0,1.00364e-06,1 +chr1 4698068 . ggaggaggagga ggaggaggaggaggagga . PASS END=4698079;RU=gga;PERIOD=3;REF=4;GRID=2,9;STUTTERUP=0.00216788;STUTTERDOWN=0.00983818;STUTTERP=0.764932;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:44:1.00001:6,6:6-6,6-6:23,16,0,4:6,23:4,3|5,1:261.501:366.612,131.36:0.0990099,0.0990099:0,5.27864e-08,1 +chr1 4699171 . ttttgttttgttttg . . PASS END=4699185;RU=ttttg;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000355742;STUTTERDOWN=0.00142295;STUTTERP=0.706087;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:56:1:3,3:3-3,3-3:40,16,0,0:3,40:NULL:305.478:366.612,131.36:0,0:0,5.41064e-12,1 +chr1 4700769 . cctcctcctcct . . PASS END=4700780;RU=cct;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000982239;STUTTERDOWN=0.00610456;STUTTERP=0.852201;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:1.00001:4,4:4-4,4-4:21,14,0,2:4,21:3,2:226.516:366.612,131.36:0,0:0,2.88555e-06,1 +chr1 4700784 . ccaccaccacca . . PASS END=4700795;RU=cca;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00197191;STUTTERDOWN=0.00394382;STUTTERP=0.552495;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:0.999947:4,4:4-4,4-4:17,13,0,3:4,17:3,3:209.523:366.612,131.36:0,0:0,2.62881e-05,0.999978 +chr1 4702033 . acacacacacacacacacacacacacacacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacac . PASS END=4702088;RU=ac;PERIOD=2;REF=28;GRID=13,30;STUTTERUP=0.0785561;STUTTERDOWN=0.252721;STUTTERP=0.746223;EXPTHRESH=28 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:19:0.949836:18,18:18-27,18-27:10,7,0,0:18,10:NULL:111.362:366.612,131.36:4.28531,4.28531:0.996482,0.00352666,0 +chr1 4704115 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt gt . PASS END=4704162;RU=gt;PERIOD=2;REF=24;GRID=1,103;STUTTERUP=0.0864184;STUTTERDOWN=0.208584;STUTTERP=0.753894;EXPTHRESH=24 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP .:.:.:.:.:.:.:.:.:.:.:. +chr1 4704841 . tctttctttctt . . PASS END=4704852;RU=tctt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000438741;STUTTERDOWN=0.00296617;STUTTERP=0.958596;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:1.00001:3,3:3-3,3-3:22,17,0,0:3,22:NULL:239.977:366.612,131.36:0,0:0,1.205e-06,1 +chr1 4706710 . aaataaataaataaataaataaat . . PASS END=4706733;RU=aaat;PERIOD=4;REF=6;GRID=3,9;STUTTERUP=0.00377401;STUTTERDOWN=0.0178632;STUTTERP=0.865986;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:0.999301:6,6:6-6,6-6:14,12,0,9:6,14:3,4|4,4|5,1:233.335:366.612,131.36:0,0:1.17776e-34,0.000402795,0.999599 +chr1 4713034 . atatatatatat . . PASS END=4713045;RU=at;PERIOD=2;REF=6;GRID=3,10;STUTTERUP=0.0240779;STUTTERDOWN=0.0160629;STUTTERP=0.921814;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:27:0.998997:6,6:6-7,6-7:14,12,0,0:6,14:NULL:161.232:366.612,131.36:0.345543,0.345543:1.41345e-23,0.000456233,0.999545 +chr1 4715718 . ttgttgttgttg . . PASS END=4715729;RU=ttg;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00106817;STUTTERDOWN=0.00213632;STUTTERP=0.866591;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:0.999965:4,4:4-4,4-4:19,16,0,0:4,19:NULL:221.081:366.612,131.36:0,0:0,3.13059e-05,0.999971 +chr1 4717842 . tctttctttctttctt . . PASS END=4717857;RU=tctt;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000482442;STUTTERDOWN=0.00465867;STUTTERP=0.905234;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:51:1:4,4:4-4,4-4:25,24,0,2:4,25:3,2:339.318:366.612,131.36:0,0:0,3.68868e-07,1 +chr1 4718882 . aactaactaact . . PASS END=4718893;RU=aact;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000426909;STUTTERDOWN=0.00206121;STUTTERP=0.719903;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:46:1:3,3:3-3,3-3:24,20,0,2:3,24:2,2:285.668:366.612,131.36:0,0:0,4.09028e-07,1 +chr1 4719899 . cacacacacacacacaca cacacacacacacacacaca . PASS END=4719916;RU=ca;PERIOD=2;REF=9;GRID=7,18;STUTTERUP=0.0323357;STUTTERDOWN=0.0558071;STUTTERP=0.872514;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:56:0.997642:10,10:10-15,10-15:34,18,0,3:10,34:9,2|15,1:344.303:366.612,131.36:2.24763,2.24763:0,1.18615e-10,1 +chr1 4722124 . aaacaaacaaacaaac aaacaaac,aaacaaacaaac . PASS END=4722139;RU=aaac;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.00289194;STUTTERDOWN=0.0181254;STUTTERP=0.96739;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:30:0.184894:2,3:1-4,2-4:0,27,0,2:NULL:3,2:288.601:366.612,131.36:0.914864,0.61098:0.38494,0.537507,0.0776752 +chr1 4725802 . acatacatacat . . PASS END=4725813;RU=acat;PERIOD=4;REF=3;GRID=1,12;STUTTERUP=0.000395774;STUTTERDOWN=0.00113058;STUTTERP=0.761601;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:49:1:3,3:3-9,3-9:32,16,0,0:3,32:NULL:276.69:366.612,131.36:2.76732,2.76732:0,2.35909e-09,1 +chr1 4726010 . ttgctttgctttgctttgctttgct ttgct . PASS END=4726034;RU=ttgct;PERIOD=5;REF=5;GRID=1,103;STUTTERUP=0.000930137;STUTTERDOWN=0.0108261;STUTTERP=0.669108;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:9:0.0189889:1,1:1-5,1-5:0,9,0,0:NULL:NULL:79.2751:366.612,131.36:1.56624,1.56624:0.226535,0.525124,0.248383 +chr1 4727699 . ataaataaataa . . PASS END=4727710;RU=ataa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000771698;STUTTERDOWN=0.00220006;STUTTERP=0.941945;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:3:0.444226:3,3:3-3,3-3:3,0,0,0:3,3:NULL:11.7222:366.612,131.36:0,0:2.47845e-10,0.222364,0.777675 +chr1 4730651 . ctcctcctcctcctcctcctcctcctcctcctcctc ctc . PASS END=4730686;RU=ctc;PERIOD=3;REF=12;GRID=1,103;STUTTERUP=0.0113163;STUTTERDOWN=0.0657889;STUTTERP=0.650163;EXPTHRESH=12 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:12:0.0285318:1,1:1-3,1-3:0,12,0,0:NULL:NULL:107.704:366.612,131.36:0.629628,0.629628:0.688685,0.293806,0.0175481 +chr1 4732027 . ctctctctctctct ctctctctctct . PASS END=4732040;RU=ct;PERIOD=2;REF=7;GRID=3,9;STUTTERUP=0.0202122;STUTTERDOWN=0.0215603;STUTTERP=0.93802;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:49:1:6,6:6-6,6-6:40,9,0,0:6,40:NULL:244.43:366.612,131.36:0,0:1,6.78159e-12,0 +chr1 4736939 . aaataaataaataaat . . PASS END=4736954;RU=aaat;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.00125741;STUTTERDOWN=0.0050295;STUTTERP=0.918556;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:0.999453:4,4:4-4,4-4:15,16,0,0:4,15:NULL:209.92:366.612,131.36:0,0:4.76441e-44,0.000465687,0.999537 +chr1 4744698 . tgttttgttttgttttgttttgttttgttt tgttttgttttgttt . PASS END=4744727;RU=tgttt;PERIOD=5;REF=6;GRID=1,6;STUTTERUP=0.000683195;STUTTERDOWN=0.00659708;STUTTERP=0.750875;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:34:0.999849:3,3:3-3,3-3:16,15,0,3:3,16:2,3:226.572:366.612,131.36:0,0:0.99998,1.92607e-05,0 +chr1 4746881 . tagatagataga . . PASS END=4746892;RU=taga;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00062169;STUTTERDOWN=0.00062169;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:32:1.00001:3,3:3-3,3-3:20,10,0,2:3,20:2,1|3,1:188.564:366.612,131.36:0,0:0,2.9315e-06,1 +chr1 4749824 . atatatatatatatatatatatatatatatatatat atatatatatatatatatatatat,atatatatatatatatatatatatatat . PASS END=4749859;RU=at;PERIOD=2;REF=18;GRID=9,22;STUTTERUP=0.082627;STUTTERDOWN=0.112392;STUTTERP=0.657199;EXPTHRESH=18 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:23:0.491197:12,14:12-19,12-19:6,15,0,0:12,2|13,2|14,2:NULL:170.202:366.612,131.36:2.80724,2.22986:0.998504,0.00150085,2.85157e-16 +chr1 4755604 . ggagggagggagggag . . PASS END=4755619;RU=ggag;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.00563435;STUTTERDOWN=0.00680354;STUTTERP=0.810869;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:7:0.303264:4,4:4-4,4-4:2,5,0,0:4,2:NULL:51.7998:366.612,131.36:0,0:1.04381e-05,0.377089,0.622955 +chr1 4755631 . gagaggagaggagaggagaggagaggagaggagaggagaggagaggagaggagaggagaggagaggagaggagaggagaggagaggagag . . PASS END=4755720;RU=gagag;PERIOD=5;REF=18;GRID=1,18;STUTTERUP=0.0170031;STUTTERDOWN=0.0514516;STUTTERP=0.932953;EXPTHRESH=18 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:8:0.0345281:18,18:1-18,1-18:0,4,0,4:NULL:7,1|13,1|15,2:63.3554:366.612,131.36:4.54331,4.54331:0.631007,0.33457,0.0345084 +chr1 4757329 . ctctctctctctctctctctctctctctctctctctctctctct ctctctctctctctctctctctctctctctctctct . PASS END=4757372;RU=ct;PERIOD=2;REF=22;GRID=18,24;STUTTERUP=0.0571241;STUTTERDOWN=0.214662;STUTTERP=0.640356;EXPTHRESH=22 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:25:0.0928393:18,18:18-21,18-21:0,24,0,0:NULL:NULL:219.478:366.612,131.36:1.4276,1.4276:0.50981,0.412801,0.0774748 +chr1 4758257 . aataaataaata aata . PASS END=4758268;RU=aata;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00128936;STUTTERDOWN=0.00257872;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:23:0.247138:1,1:1-3,1-3:0,22,0,0:NULL:NULL:224.468:366.612,131.36:0.911644,0.911644:0.474337,0.438266,0.0875358 +chr1 4761246 . tttgtttgtttg tttgtttg . PASS END=4761257;RU=tttg;PERIOD=4;REF=3;GRID=1,5;STUTTERUP=0.00186974;STUTTERDOWN=0.00136523;STUTTERP=0.985668;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:24:0.999753:2,2:2-2,2-2:15,9,0,0:2,15:NULL:139.97:366.612,131.36:0,0:0.999841,0.000161256,4.76441e-44 +chr1 4765570 . aaagaaaagaaaagaaaagaaaagaaaagaaaagaaaaga aaaga . PASS END=4765609;RU=aaaga;PERIOD=5;REF=8;GRID=1,103;STUTTERUP=0.00819406;STUTTERDOWN=0.0163651;STUTTERP=0.999;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:9:0.0327166:1,1:1-5,1-5:0,9,0,0:NULL:NULL:86.9262:366.612,131.36:1.26307,1.26307:0.53443,0.419224,0.0465006 +chr1 4767274 . ttttgttttgttttg ttttgttttg . PASS END=4767288;RU=ttttg;PERIOD=5;REF=3;GRID=1,5;STUTTERUP=0.00109054;STUTTERDOWN=0.00198711;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:33:1.00001:2,2:2-2,2-2:22,11,0,0:2,22:NULL:183.799:366.612,131.36:0,0:1,1.05278e-06,0 +chr1 4769727 . tttttttgtttttttgtttttttg tttttttg . PASS END=4769750;RU=tttttttg;PERIOD=8;REF=3;GRID=1,103;STUTTERUP=0.00147891;STUTTERDOWN=0.0073391;STUTTERP=0.718087;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:27:0.164897:1,1:1-2,1-2:0,27,0,0:NULL:NULL:231.409:366.612,131.36:0.412766,0.412766:0.544221,0.398179,0.057756 +chr1 4772542 . aataaataaataaataaataaataaata . . PASS END=4772569;RU=aata;PERIOD=4;REF=7;GRID=4,10;STUTTERUP=0.00446998;STUTTERDOWN=0.0240042;STUTTERP=0.704795;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:6:0.275424:7,7:7-8,7-8:2,2,0,2:7,2:3,1|5,1:43.124:366.612,131.36:0.371782,0.371782:6.84117e-06,0.345865,0.654163 +chr1 4777183 . tctctctctctctctctctctctctctctctctc tctctctctctctctc . PASS END=4777216;RU=tc;PERIOD=2;REF=17;GRID=5,11;STUTTERUP=0.0378193;STUTTERDOWN=0.109338;STUTTERP=0.71892;EXPTHRESH=17 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:28:0.998464:8,8:8-8,8-8:13,12,0,3:8,13:7,3:186.353:366.612,131.36:0,0:1,0,0 +chr1 4778087 . tgtgtgtgtgtg tgtgtgtgtgtgtg,tgtgtgtgtgtgtgtgtg . PASS END=4778098;RU=tg;PERIOD=2;REF=6;GRID=4,12;STUTTERUP=0.0822043;STUTTERDOWN=0.00176273;STUTTERP=0.912734;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:30:0.982749:7,9:7-9,7-9:4,23,0,2:7,2|9,2:6,2:239.527:366.612,131.36:0.5634,0.665211:4.26849e-27,6.03865e-05,0.999941 +chr1 4779799 . tgtgtgtgtgtgtg . . PASS END=4779812;RU=tg;PERIOD=2;REF=7;GRID=4,10;STUTTERUP=0.0120072;STUTTERDOWN=0.0220761;STUTTERP=0.948775;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:30:0.999841:7,7:7-7,7-7:16,14,0,0:7,16:NULL:192.429:366.612,131.36:0,0:2.56299e-31,8.08966e-05,0.999919 +chr1 4780052 . gtttgtttgttt . . PASS END=4780063;RU=gttt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000496751;STUTTERDOWN=0.000496751;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:0.999904:3,3:3-3,3-3:17,19,0,0:3,17:NULL:238.62:366.612,131.36:0,0:0,7.31266e-05,0.999926 +chr1 4781290 . aaaacaaaacaaaacaaaac aaaac . PASS END=4781309;RU=aaaac;PERIOD=5;REF=4;GRID=1,6;STUTTERUP=0.000574847;STUTTERDOWN=0.00410156;STUTTERP=0.963962;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:10:0.077236:1,1:1-3,1-3:0,9,0,0:NULL:NULL:83.6948:366.612,131.36:0.885129,0.885129:0.393228,0.473883,0.132974 +chr1 4783247 . atatatatatatat atatatatatatatatatatatatatatat,atatatatatatatatatatatatatatatat . PASS END=4783260;RU=at;PERIOD=2;REF=7;GRID=12,19;STUTTERUP=0.0664448;STUTTERDOWN=0.0892668;STUTTERP=0.702159;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:15:0.914663:15,16:15-16,15-16:5,10,0,0:15,3|16,2:NULL:117.259:366.612,131.36:0.38423,0.661813:0,0,1 +chr1 4783908 . aaaaaacaaaaaacaaaaaac aaaaaac . PASS END=4783928;RU=aaaaaac;PERIOD=7;REF=3;GRID=1,103;STUTTERUP=0.000768565;STUTTERDOWN=0.00207938;STUTTERP=0.551476;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:13:0.121674:1,1:1-2,1-2:0,13,0,0:NULL:NULL:122.189:366.612,131.36:0.38244,0.38244:0.327036,0.514355,0.158633 +chr1 4789575 . tgaatgaatgaa . . PASS END=4789586;RU=tgaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000469064;STUTTERDOWN=0.000469064;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:1:3,3:3-3,3-3:23,8,0,0:3,23:NULL:161.544:366.612,131.36:0,0:0,7.52438e-07,1 +chr1 4790408 . aagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaag aagaagaagaagaagaagaagaagaagaagaagaagaagaag . PASS END=4790503;RU=aag;PERIOD=3;REF=32;GRID=12,19;STUTTERUP=0.0352306;STUTTERDOWN=0.121336;STUTTERP=0.890105;EXPTHRESH=32 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:19:0.0413989:14,14:14-16,14-16:0,14,0,3:NULL:5,1|12,1|14,1:150.9:366.612,131.36:0.752866,0.752866:1,0,0 +chr1 4790591 . aataataataataataat aataataataataat . PASS END=4790608;RU=aat;PERIOD=3;REF=6;GRID=2,8;STUTTERUP=0.00588472;STUTTERDOWN=0.0111886;STUTTERP=0.91257;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:32:1.00001:5,5:5-5,5-5:22,10,0,0:5,22:NULL:183.042:366.612,131.36:0,0:1,1.20863e-06,9.80909e-45 +chr1 4794293 . agacagacagacagacagac agacagacagacagacagacagacagac . PASS END=4794312;RU=agac;PERIOD=4;REF=5;GRID=4,10;STUTTERUP=0.00087825;STUTTERDOWN=0.0196511;STUTTERP=0.869513;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:41:1:7,7:7-7,7-7:20,16,0,5:7,20:2,1|3,2|6,2:262.128:366.612,131.36:0,0:0,8.52709e-07,1 +chr1 4795085 . agatagatagatagatagatagatagatagatagatagatagatagat agatagatagatagatagatagatagatagatagatagatagat . PASS END=4795132;RU=agat;PERIOD=4;REF=12;GRID=7,14;STUTTERUP=0.005603;STUTTERDOWN=0.0231525;STUTTERP=0.558153;EXPTHRESH=12 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:23:0.983372:11,11:10-11,10-11:10,7,0,5:11,10:2,1|4,1|6,2|8,1:148.19:366.612,131.36:0.374147,0.374147:0.993804,0.00621315,1.9132e-19 +chr1 4795238 . gttttgttttgttttgtttt gttttgtttt . PASS END=4795257;RU=gtttt;PERIOD=5;REF=4;GRID=1,103;STUTTERUP=0.000619729;STUTTERDOWN=0.00177026;STUTTERP=0.76161;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:10:0.0361998:2,2:1-2,1-2:0,10,0,0:NULL:NULL:91.2136:366.612,131.36:0.497026,0.497026:0.251267,0.543828,0.204912 +chr1 4796020 . tttgtttgtttgtttgtttgtttg tttgtttgtttgtttgtttg . PASS END=4796043;RU=tttg;PERIOD=4;REF=6;GRID=2,8;STUTTERUP=0.00270253;STUTTERDOWN=0.00963792;STUTTERP=0.759332;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:37:1.00001:5,5:5-5,5-5:21,14,0,2:5,21:2,2:223.615:366.612,131.36:0,0:1,1.53343e-06,0 +chr1 4802916 . tctctctctctctc tctctctctc,tctctctctctctctc . PASS END=4802929;RU=tc;PERIOD=2;REF=7;GRID=2,11;STUTTERUP=0.0734298;STUTTERDOWN=0.030894;STUTTERP=0.805709;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:23:0.942033:5,8:5-8,7-8:8,14,0,0:5,2|7,2|8,4:NULL:166.965:366.612,131.36:0.907009,0.442564:2.56506e-07,0.96656,0.0335034 +chr1 4804071 . aaaccaaaccaaaccaaaccaaacc . . PASS END=4804095;RU=aaacc;PERIOD=5;REF=5;GRID=1,7;STUTTERUP=0.000645296;STUTTERDOWN=0.00320256;STUTTERP=0.547905;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:15:0.0894039:5,5:2-5,2-5:0,11,0,4:NULL:4,4:127.203:366.612,131.36:0.778346,0.778346:0.129595,0.474151,0.396449 +chr1 4804879 . aaaaacaaaaacaaaaac . . PASS END=4804896;RU=aaaaac;PERIOD=6;REF=3;GRID=1,6;STUTTERUP=0.000636167;STUTTERDOWN=0.00363459;STUTTERP=0.829224;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:34:0.999446:3,3:3-3,3-3:14,20,0,0:3,14:NULL:236.542:366.612,131.36:0,0:0,0.000471379,0.99953 +chr1 4805189 . atttatttattt atttatttatttattt . PASS END=4805200;RU=attt;PERIOD=4;REF=3;GRID=1,7;STUTTERUP=0.000674417;STUTTERDOWN=0.0416099;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/1:25:0.999411:3,4:3-4,4-4:18,5,0,2:3,6|4,12:2,2:141.207:366.612,131.36:0.323567,0:0,7.80262e-09,1 +chr1 4806133 . tgtgtgtgtgtgtg . . PASS END=4806146;RU=tg;PERIOD=2;REF=7;GRID=4,10;STUTTERUP=0.00927525;STUTTERDOWN=0.0313905;STUTTERP=0.968617;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:30:0.995514:7,7:7-7,7-7:11,16,0,3:7,11:5,2|6,1:212.496:366.612,131.36:0,0:9.26685e-23,0.00238463,0.997624 +chr1 4806257 . ctgactgactga . . PASS END=4806268;RU=ctga;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00102114;STUTTERDOWN=0.00145853;STUTTERP=0.959076;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:1:3,3:3-3,3-3:24,7,0,0:3,24:NULL:159.946:366.612,131.36:0,0:0,2.69918e-07,1 +chr1 4806381 . ttctttctttctttctttctttctttctttct ttct . PASS END=4806412;RU=ttct;PERIOD=4;REF=8;GRID=1,103;STUTTERUP=0.0875777;STUTTERDOWN=0.0161799;STUTTERP=0.95956;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:9:0.0223139:1,1:1-2,1-2:0,9,0,0:NULL:NULL:81.0159:366.612,131.36:0.486863,0.486863:0.428852,0.485257,0.0860298 +chr1 4808103 . gcctgcctgcct . . PASS END=4808114;RU=gcct;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000420909;STUTTERDOWN=0.000420909;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:34:1:3,3:3-3,3-3:23,11,0,0:3,23:NULL:189.832:366.612,131.36:0,0:0,6.95971e-07,1 +chr1 4809703 . atgaatgaatgaatga . . PASS END=4809718;RU=atga;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000495785;STUTTERDOWN=0.00729224;STUTTERP=0.975956;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:24:0.999994:4,4:4-4,4-4:19,5,0,0:4,19:NULL:118.253:366.612,131.36:0,0:0,1.32162e-05,0.999987 +chr1 4809829 . gttttgttttgttttgtttt . . PASS END=4809848;RU=gtttt;PERIOD=5;REF=4;GRID=1,7;STUTTERUP=0.00107231;STUTTERDOWN=0.00476834;STUTTERP=0.922246;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:1.00001:4,4:4-4,4-4:20,13,0,3:4,20:2,1|3,2:222.309:366.612,131.36:0,0:0,3.33137e-06,1 +chr1 4809864 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=4809903;RU=tg;PERIOD=2;REF=20;GRID=15,23;STUTTERUP=0.0875468;STUTTERDOWN=0.152098;STUTTERP=0.7978;EXPTHRESH=20 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:44:0.88101:19,19:18-20,18-20:14,15,0,14:18,3|19,11:4,1|6,2|8,1|9,1|10,2|13,1|14,1|15,1|16,2|17,1|18,1:319.085:366.612,131.36:0.410384,0.410384:0.998451,0.00155301,1.22279e-11 +chr1 4810353 . tttgtttgtttg . . PASS END=4810364;RU=tttg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00040495;STUTTERDOWN=0.00040495;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:42:1:3,3:3-3,3-3:24,16,0,2:3,24:2,2:248.206:366.612,131.36:0,0:0,2.23073e-07,1 +chr1 4810746 . catgcatgcatg . . PASS END=4810757;RU=catg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000687401;STUTTERDOWN=0.000687401;STUTTERP=0.976453;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:50:1:3,3:3-3,3-3:25,25,0,0:3,25:NULL:311.433:366.612,131.36:0,0:0,1.80033e-07,1 +chr1 4810950 . ttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctcc ttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctcc,ttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctccttctcc . PASS END=4811123;RU=ttctcc;PERIOD=6;REF=29;GRID=4,22;STUTTERUP=0.05;STUTTERDOWN=0.05;STUTTERP=0.9;EXPTHRESH=29 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:21:0.284642:15,19:7-15,7-21:3,3,0,14:15,3:4,1|5,2|6,2|7,3|8,2|9,1|10,1|13,1|19,1:141.767:366.612,131.36:3.80837,5.76309:1,0,0 +chr1 4811609 . gagagagagagagagagagagagagagagagagagagagaga . . PASS END=4811650;RU=ga;PERIOD=2;REF=21;GRID=16,24;STUTTERUP=0.0166013;STUTTERDOWN=0.19036;STUTTERP=0.483921;EXPTHRESH=21 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:25:0.795355:21,21:19-21,19-21:6,12,0,6:21,6:4,1|8,1|12,1|14,1|15,1|16,1:187.852:366.612,131.36:0.825531,0.825531:1.10236e-12,0.124233,0.875868 +chr1 4811806 . ttttgttttgttttg . . PASS END=4811820;RU=ttttg;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000483501;STUTTERDOWN=0.00193398;STUTTERP=0.987382;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:1:3,3:3-3,3-3:26,9,0,3:3,26:2,3:205.931:366.612,131.36:0,0:0,2.39576e-08,1 +chr1 4814327 . aaataaataaat aaataaat . PASS END=4814338;RU=aaat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000671617;STUTTERDOWN=0.00191856;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/0:26:0.999999:2,3:2-2,2-3:12,14,0,0:2,9|3,3:NULL:181.575:366.612,131.36:0,0.36513:8.4454e-07,1,1.92825e-22 +chr1 4815548 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=4815577;RU=gt;PERIOD=2;REF=15;GRID=10,19;STUTTERUP=0.0439746;STUTTERDOWN=0.174802;STUTTERP=0.782972;EXPTHRESH=15 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:24:0.978896:16,16:13-16,13-16:13,7,0,2:15,2|16,11:11,1|13,1:143.644:366.612,131.36:1.12671,1.12671:5.2269e-24,0.00115283,0.998853 +chr1 4817565 . cagcagcagcag . . PASS END=4817576;RU=cag;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000487118;STUTTERDOWN=0.00139152;STUTTERP=0.941457;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:41:0.999968:4,4:4-4,4-4:19,22,0,0:4,19:NULL:273.457:366.612,131.36:0,0:0,3.97051e-05,0.999963 +chr1 4819449 . tttgtttgtttgtttgtttgtttg tttgtttgtttgtttg . PASS END=4819472;RU=tttg;PERIOD=4;REF=6;GRID=1,7;STUTTERUP=0.00250357;STUTTERDOWN=0.0046205;STUTTERP=0.644549;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:19:0.630721:4,4:3-4,3-4:4,13,0,2:4,4:3,2:153.492:366.612,131.36:0.330165,0.330165:0.92114,0.0789544,1.7293e-13 +chr1 4820555 . gtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgt . PASS END=4820572;RU=gt;PERIOD=2;REF=9;GRID=6,13;STUTTERUP=0.0252827;STUTTERDOWN=0.0751166;STUTTERP=0.888218;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:32:0.99982:10,10:10-10,10-10:16,10,0,5:10,16:6,1|7,2|9,2:200.216:366.612,131.36:0,0:0,2.30314e-05,0.999979 +chr1 4822262 . tgtttgtttgtt tgtt . PASS END=4822273;RU=tgtt;PERIOD=4;REF=3;GRID=1,103;STUTTERUP=0.000392174;STUTTERDOWN=0.000392174;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:25:0.0821131:1,1:1-3,1-3:0,25,0,0:NULL:NULL:224.832:366.612,131.36:0.556749,0.556749:0.273043,0.514863,0.212099 +chr1 4822494 . cacacacacaca . . PASS END=4822505;RU=ca;PERIOD=2;REF=6;GRID=3,9;STUTTERUP=0.00729847;STUTTERDOWN=0.00335469;STUTTERP=0.949753;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:42:1:6,6:6-6,6-6:29,13,0,0:6,29:NULL:234.205:366.612,131.36:0,0:0,1.70101e-08,1 +chr1 4823989 . tgtctgtctgtctgtctgtctgtc tgtctgtctgtctgtctgtctgtctgtctgtc . PASS END=4824012;RU=tgtc;PERIOD=4;REF=6;GRID=4,11;STUTTERUP=0.00273929;STUTTERDOWN=0.0351602;STUTTERP=0.868423;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:41:1.00001:8,8:8-8,8-8:22,11,0,7:8,22:2,1|3,2|4,1|5,1|6,2:243.729:366.612,131.36:0.0990099,0.0990099:0,3.8867e-07,1 +chr1 4831112 . ctggctggctgg . . PASS END=4831123;RU=ctgg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00041194;STUTTERDOWN=0.00041194;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:46:1:3,3:3-3,3-3:27,19,0,0:3,27:NULL:275.992:366.612,131.36:0,0:0,5.25396e-08,1 +chr1 4832670 . ctccctccctcc . . PASS END=4832681;RU=ctcc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000430106;STUTTERDOWN=0.00122866;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:50:1:3,3:3-3,3-3:25,23,0,2:3,25:2,2:329.873:366.612,131.36:0,0:0,1.7607e-07,1 +chr1 4835862 . ttttgttttgttttg . . PASS END=4835876;RU=ttttg;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000552742;STUTTERDOWN=0.00110548;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:1:3,3:3-3,3-3:25,11,0,0:3,25:NULL:194.431:366.612,131.36:0,0:0,1.38502e-07,1 +chr1 4836013 . tttcttttcttttct . . PASS END=4836027;RU=tttct;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.00059378;STUTTERDOWN=0.0028669;STUTTERP=0.984306;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:23:0.99706:3,3:3-3,3-3:11,10,0,2:3,11:2,2:144.957:366.612,131.36:0,0:4.62434e-36,0.00126048,0.998746 +chr1 4836682 . tttatttattta . . PASS END=4836693;RU=ttta;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000511424;STUTTERDOWN=0.000511424;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:0.999993:3,3:3-3,3-3:19,17,0,0:3,19:NULL:231.07:366.612,131.36:0,0:0,1.7298e-05,0.999986 +chr1 4837261 . ttcattcattcattcattca ttca . PASS END=4837280;RU=ttca;PERIOD=4;REF=5;GRID=1,103;STUTTERUP=0.00173446;STUTTERDOWN=0.00587199;STUTTERP=0.908916;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:16:0.0690482:1,1:1-1,1-1:0,16,0,0:NULL:NULL:142.057:366.612,131.36:0.19802,0.19802:0.394443,0.481659,0.12399 +chr1 4840709 . aataaataaata . . PASS END=4840720;RU=aata;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000509794;STUTTERDOWN=0.00291259;STUTTERP=0.969616;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:0.999165:3,3:3-3,3-3:13,16,0,0:3,13:NULL:199.55:366.612,131.36:0,0:1.35926e-43,0.000665667,0.999339 +chr1 4841846 . aaagaaagaaag aaagaaag . PASS END=4841857;RU=aaag;PERIOD=4;REF=3;GRID=1,5;STUTTERUP=0.000509226;STUTTERDOWN=0.00101158;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:36:1.00001:2,2:2-2,2-2:22,14,0,0:2,22:NULL:212.561:366.612,131.36:0,0:1,7.47019e-07,0 +chr1 4843541 . tttgtttgtttg . . PASS END=4843552;RU=tttg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000489041;STUTTERDOWN=0.00139701;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:42:1:3,3:3-3,3-3:28,14,0,0:3,28:NULL:240.43:366.612,131.36:0,0:0,1.4138e-08,1 +chr1 4844779 . aaaataaaataaaat . . PASS END=4844793;RU=aaaat;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.00121984;STUTTERDOWN=0.00348463;STUTTERP=0.952743;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:26:0.999617:3,3:3-3,3-3:15,11,0,0:3,15:NULL:162.206:366.612,131.36:0,0:6.30584e-44,0.000244671,0.999758 +chr1 4845843 . aaacaaacaaacaaacaaac . . PASS END=4845862;RU=aaac;PERIOD=4;REF=5;GRID=2,8;STUTTERUP=0.000441217;STUTTERDOWN=0.0105166;STUTTERP=0.706571;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:52:1:5,5:5-5,5-5:23,27,0,2:5,23:3,1|4,1:355.553:366.612,131.36:0,0:0,5.15931e-07,1 +chr1 4846452 . ccaaccaaccaa . . PASS END=4846463;RU=ccaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000539924;STUTTERDOWN=0.00107985;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:22:0.981252:3,3:3-3,3-3:9,11,0,2:3,9:2,2:146.9:366.612,131.36:0,0:1.18375e-29,0.00809632,0.991921 +chr1 4848400 . tgtttgtttgtttgtttgtttgtttgtttgtttgtt tgtttgtttgtttgtttgtttgtttgtt . PASS END=4848435;RU=tgtt;PERIOD=4;REF=9;GRID=4,10;STUTTERUP=0.00250898;STUTTERDOWN=0.0227987;STUTTERP=0.688377;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:51:1:7,7:7-7,7-7:21,25,0,5:7,21:3,1|4,2|5,1|6,1:348.189:366.612,131.36:0,0:1,1.1066e-06,0 +chr1 4849030 . aaagaaagaaagaaag . . PASS END=4849045;RU=aaag;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000985576;STUTTERDOWN=0.00563085;STUTTERP=0.834179;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:1:4,4:4-4,4-4:22,17,0,0:4,22:NULL:245.114:366.612,131.36:0,0:0,2.42971e-06,1 +chr1 4849772 . caacaacaacaacaacaacaacaacaa caacaacaacaacaa . PASS END=4849798;RU=caa;PERIOD=3;REF=9;GRID=2,8;STUTTERUP=0.00443539;STUTTERDOWN=0.0199193;STUTTERP=0.64304;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:26:0.999796:5,5:5-5,5-5:16,10,0,0:5,16:NULL:158.209:366.612,131.36:0,0:1,0,0 +chr1 4850587 . cacacacacacacacacacacacacacaca cacacacacacacacacacacacacacacacacacacacacaca,cacacacacacacacacacacacacacacacacacacacacacacaca . PASS END=4850616;RU=ca;PERIOD=2;REF=15;GRID=19,29;STUTTERUP=0.0559486;STUTTERDOWN=0.115217;STUTTERP=0.900568;EXPTHRESH=15 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:26:0.935192:22,24:22-26,24-26:7,7,0,11:22,2|24,5:4,1|8,1|10,2|13,1|16,1|18,1|19,1|20,1|23,1|24,1:190.511:366.612,131.36:1.82006,0.507951:0,0,1 +chr1 4858043 . gggccgggccgggccgggcc gggccgggccgggcc . PASS END=4858062;RU=gggcc;PERIOD=5;REF=4;GRID=1,7;STUTTERUP=0.000802261;STUTTERDOWN=0.00320901;STUTTERP=0.91856;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/0:54:1:3,4:3-4,4-4:35,19,0,0:3,6|4,29:NULL:341.472:366.612,131.36:0.390807,0:0,1,3.05897e-06 +chr1 4858328 . gctgctgctgct . . PASS END=4858339;RU=gct;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000450687;STUTTERDOWN=0.00128745;STUTTERP=0.941457;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:55:1:4,4:4-4,4-4:29,23,0,3:4,29:3,3:364.467:366.612,131.36:0,0:0,5.83154e-09,1 +chr1 4859454 . caaacaaacaaa . . PASS END=4859465;RU=caaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000627909;STUTTERDOWN=0.00125582;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:22:0.997279:3,3:3-3,3-3:12,10,0,0:3,12:NULL:137.94:366.612,131.36:0,0:1.15188e-38,0.00183885,0.998169 +chr1 4859713 . ctctctctctctctct . . PASS END=4859728;RU=ct;PERIOD=2;REF=8;GRID=5,11;STUTTERUP=0.0140642;STUTTERDOWN=0.0354523;STUTTERP=0.852793;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:25:0.997518:8,8:8-8,8-8:13,12,0,0:8,13:NULL:164.513:366.612,131.36:0,0:6.90662e-25,0.0017479,0.99826 +chr1 4861410 . ttctttctttct . . PASS END=4861421;RU=ttct;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000441641;STUTTERDOWN=0.00298578;STUTTERP=0.958596;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:40:1:3,3:3-3,3-3:28,12,0,0:3,28:NULL:224.402:366.612,131.36:0,0:0,2.06593e-08,1 +chr1 4862097 . acacacacacacacacac . . PASS END=4862114;RU=ac;PERIOD=2;REF=9;GRID=5,13;STUTTERUP=0.0193026;STUTTERDOWN=0.0481493;STUTTERP=0.856985;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:52:1:9,9:9-9,9-9:26,20,0,4:9,26:6,1|7,2|8,1:325.837:366.612,131.36:0.172061,0.172061:0,4.50161e-08,1 +chr1 4862140 . acacacacacacac acacacacacacacacac . PASS END=4862153;RU=ac;PERIOD=2;REF=7;GRID=4,12;STUTTERUP=0.00786056;STUTTERDOWN=0.0211062;STUTTERP=0.829857;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/1:44:0.475531:7,9:7-7,8-9:16,22,0,5:7,16:8,4|9,1:320.291:366.612,131.36:0,0.510837:0,2.3204e-33,1 +chr1 4864608 . aaacaaacaaac . . PASS END=4864619;RU=aaac;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000399644;STUTTERDOWN=0.00228326;STUTTERP=0.829231;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:1:3,3:3-3,3-3:25,10,0,2:3,25:2,2:205.564:366.612,131.36:0,0:0,1.127e-07,1 +chr1 4866501 . ccaggctggcctccaggctggcctccaggctggcct ccaggctggcctccaggctggcct . PASS END=4866536;RU=ccaggctggcct;PERIOD=12;REF=3;GRID=1,5;STUTTERUP=0.05;STUTTERDOWN=0.05;STUTTERP=0.9;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:25:0.999145:2,2:2-2,2-2:13,12,0,0:2,13:NULL:158.09:366.612,131.36:0,0:0.999728,0.000272618,2.5201e-19 +chr1 4867295 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg,tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=4867334;RU=tg;PERIOD=2;REF=20;GRID=1,25;STUTTERUP=0.0714711;STUTTERDOWN=0.274865;STUTTERP=0.585572;EXPTHRESH=20 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:32:0.102623:22,23:10-23,10-24:0,18,0,14:NULL:5,1|6,2|7,2|8,1|10,2|16,1|17,2|20,2|22,1:279.652:366.612,131.36:2.91557,2.97962:1.37974e-22,0.306397,0.693615 +chr1 4867339 . tacatacatacataca tacatacatacatacataca . PASS END=4867354;RU=taca;PERIOD=4;REF=4;GRID=1,8;STUTTERUP=0.00119654;STUTTERDOWN=0.0297031;STUTTERP=0.941178;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:50:0.999979:5,5:5-5,5-5:27,21,0,2:4,2|5,25:3,2:323.082:366.612,131.36:0,0:0,4.58403e-08,1 +chr1 4870254 . tatttatttatt . . PASS END=4870265;RU=tatt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000580258;STUTTERDOWN=0.00165758;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:0.999596:3,3:3-3,3-3:14,14,0,3:3,14:2,3:203.164:366.612,131.36:0,0:1.4013e-45,0.000216245,0.999788 +chr1 4871522 . tcctcctcctcc . . PASS END=4871533;RU=tcc;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.001839;STUTTERDOWN=0.0067623;STUTTERP=0.900294;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:60:1:4,4:4-4,4-4:31,29,0,0:4,31:NULL:387.375:366.612,131.36:0,0:0,6.72445e-09,1 +chr1 4874307 . ggaaggaaggaa . . PASS END=4874318;RU=ggaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00053123;STUTTERDOWN=0.00106246;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:27:0.999255:3,3:3-3,3-3:14,13,0,0:3,14:NULL:179.186:366.612,131.36:0,0:1.4013e-45,0.000496271,0.999507 +chr1 4874466 . aacaacaacaacaac aacaacaacaac . PASS END=4874480;RU=aac;PERIOD=3;REF=5;GRID=1,8;STUTTERUP=0.00128602;STUTTERDOWN=0.0062092;STUTTERP=0.915698;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/0:37:0.993994:4,5:4-5,5-5:17,20,0,0:4,3|5,14:NULL:266.538:366.612,131.36:0.398507,0:1.51296e-36,0.993994,0.00601875 +chr1 4877242 . tatttatttatttatt tatt,tatttatttatt . PASS END=4877257;RU=tatt;PERIOD=4;REF=4;GRID=1,103;STUTTERUP=0.00118704;STUTTERDOWN=0.00237404;STUTTERP=0.866593;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:6:0.0150407:1,3:1-3,1-3:0,6,0,0:NULL:NULL:53.3083:366.612,131.36:0.825769,0.877677:0.0641034,0.438012,0.498075 +chr1 4878697 . ctcttctcttctcttctcttctcttctcttctcttctcttctcttctcttctcttctcttctcttctctt ctcttctcttctcttctcttctcttctcttctcttctcttctcttctcttctcttctcttctctt . PASS END=4878766;RU=ctctt;PERIOD=5;REF=14;GRID=10,16;STUTTERUP=0.00341239;STUTTERDOWN=0.0241124;STUTTERP=0.42172;EXPTHRESH=14 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:34:0.98803:13,13:13-13,13-13:10,13,0,11:13,10:2,2|4,1|6,1|8,1|9,2|10,1|11,3:246.043:366.612,131.36:0,0:0.996172,0.00383706,7.51694e-21 +chr1 4878791 . ctccctccctccctccctccctccctccctcc ctccctccctccctccctccctccctccctccctccctcc . PASS END=4878822;RU=ctcc;PERIOD=4;REF=8;GRID=1,13;STUTTERUP=0.046796;STUTTERDOWN=0.0401574;STUTTERP=0.760242;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:21:0.227777:10,10:3-10,3-10:5,14,0,0:10,5:NULL:149.658:366.612,131.36:3.15514,3.15514:4.32064e-13,0.665501,0.334514 +chr1 4880388 . cttcttcttctt . . PASS END=4880399;RU=ctt;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000547172;STUTTERDOWN=0.00625227;STUTTERP=0.902756;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:0.99948:4,4:4-4,4-4:15,16,0,0:4,15:NULL:206.169:366.612,131.36:0,0:0,0.000409236,0.999591 +chr1 4881181 . tgttttgttttgttt . . PASS END=4881195;RU=tgttt;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000427153;STUTTERDOWN=0.00122022;STUTTERP=0.761601;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:54:1:3,3:3-3,3-3:27,27,0,0:3,27:NULL:352.532:366.612,131.36:0,0:0,1.58999e-07,1 +chr1 4882279 . ttattattatta . . PASS END=4882290;RU=tta;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00101288;STUTTERDOWN=0.00289343;STUTTERP=0.952743;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:14:0.407704:4,4:3-4,3-4:3,11,0,0:4,3:NULL:117.024:366.612,131.36:0.169767,0.169767:7.928e-10,0.348483,0.65155 +chr1 4885247 . tatctatctatctatctatctatctatctatctatctatc tatctatctatctatctatctatctatctatc,tatctatctatctatctatctatctatctatctatc . PASS END=4885286;RU=tatc;PERIOD=4;REF=10;GRID=5,13;STUTTERUP=0.011663;STUTTERDOWN=0.0209528;STUTTERP=0.778357;EXPTHRESH=10 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:36:0.950189:8,9:8-10,9-9:15,17,0,3:8,3|9,12:4,1|6,1|7,1:247.157:366.612,131.36:0.653465,0:0.999994,7.2535e-06,3.8647e-26 +chr1 4885324 . ttagttagttagttagttagttag ttagttagttagttagttag,ttagttagttagttagttagttagttag . PASS END=4885347;RU=ttag;PERIOD=4;REF=6;GRID=2,10;STUTTERUP=0.0106893;STUTTERDOWN=0.0102488;STUTTERP=0.797284;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:38:0.874592:5,7:5-7,7-7:18,12,0,7:5,2|7,16:3,4|4,3:251.737:366.612,131.36:0.899738,0:6.23911e-39,0.87467,0.125428 +chr1 4890962 . tgtttgtttgtttgtttgtttgtttgtttgtttgtt tgtttgtttgtttgtttgtttgtttgtttgtt . PASS END=4890997;RU=tgtt;PERIOD=4;REF=9;GRID=5,11;STUTTERUP=0.00118841;STUTTERDOWN=0.0249109;STUTTERP=0.671303;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:33:1:8,8:8-8,8-8:19,7,0,7:8,19:2,1|3,4|6,1|7,1:192.509:366.612,131.36:0,0:0.999993,9.55034e-06,7.84969e-35 +chr1 4894530 . gttggttggttg . . PASS END=4894541;RU=gttg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000375324;STUTTERDOWN=0.00214433;STUTTERP=0.829224;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:46:1:3,3:3-3,3-3:23,21,0,2:3,23:2,2:290.005:366.612,131.36:0,0:0,5.67316e-07,1 +chr1 4895853 . ctcactcactca . . PASS END=4895864;RU=ctca;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000498651;STUTTERDOWN=0.000498651;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:24:0.999177:3,3:3-3,3-3:13,11,0,0:3,13:NULL:150.405:366.612,131.36:0,0:7.84727e-44,0.000490639,0.999514 +chr1 4899661 . acacacacacacacac acacacacacacac . PASS END=4899676;RU=ac;PERIOD=2;REF=8;GRID=3,10;STUTTERUP=0.0155941;STUTTERDOWN=0.0354213;STUTTERP=0.907526;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:46:1.00001:7,7:7-7,7-7:22,19,0,4:7,22:5,1|6,2|7,1:294.528:366.612,131.36:0.0990099,0.0990099:1,1.37938e-06,1.61122e-33 +chr1 4902415 . gagagagagagagagaga . . PASS END=4902432;RU=ga;PERIOD=2;REF=9;GRID=5,13;STUTTERUP=0.0200385;STUTTERDOWN=0.0479256;STUTTERP=0.874408;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:22:0.881129:9,9:8-10,8-10:7,11,0,2:9,7:6,1|8,1:146.361:366.612,131.36:0.696456,0.696456:1.12057e-12,0.0606104,0.939477 +chr1 4902708 . tgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtg . PASS END=4902725;RU=tg;PERIOD=2;REF=9;GRID=4,10;STUTTERUP=0.0222262;STUTTERDOWN=0.0458763;STUTTERP=0.866805;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:19:0.413074:7,7:5-7,5-7:3,14,0,2:7,3:5,2:154.668:366.612,131.36:0.634282,0.634282:0.822065,0.178005,7.49676e-08 +chr1 4903639 . tttttgtttttgtttttgtttttgtttttgtttttg tttttgtttttgtttttgtttttgtttttgtttttgtttttg . PASS END=4903674;RU=tttttg;PERIOD=6;REF=6;GRID=4,10;STUTTERUP=0.00178759;STUTTERDOWN=0.02256;STUTTERP=0.681159;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:12:0.239431:7,7:4-7,4-7:2,10,0,0:7,2:NULL:101.832:366.612,131.36:0.949876,0.949876:3.28881e-07,0.444397,0.555709 +chr1 4903855 . tttgtttgtttg . . PASS END=4903866;RU=tttg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000458804;STUTTERDOWN=0.00221521;STUTTERP=0.984306;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:32:1:3,3:3-3,3-3:20,12,0,0:3,20:NULL:185.345:366.612,131.36:0,0:0,7.09136e-06,0.999994 +chr1 4905039 . tacatacataca . . PASS END=4905050;RU=taca;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000399958;STUTTERDOWN=0.000399958;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:1:3,3:3-3,3-3:23,13,0,0:3,23:NULL:208.626:366.612,131.36:0,0:0,6.88669e-07,1 +chr1 4905095 . tggatggatgga . . PASS END=4905106;RU=tgga;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000455772;STUTTERDOWN=0.00130197;STUTTERP=0.761601;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:0.999923:3,3:3-3,3-3:17,12,0,0:3,17:NULL:174.614:366.612,131.36:0,0:0,4.30267e-05,0.999957 +chr1 4909777 . acacacacacacacacacacacacacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacacacacacacacac,acacacacacacacacacacacacacacacacacacacacacacacacacacac . PASS END=4909828;RU=ac;PERIOD=2;REF=26;GRID=10,30;STUTTERUP=0.0821162;STUTTERDOWN=0.255666;STUTTERP=0.651551;EXPTHRESH=26 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:32:0.430922:25,27:13-25,13-27:9,7,0,15:25,9:5,1|6,1|7,1|10,1|14,1|15,1|16,1|17,2|19,3|23,1|25,1|27,1:229.804:366.612,131.36:4.01858,5.57861:4.85751e-06,0.999988,1.00647e-05 +chr1 4909833 . atgcatgcatgc . . PASS END=4909844;RU=atgc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000600075;STUTTERDOWN=0.0235124;STUTTERP=0.879853;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:25:0.997586:3,3:3-3,3-3:12,13,0,0:3,12:NULL:161.285:366.612,131.36:0,0:1.12194e-39,0.00116656,0.998838 +chr1 4914303 . aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag . PASS END=4914366;RU=aaag;PERIOD=4;REF=16;GRID=10,16;STUTTERUP=0.00870114;STUTTERDOWN=0.0439081;STUTTERP=0.78929;EXPTHRESH=16 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:41:0.963093:13,13:13-13,13-13:8,20,0,13:13,8:3,1|4,2|5,1|8,1|9,1|10,2|11,1|12,4:314.081:366.612,131.36:0,0:0.995673,0.00433868,3.36631e-24 +chr1 4914896 . ggaggaggagga . . PASS END=4914907;RU=gga;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.0010654;STUTTERDOWN=0.0072028;STUTTERP=0.803986;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:49:1:4,4:4-4,4-4:21,28,0,0:4,21:NULL:340.103:366.612,131.36:0,0:0,6.01108e-06,0.999995 +chr1 4916037 . tacatacatacataca . . PASS END=4916052;RU=taca;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000423716;STUTTERDOWN=0.00445084;STUTTERP=0.977258;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:58:1:4,4:4-4,4-4:30,25,0,3:4,30:3,3:372.561:366.612,131.36:0,0:0,5.3936e-09,1 +chr1 4918464 . ggagggagggagggagggagggagggag . . PASS END=4918491;RU=ggag;PERIOD=4;REF=7;GRID=4,10;STUTTERUP=0.0162482;STUTTERDOWN=0.0193535;STUTTERP=0.798653;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:28:0.974661:7,7:7-7,7-7:9,16,0,3:7,9:2,1|3,1|6,1:208.115:366.612,131.36:0,0:4.71002e-17,0.0165889,0.983445 +chr1 4918494 . gagagagagagagagagagagagagagagagagagagagagagagagagaga ga,gagagagagagagagaga . PASS END=4918545;RU=ga;PERIOD=2;REF=26;GRID=1,103;STUTTERUP=0.0404704;STUTTERDOWN=0.174526;STUTTERP=0.63313;EXPTHRESH=26 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:5:0.00284588:1,9:1-13,1-13:0,5,0,0:NULL:NULL:45.8483:366.612,131.36:4.3402,4.33937:0.395201,0.511789,0.0931213 +chr1 4920839 . ttattattatta . . PASS END=4920850;RU=tta;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00094574;STUTTERDOWN=0.00228312;STUTTERP=0.843423;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:22:0.999195:4,4:2-4,2-4:14,7,0,0:4,14:NULL:119.597:366.612,131.36:0.973726,0.973726:7.70714e-44,0.000479133,0.999523 +chr1 4920879 . tggctggctggc . . PASS END=4920890;RU=tggc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.0026921;STUTTERDOWN=0.00802089;STUTTERP=0.968544;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:25:0.999941:3,3:3-3,3-3:17,8,0,0:3,17:NULL:140.755:366.612,131.36:0,0:4.2039e-44,3.98504e-05,0.999963 +chr1 4920889 . gccagccagcca . . PASS END=4920900;RU=gcca;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000477539;STUTTERDOWN=0.0118716;STUTTERP=0.942138;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:27:1:3,3:3-3,3-3:19,8,0,0:3,19:NULL:148.616:366.612,131.36:0,0:0,9.76148e-06,0.999993 +chr1 4921013 . atttatttattt . . PASS END=4921024;RU=attt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000752955;STUTTERDOWN=0.00363543;STUTTERP=0.984306;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:26:0.906659:3,3:3-3,3-3:6,20,0,0:3,6:NULL:204.332:366.612,131.36:0,0:1.3993e-19,0.0448965,0.955176 +chr1 4921202 . ttcttcttcttc . . PASS END=4921213;RU=ttc;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000650795;STUTTERDOWN=0.00371816;STUTTERP=0.969616;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:30:0.999931:4,4:4-4,4-4:17,13,0,0:4,17:NULL:190.356:366.612,131.36:0,0:0,3.68238e-05,0.999964 +chr1 4921293 . atttatttatttattt . . PASS END=4921308;RU=attt;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.00238977;STUTTERDOWN=0.00288461;STUTTERP=0.87689;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:0.983004:4,4:4-4,4-4:9,19,0,3:4,9:3,3:231.443:366.612,131.36:0,0:1.93803e-24,0.00857355,0.991448 +chr1 4922764 . aaataaataaat . . PASS END=4922775;RU=aaat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000598908;STUTTERDOWN=0.00239164;STUTTERP=0.986941;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:30:0.999992:3,3:3-3,3-3:18,12,0,0:3,18:NULL:180.383:366.612,131.36:0,0:0,1.69412e-05,0.999986 +chr1 4925089 . attcattcattcattcattc . . PASS END=4925108;RU=attc;PERIOD=4;REF=5;GRID=2,8;STUTTERUP=0.000827896;STUTTERDOWN=0.00869646;STUTTERP=0.812962;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:50:1.00001:5,5:5-5,5-5:21,26,0,3:5,21:4,3:340.176:366.612,131.36:0,0:0,2.28456e-06,1 +chr1 4930713 . atctatctatct . . PASS END=4930724;RU=atct;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000914429;STUTTERDOWN=0.000914429;STUTTERP=0.580603;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:55:1:3,3:3-3,3-3:30,21,0,4:3,30:2,4:335.927:366.612,131.36:0,0:0,3.17815e-09,1 +chr1 4931717 . agagagagagagag agagagagagag . PASS END=4931730;RU=ag;PERIOD=2;REF=7;GRID=3,10;STUTTERUP=0.00975188;STUTTERDOWN=0.0525836;STUTTERP=0.805557;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/0:61:1:6,7:6-6,7-7:32,29,0,0:6,13|7,19:NULL:403.191:366.612,131.36:0.0990099,0:7.75488e-31,1,1.62485e-09 +chr1 4931731 . acacacacacac . . PASS END=4931742;RU=ac;PERIOD=2;REF=6;GRID=2,10;STUTTERUP=0.00810247;STUTTERDOWN=0.00388432;STUTTERP=0.721291;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:58:1.00001:6,6:5-7,5-7:20,31,0,5:6,20:5,3|6,2:390.258:366.612,131.36:0.342408,0.342408:0,1.01925e-06,1 +chr1 4935229 . ctccctccctccctcc . . PASS END=4935244;RU=ctcc;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000422507;STUTTERDOWN=0.00965556;STUTTERP=0.977178;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:50:1:4,4:4-4,4-4:28,21,0,0:4,28:NULL:301.091:366.612,131.36:0.0990099,0.0990099:0,3.72473e-08,1 +chr1 4936747 . aaacaaacaaac . . PASS END=4936758;RU=aaac;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000417006;STUTTERDOWN=0.00083401;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:48:1:3,3:3-3,3-3:27,18,0,3:3,27:2,3:293.25:366.612,131.36:0,0:0,2.01391e-08,1 +chr1 4937389 . aacaacaacaacaacaac . . PASS END=4937406;RU=aac;PERIOD=3;REF=6;GRID=3,9;STUTTERUP=0.00453893;STUTTERDOWN=0.0214842;STUTTERP=0.908968;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:48:1:6,6:6-6,6-6:31,15,0,2:6,31:5,2:276.512:366.612,131.36:0,0:0,3.35845e-09,1 +chr1 4938098 . agaaagaaagaa . . PASS END=4938109;RU=agaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000594263;STUTTERDOWN=0.00118852;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:1.00001:3,3:3-3,3-3:22,14,0,0:3,22:NULL:218.478:366.612,131.36:0,0:0,2.99825e-06,1 +chr1 4940874 . aaaacaaaacaaaacaaaacaaaacaaaacaaaacaaaacaaaac . . PASS END=4940918;RU=aaaac;PERIOD=5;REF=9;GRID=5,12;STUTTERUP=0.0027175;STUTTERDOWN=0.0183435;STUTTERP=0.617934;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:0.976025:9,9:8-9,8-9:9,14,0,9:9,9:2,1|3,1|4,2|5,2|6,2|8,1:234.928:366.612,131.36:0.46122,0.46122:4.70087e-25,0.0183276,0.98171 +chr1 4941227 . ttgttgttgttg . . PASS END=4941238;RU=ttg;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00100169;STUTTERDOWN=0.00241819;STUTTERP=0.986219;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:34:1:4,4:4-4,4-4:20,11,0,3:4,20:3,3:202.89:366.612,131.36:0,0:0,4.02136e-06,0.999995 +chr1 4941826 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=4941867;RU=gt;PERIOD=2;REF=21;GRID=16,25;STUTTERUP=0.0661015;STUTTERDOWN=0.204766;STUTTERP=0.714787;EXPTHRESH=21 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/0:48:0.869733:20,21:20-22,20-22:13,22,0,12:20,7|21,4|22,2:6,1|7,1|9,1|13,2|14,1|15,2|18,1|19,2|21,1:379.236:366.612,131.36:0.575281,0.55233:1.04935e-10,0.99145,0.00856707 +chr1 4943920 . tctctctctctctctctctctctc . . PASS END=4943943;RU=tc;PERIOD=2;REF=12;GRID=6,15;STUTTERUP=0.0363797;STUTTERDOWN=0.159549;STUTTERP=0.738181;EXPTHRESH=12 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:65:0.93824:12,12:11-12,11-12:18,32,0,14:11,4|12,14:4,1|5,2|6,2|8,1|9,3|10,3|11,2:491.696:366.612,131.36:0.460582,0.460582:1.00657e-17,0.0617049,0.938387 +chr1 4944834 . aaacaaacaaacaaacaaacaaac . . PASS END=4944857;RU=aaac;PERIOD=4;REF=6;GRID=3,9;STUTTERUP=0.00201142;STUTTERDOWN=0.0239717;STUTTERP=0.856733;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:58:1:6,6:6-6,6-6:24,24,0,10:6,24:2,1|3,3|4,4|5,2:388.368:366.612,131.36:0,0:0,2.95896e-07,1 +chr1 4946471 . ataacatataacatataacat . . PASS END=4946491;RU=ataacat;PERIOD=7;REF=3;GRID=1,6;STUTTERUP=0.000983701;STUTTERDOWN=0.00140504;STUTTERP=0.959079;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:45:1:3,3:3-3,3-3:25,20,0,0:3,25:NULL:283.248:366.612,131.36:0,0:0,3.02506e-07,1 +chr1 4957150 . aaacaaacaaac . . PASS END=4957161;RU=aaac;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000390851;STUTTERDOWN=0.000781701;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:47:1:3,3:3-3,3-3:33,12,0,2:3,33:2,2:253.018:366.612,131.36:0,0:0,3.93596e-10,1 +chr1 4958201 . gaggcagaggcagaggca . . PASS END=4958218;RU=gaggca;PERIOD=6;REF=3;GRID=1,6;STUTTERUP=0.000412319;STUTTERDOWN=0.00164926;STUTTERP=0.987382;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:42:1:3,3:3-3,3-3:33,9,0,0:3,33:NULL:219.278:366.612,131.36:0,0:0,5.27952e-10,1 +chr1 4960946 . acacacacacacacacacacacac . . PASS END=4960969;RU=ac;PERIOD=2;REF=12;GRID=8,16;STUTTERUP=0.0251455;STUTTERDOWN=0.0841098;STUTTERP=0.89182;EXPTHRESH=12 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:0.998459:12,12:12-13,12-13:14,14,0,5:12,14:5,2|9,2|11,1:228.619:366.612,131.36:0.19802,0.19802:9.682e-23,0.000546971,0.999454 +chr1 4967461 . ggtggtggtggt . . PASS END=4967472;RU=ggt;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000438827;STUTTERDOWN=0.000877652;STUTTERP=0.999;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:54:1:4,4:4-4,4-4:30,22,0,2:4,30:3,2:335.899:366.612,131.36:0,0:0,5.93903e-09,1 +chr1 4967521 . cttgcttgcttg . . PASS END=4967532;RU=cttg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000445067;STUTTERDOWN=0.00127139;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:50:1:3,3:3-3,3-3:33,16,0,0:3,33:NULL:276.484:366.612,131.36:0.0990099,0.0990099:0,7.17683e-10,1 +chr1 4976938 . cacacacacacacacacacacacacaca cacacacacacacacacacacacacacacacacacacacacacacacacacaca . PASS END=4976965;RU=ca;PERIOD=2;REF=14;GRID=25,31;STUTTERUP=0.066377;STUTTERDOWN=0.106135;STUTTERP=0.708048;EXPTHRESH=14 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:47:0.0489368:27,27:25-29,25-29:0,17,0,29:NULL:5,2|6,2|7,3|9,2|10,1|11,1|12,1|13,3|14,2|15,1|17,3|20,1|21,2|23,2|24,1|26,1|27,1:379.606:366.612,131.36:0.896245,0.896245:0,0,1 +chr1 4977099 . agagagagagagagagagagagagagagagagagagagagagagag agagagagagagagagagagagagagagagagagagagagagag . PASS END=4977144;RU=ag;PERIOD=2;REF=23;GRID=18,29;STUTTERUP=0.131194;STUTTERDOWN=0.18466;STUTTERP=0.617448;EXPTHRESH=23 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:21:0.0233624:22,22:21-26,21-26:0,9,0,9:NULL:6,1|8,1|11,1|12,2|13,2|18,1|22,1:149.084:366.612,131.36:1.98761,1.98761:0.11419,0.539167,0.346797 +chr1 4977990 . tcatcatcatcatca . . PASS END=4978004;RU=tca;PERIOD=3;REF=5;GRID=1,8;STUTTERUP=0.00183321;STUTTERDOWN=0.00962838;STUTTERP=0.911119;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:53:0.999972:5,5:4-5,4-5:30,19,0,4:4,2|5,28:4,4:338.446:366.612,131.36:0.195027,0.195027:0,2.72889e-05,0.999972 +chr1 4983563 . catcatcatcat . . PASS END=4983574;RU=cat;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00177423;STUTTERDOWN=0.00036747;STUTTERP=0.984306;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:58:1:4,4:4-4,4-4:30,26,0,2:4,30:3,2:372.273:366.612,131.36:0,0:0,5.35047e-09,1 +chr1 4985196 . tttgtttgtttg . . PASS END=4985207;RU=tttg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00111968;STUTTERDOWN=0.000559842;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:24:1:3,3:3-3,3-3:19,5,0,0:3,19:NULL:117.877:366.612,131.36:0,0:0,7.5934e-06,0.999994 +chr1 4996877 . tatatatatatatatata tatatatatatata . PASS END=4996894;RU=ta;PERIOD=2;REF=9;GRID=4,10;STUTTERUP=0.0811855;STUTTERDOWN=0.0535307;STUTTERP=0.834777;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:23:0.447467:7,7:5-7,5-7:4,19,0,0:7,4:NULL:192.185:366.612,131.36:0.658248,0.658248:0.876695,0.123405,3.28883e-09 +chr1 4998367 . ctccctccctcc . . PASS END=4998378;RU=ctcc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000423738;STUTTERDOWN=0.00121047;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:25:1:3,3:3-3,3-3:19,6,0,0:3,19:NULL:127.455:366.612,131.36:0,0:0,8.23697e-06,0.999994 +chr1 5001697 . ttttgttttgttttg . . PASS END=5001711;RU=ttttg;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.00097714;STUTTERDOWN=0.00433704;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:40:0.999987:3,3:3-3,3-3:19,21,0,0:3,19:NULL:274.069:366.612,131.36:0,0:0,1.95025e-05,0.99998 +chr1 5003140 . acacacacacacacacacacacacacac acacacacacacacacacacacacac . PASS END=5003167;RU=ac;PERIOD=2;REF=14;GRID=9,16;STUTTERUP=0.0380541;STUTTERDOWN=0.0735496;STUTTERP=0.804637;EXPTHRESH=14 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:50:0.999859:13,13:13-13,13-13:23,24,0,3:12,2|13,21:8,1|9,1|10,1:344.393:366.612,131.36:0,0:1,1.05659e-06,1.4696e-27 +chr1 5005661 . gaggaggaggag . . PASS END=5005672;RU=gag;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000515117;STUTTERDOWN=0.00103023;STUTTERP=0.999;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:22:0.992028:4,4:4-4,4-4:11,11,0,0:4,11:NULL:141.326:366.612,131.36:0,0:1.67609e-36,0.00433231,0.99568 +chr1 5007022 . tttattttattttat . . PASS END=5007036;RU=tttat;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000566783;STUTTERDOWN=0.00113356;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:25:0.998728:3,3:3-3,3-3:13,12,0,0:3,13:NULL:164.765:366.612,131.36:0,0:1.54703e-42,0.000819146,0.999187 +chr1 5008480 . aaacaaacaaacaaacaaacaaacaaacaaac aaacaaacaaacaaacaaacaaacaaac . PASS END=5008511;RU=aaac;PERIOD=4;REF=8;GRID=4,10;STUTTERUP=0.0019428;STUTTERDOWN=0.0193964;STUTTERP=0.815865;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:42:0.999985:7,7:7-7,7-7:18,17,0,7:7,18:2,1|4,5|6,1:280.991:366.612,131.36:0,0:0.999987,1.30011e-05,1.28651e-33 +chr1 5011517 . cacacacacacacacacacacacacacacacacacacacacaca cacacacacacacacacacacacacacacacacacacacaca . PASS END=5011560;RU=ca;PERIOD=2;REF=22;GRID=17,24;STUTTERUP=0.082955;STUTTERDOWN=0.163686;STUTTERP=0.722619;EXPTHRESH=22 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:42:0.781628:21,21:20-21,20-21:10,16,0,16:20,2|21,8:4,1|5,1|6,1|7,2|8,2|11,2|14,1|15,1|16,2|17,1|18,1|19,1:329.553:366.612,131.36:0.35561,0.35561:0.986623,0.0134052,2.41062e-08 +chr1 5011684 . aaaacaaaacaaaacaaaac . . PASS END=5011703;RU=aaaac;PERIOD=5;REF=4;GRID=1,7;STUTTERUP=0.000652366;STUTTERDOWN=0.00314977;STUTTERP=0.719903;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:0.999956:4,4:4-4,4-4:17,19,0,3:4,17:2,1|3,2:265.456:366.612,131.36:0,0:0,4.14353e-05,0.999963 +chr1 5012007 . ctttctttctttctttctttctttctttctttctttctttctttctttctttcttt ctttctttctttctttctttctttctttctttctttcttt,ctttctttctttctttctttctttctttctttctttctttctttcttt . PASS END=5012062;RU=cttt;PERIOD=4;REF=14;GRID=1,15;STUTTERUP=0.00480351;STUTTERDOWN=0.0358318;STUTTERP=0.783942;EXPTHRESH=14 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:25:0.0683737:10,12:1-13,1-13:0,18,0,7:NULL:5,1|6,1|7,2|8,1|12,2:219.863:366.612,131.36:3.69494,2.58175:0.597251,0.37845,0.0244016 +chr1 5013650 . cagagcagagcagagcagagcagagcagag cagagcagagcagagcagagcagag . PASS END=5013679;RU=cagag;PERIOD=5;REF=6;GRID=2,8;STUTTERUP=0.000566388;STUTTERDOWN=0.0109596;STUTTERP=0.716683;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:32:0.999973:5,5:5-5,5-5:18,12,0,2:5,18:4,2:195.346:366.612,131.36:0,0:0.999986,1.7778e-05,5.31604e-39 +chr1 5014848 . cacacacacacacacacacacacacacacacacacacacacaca cacacacacacacacacacacacacacacacacacacacacacacacacaca . PASS END=5014891;RU=ca;PERIOD=2;REF=22;GRID=22,30;STUTTERUP=0.0862458;STUTTERDOWN=0.217284;STUTTERP=0.660877;EXPTHRESH=22 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:62:0.591369:26,26:25-27,25-27:11,24,0,26:25,3|26,8:5,3|6,1|9,2|10,2|13,2|15,1|16,2|17,2|18,3|20,5|21,1|22,1|24,1:478.783:366.612,131.36:0.515042,0.515042:0,0,1 +chr1 5019542 . cgctcgctcgct . . PASS END=5019553;RU=cgct;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000272412;STUTTERDOWN=0.000272412;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:64:1:3,3:3-3,3-3:28,33,0,3:3,28:2,3:436.889:366.612,131.36:0,0:0,1.82732e-08,1 +chr1 5020039 . gccagccagcca . . PASS END=5020050;RU=gcca;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000225486;STUTTERDOWN=0.00064413;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:81:1:3,3:3-3,3-3:50,31,0,0:3,50:NULL:489.516:366.612,131.36:0,0:0,1.08271e-14,1 +chr1 5022514 . ttgttgttgttg . . PASS END=5022525;RU=ttg;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000513738;STUTTERDOWN=0.00102747;STUTTERP=0.999;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:27:0.999007:4,4:4-4,4-4:14,13,0,0:4,14:NULL:169.733:366.612,131.36:0,0:0,0.000700097,0.999302 +chr1 5023422 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=5023467;RU=tg;PERIOD=2;REF=23;GRID=14,21;STUTTERUP=0.0662529;STUTTERDOWN=0.23178;STUTTERP=0.754251;EXPTHRESH=23 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:61:0.928802:18,18:17-18,17-18:20,29,0,12:17,5|18,15:5,1|6,1|8,1|10,3|11,2|12,1|13,1|14,2:459.163:366.612,131.36:0.36513,0.36513:1,0,0 +chr1 5024078 . aataataataataataataataataataataataataataat . . PASS END=5024119;RU=aat;PERIOD=3;REF=14;GRID=11,17;STUTTERUP=0.0413473;STUTTERDOWN=0.132626;STUTTERP=0.639613;EXPTHRESH=14 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:23:0.867285:14,14:14-14,14-14:6,9,0,8:14,6:6,2|8,3|12,1|13,2:167.018:366.612,131.36:0,0:8.86682e-10,0.0435721,0.956499 +chr1 5026610 . ctctctctctctctctctctct ctctctctctctctctct,ctctctctctctctctctctctctct . PASS END=5026631;RU=ct;PERIOD=2;REF=11;GRID=4,16;STUTTERUP=0.0432837;STUTTERDOWN=0.0712442;STUTTERP=0.656322;EXPTHRESH=11 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:40:0.995281:9,13:9-9,12-13:10,23,0,4:9,8|13,2:4,1|7,1|10,1|12,1:294.328:366.612,131.36:0,0.611622:1.05571e-11,1,2.1268e-14 +chr1 5030577 . tccctccctccctccctccctccctccctccctccctccctccctccctccctccctccctccctccc tccc . PASS END=5030644;RU=tccc;PERIOD=4;REF=17;GRID=1,103;STUTTERUP=0.05;STUTTERDOWN=0.05;STUTTERP=0.9;EXPTHRESH=17 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:2:0.00122163:1,1:1-1,1-1:0,2,0,0:NULL:NULL:16.7026:366.612,131.36:0,0:0.157866,0.613891,0.228323 +chr1 5032870 . cacacacacacacacacacacacacacacacacacacacacacacacaca cacacacacacacacacacacacacacacacacacacaca,cacacacacacacacacacacacacacacacacacacacacacacacacaca . PASS END=5032919;RU=ca;PERIOD=2;REF=25;GRID=15,29;STUTTERUP=0.0641016;STUTTERDOWN=0.211413;STUTTERP=0.665765;EXPTHRESH=25 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:42:0.361478:20,26:20-22,21-26:9,14,0,16:19,2|20,7:4,1|6,2|8,1|11,1|12,1|14,1|15,1|16,1|17,3|21,1|23,2|26,1:304.689:366.612,131.36:0.352008,1.57945:6.5147e-08,1,5.81691e-23 +chr1 5034803 . acccacccaccc . . PASS END=5034814;RU=accc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00111913;STUTTERDOWN=0.00220992;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:25:0.994095:3,3:3-3,3-3:11,14,0,0:3,11:NULL:173.794:366.612,131.36:0,0:1.24098e-32,0.00394774,0.996065 +chr1 5042658 . ttgtttgtttgtttgtttgt . . PASS END=5042677;RU=ttgt;PERIOD=4;REF=5;GRID=1,8;STUTTERUP=0.000709739;STUTTERDOWN=0.0067136;STUTTERP=0.784069;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:15:0.149815:5,5:1-5,1-5:2,12,0,0:5,2:NULL:118.069:366.612,131.36:1.10262,1.10262:4.18241e-07,0.608055,0.392004 +chr1 5043950 . gtttgtttgtttgttt . . PASS END=5043965;RU=gttt;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000854786;STUTTERDOWN=0.00628631;STUTTERP=0.959998;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:27:1:4,4:4-4,4-4:20,7,0,0:4,20:NULL:141.455:366.612,131.36:0,0:0,8.42021e-06,0.999994 +chr1 5046122 . ctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctct ctctctctctctctctctctctctctctctctctctctctctctctctctct . PASS END=5046183;RU=ct;PERIOD=2;REF=31;GRID=23,31;STUTTERUP=0.0772172;STUTTERDOWN=0.172855;STUTTERP=0.700092;EXPTHRESH=31 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:7:0.0180503:26,26:26-28,26-28:0,5,0,0:NULL:NULL:44.9841:366.612,131.36:1.02378,1.02378:0.807671,0.182256,0.0101442 +chr1 5046685 . gtggtggtggtg gtggtggtggtggtg . PASS END=5046696;RU=gtg;PERIOD=3;REF=4;GRID=1,8;STUTTERUP=0.0171602;STUTTERDOWN=0.00177499;STUTTERP=0.97711;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/1:56:0.830985:4,5:4-4,4-5:16,40,0,0:4,13|5,3:NULL:431.746:366.612,131.36:0,0.489073:2.65866e-29,4.68503e-05,0.999956 +chr1 5047709 . tatatatatatata . . PASS END=5047722;RU=ta;PERIOD=2;REF=7;GRID=4,10;STUTTERUP=0.0299767;STUTTERDOWN=0.0184794;STUTTERP=0.906729;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:24:0.997365:7,7:7-7,7-7:12,12,0,0:7,12:NULL:161.03:366.612,131.36:0,0:7.77904e-19,0.00182557,0.998178 +chr1 5055484 . tgctgctgctgc . . PASS END=5055495;RU=tgc;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00121365;STUTTERDOWN=0.00346696;STUTTERP=0.952743;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:23:0.999749:4,4:4-4,4-4:15,8,0,0:4,15:NULL:135.046:366.612,131.36:0,0:1.26117e-44,0.00018649,0.999818 +chr1 5064770 . ggctggctggct . . PASS END=5064781;RU=ggct;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000515794;STUTTERDOWN=0.00103159;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:23:0.997253:3,3:3-3,3-3:11,9,0,3:3,11:2,2|3,1:146.383:366.612,131.36:0,0:2.52234e-44,0.000676736,0.999325 +chr1 5066467 . tttccttttccttttccttttccttttccttttcct tttccttttcct . PASS END=5066502;RU=tttcct;PERIOD=6;REF=6;GRID=1,103;STUTTERUP=0.00121116;STUTTERDOWN=0.00409402;STUTTERP=0.870179;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:13:0.0731375:2,2:1-2,1-2:0,13,0,0:NULL:NULL:123.218:366.612,131.36:0.486863,0.486863:0.646631,0.326493,0.0269461 +chr1 5068662 . ctctctctctctctctct ctctctctctctctctctctctctctctctctct,ctctctctctctctctctctctctctctctctctct . PASS END=5068679;RU=ct;PERIOD=2;REF=9;GRID=12,22;STUTTERUP=0.00617843;STUTTERDOWN=0.051731;STUTTERP=0.801909;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:23:0.370893:17,18:15-19,15-19:2,17,0,2:17,2:17,1|18,1:185.617:366.612,131.36:1.48337,1.16983:0,0,1 +chr1 5071017 . atttatttattt . . PASS END=5071028;RU=attt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00139045;STUTTERDOWN=0.00194695;STUTTERP=0.990318;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:19:0.192677:3,3:1-3,1-3:2,17,0,0:3,2:NULL:160.902:366.612,131.36:0.877453,0.877453:4.0823e-06,0.603197,0.396863 +chr1 5073289 . cttccttccttc cttccttc . PASS END=5073300;RU=cttc;PERIOD=4;REF=3;GRID=1,103;STUTTERUP=0.00169221;STUTTERDOWN=0.00397481;STUTTERP=0.874307;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:11:0.0309734:2,2:1-5,1-5:0,11,0,0:NULL:NULL:99.0037:366.612,131.36:0.808615,0.808615:0.0839852,0.432101,0.484103 +chr1 5073332 . ccctctccctctccctctccctct ccctct . PASS END=5073355;RU=ccctct;PERIOD=6;REF=4;GRID=1,103;STUTTERUP=0.0277575;STUTTERDOWN=0.0213607;STUTTERP=0.885324;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:14:0.0763815:1,1:1-2,1-2:0,14,0,0:NULL:NULL:124.041:366.612,131.36:0.44763,0.44763:0.389388,0.484308,0.126391 +chr1 5074855 . aaacaaacaaacaaac aaacaaacaaacaaacaaacaaac . PASS END=5074870;RU=aaac;PERIOD=4;REF=4;GRID=3,9;STUTTERUP=0.000635832;STUTTERDOWN=0.0133619;STUTTERP=0.709421;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:18:0.991707:6,6:6-6,6-6:11,7,0,0:6,11:NULL:109.741:366.612,131.36:0,0:0,0.00239985,0.997608 +chr1 5075461 . acacacacacacacacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacacacacacac . PASS END=5075502;RU=ac;PERIOD=2;REF=21;GRID=19,26;STUTTERUP=0.0506451;STUTTERDOWN=0.282808;STUTTERP=0.688373;EXPTHRESH=21 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:21:0.301404:23,23:19-23,19-23:3,15,0,2:23,3:4,1|11,1:166.597:366.612,131.36:1.03975,1.03975:1.26872e-07,0.221528,0.778513 +chr1 5076742 . aaacaaaacaaaaca . . PASS END=5076756;RU=aaaca;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000825507;STUTTERDOWN=0.001651;STUTTERP=0.732347;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:15:0.999445:3,3:3-3,3-3:14,1,0,0:3,14:NULL:64.0851:366.612,131.36:0,0:1.4013e-45,0.000246601,0.999757 +chr1 5083412 . gggccgggccgggccgggcc . . PASS END=5083431;RU=gggcc;PERIOD=5;REF=4;GRID=1,7;STUTTERUP=0.00053456;STUTTERDOWN=0.00427643;STUTTERP=0.966403;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:50:1:4,4:4-4,4-4:28,16,0,6:4,28:2,2|3,4:304.674:366.612,131.36:0,0:0,1.98004e-08,1 +chr1 5084805 . atgtatgtatgt . . PASS END=5084816;RU=atgt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000465041;STUTTERDOWN=0.00132845;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:46:1:3,3:3-3,3-3:22,20,0,4:3,22:2,4:302.177:366.612,131.36:0,0:0,4.10807e-07,1 +chr1 5087801 . ctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttc ctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttc . PASS END=5087900;RU=ctttc;PERIOD=5;REF=20;GRID=14,20;STUTTERUP=0.0065069;STUTTERDOWN=0.0526096;STUTTERP=0.931221;EXPTHRESH=20 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:45:0.423483:17,17:14-17,14-17:3,25,0,17:17,3:3,1|5,2|6,1|7,3|9,2|10,2|11,1|12,1|14,2|15,1|16,1:371.198:366.612,131.36:0.712734,0.712734:0.949726,0.0503559,3.15541e-13 +chr1 5087905 . tgttgttgttgttgttgttgttgttgttgttgttgttgt tgttgttgttgttgttgttgttgttgttgttgttgt . PASS END=5087943;RU=tgt;PERIOD=3;REF=13;GRID=8,15;STUTTERUP=0.00879339;STUTTERDOWN=0.0391862;STUTTERP=0.96968;EXPTHRESH=13 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:21:0.8976:12,12:11-12,11-12:7,13,0,0:12,7:NULL:150.871:366.612,131.36:0.419363,0.419363:0.970468,0.0295872,7.15236e-11 +chr1 5089647 . tttattttattttat . . PASS END=5089661;RU=tttat;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000556196;STUTTERDOWN=0.00222476;STUTTERP=0.844424;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:25:0.973746:3,3:3-3,3-3:9,16,0,0:3,9:NULL:185.953:366.612,131.36:0.19802,0.19802:6.29408e-30,0.0208076,0.979234 +chr1 5093894 . attttattttatttt . . PASS END=5093908;RU=atttt;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.00204207;STUTTERDOWN=0.00246492;STUTTERP=0.948224;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:23:0.999851:3,3:3-3,3-3:16,7,0,0:3,16:NULL:127.757:366.612,131.36:0,0:9.10844e-44,8.21706e-05,0.999918 +chr1 5094712 . atatatatatatatatatatatatatatatat atatatatatatatatatatatatatatatatatatat . PASS END=5094743;RU=at;PERIOD=2;REF=16;GRID=16,25;STUTTERUP=0.107394;STUTTERDOWN=0.206037;STUTTERP=0.547978;EXPTHRESH=16 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:18:0.17472:19,19:19-22,19-22:2,13,0,0:19,2:NULL:127.165:366.612,131.36:1.09834,1.09834:0,0,1 +chr1 5094744 . acacacacacacacac acacacacacacacacacacacacac . PASS END=5094759;RU=ac;PERIOD=2;REF=8;GRID=5,16;STUTTERUP=0.0501745;STUTTERDOWN=0.0880314;STUTTERP=0.719602;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/1:29:0.998935:8,13:8-12,11-13:9,16,0,3:8,3|11,2|13,4:7,1|8,1|12,1:217.207:366.612,131.36:1.52861,0.57834:9.98027e-36,3.49991e-05,0.999964 +chr1 5094790 . acacacacacacac acacacacacacacac . PASS END=5094803;RU=ac;PERIOD=2;REF=7;GRID=4,12;STUTTERUP=0.0156039;STUTTERDOWN=0.0637734;STUTTERP=0.892451;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:32:0.999827:8,8:8-9,8-9:17,13,0,0:8,17:NULL:188.976:366.612,131.36:0.21692,0.21692:0,8.64003e-05,0.999917 +chr1 5097446 . tttatttattta . . PASS END=5097457;RU=ttta;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000470763;STUTTERDOWN=0.00376606;STUTTERP=0.966669;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:44:0.999863:3,3:3-3,3-3:15,27,0,2:3,15:2,2:320.643:366.612,131.36:0,0:0,9.35685e-05,0.99991 +chr1 5102138 . attttattttattttatttt . . PASS END=5102157;RU=atttt;PERIOD=5;REF=4;GRID=1,7;STUTTERUP=0.00066535;STUTTERDOWN=0.00698903;STUTTERP=0.772892;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:27:0.999837:4,4:4-4,4-4:16,11,0,0:4,16:NULL:162.302:366.612,131.36:0,0:0,0.000129928,0.999872 +chr1 5106170 . atttatttattt . . PASS END=5106181;RU=attt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000505262;STUTTERDOWN=0.00101052;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:19:0.993565:3,3:3-3,3-3:11,8,0,0:3,11:NULL:117.455:366.612,131.36:0,0:1.93051e-36,0.00365293,0.996354 +chr1 5119029 . tgtatgtatgta tgtatgtatgtatgta . PASS END=5119040;RU=tgta;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000418028;STUTTERDOWN=0.000418028;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:23:0.0766832:4,4:1-4,1-4:0,20,0,2:NULL:2,2:194.997:366.612,131.36:0.648798,0.648798:0.129674,0.484023,0.38649 +chr1 5120108 . ttttgttttgttttgttttgttttg ttttgttttgttttgttttgttttgttttg . PASS END=5120132;RU=ttttg;PERIOD=5;REF=5;GRID=3,9;STUTTERUP=0.000559791;STUTTERDOWN=0.0171076;STUTTERP=0.850582;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:21:0.999993:6,6:6-6,6-6:19,2,0,0:6,19:NULL:97.5754:366.612,131.36:0,0:0,8.88581e-06,0.999994 +chr1 5122238 . attttattttatttt . . PASS END=5122252;RU=atttt;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000588098;STUTTERDOWN=0.00117619;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:0.999732:3,3:3-3,3-3:15,14,0,0:3,15:NULL:187.866:366.612,131.36:0,0:0,0.000213579,0.999788 +chr1 5124506 . gtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgt . PASS END=5124523;RU=gt;PERIOD=2;REF=9;GRID=7,14;STUTTERUP=0.0307966;STUTTERDOWN=0.0503984;STUTTERP=0.824465;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:35:0.611604:11,11:10-11,10-11:15,17,0,3:10,3|11,12:5,1|7,1|11,1:250.286:366.612,131.36:0.465241,0.465241:0,0.000149354,0.99985 +chr1 5130293 . ttgttgttgttgttgttgttg ttgttgttgttgttgttgttgttg . PASS END=5130313;RU=ttg;PERIOD=3;REF=7;GRID=5,11;STUTTERUP=0.00608613;STUTTERDOWN=0.0302219;STUTTERP=0.878055;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:28:0.978104:8,8:8-8,8-8:9,14,0,5:8,9:3,1|5,1|6,1|7,2:202.051:366.612,131.36:0,0:1.93379e-43,0.00381364,0.996195 +chr1 5131927 . tttatttatttatttatttattta tttatttatttatttatttatttattta . PASS END=5131950;RU=ttta;PERIOD=4;REF=6;GRID=4,10;STUTTERUP=0.00288162;STUTTERDOWN=0.0200334;STUTTERP=0.793559;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:35:0.999788:7,7:7-7,7-7:15,14,0,6:7,15:3,2|5,2|6,2:231.075:366.612,131.36:0,0:0,4.31738e-05,0.999957 +chr1 5136692 . taattaattaattaat . . PASS END=5136707;RU=taat;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.00182444;STUTTERDOWN=0.0072978;STUTTERP=0.921308;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:0.998591:4,4:4-4,4-4:14,24,0,0:4,14:NULL:285.967:366.612,131.36:0,0:1.12765e-38,0.0011807,0.998823 +chr1 5136778 . tttgtttgtttgtttg . . PASS END=5136793;RU=tttg;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000446129;STUTTERDOWN=0.00356899;STUTTERP=0.826703;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:30:0.893922:4,4:4-4,4-4:6,20,0,4:4,6:2,1|3,3:240.676:366.612,131.36:0.0990099,0.0990099:8.65602e-21,0.0682427,0.931854 +chr1 5137285 . aacaaaacaaaacaaaacaaaacaaaacaaaacaaaacaa . . PASS END=5137324;RU=aacaa;PERIOD=5;REF=8;GRID=5,11;STUTTERUP=0.000609373;STUTTERDOWN=0.0179312;STUTTERP=0.588193;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:0.984495:8,8:8-8,8-8:11,22,0,5:8,11:3,1|5,3|6,1:288.126:366.612,131.36:0.29703,0.29703:2.79445e-37,0.0136302,0.9864 +chr1 5138729 . aaataaataaat . . PASS END=5138740;RU=aaat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00048737;STUTTERDOWN=0.000974738;STUTTERP=0.597956;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:32:0.999729:3,3:3-3,3-3:15,14,0,3:3,15:2,3:203.069:366.612,131.36:0,0:0,0.00013237,0.999871 +chr1 5139656 . cacacacacacacacacacacacacacacacacaca cacacacacacacacacacacacacacacacacacacacacaca,cacacacacacacacacacacacacacacacacacacacacacaca . PASS END=5139691;RU=ca;PERIOD=2;REF=18;GRID=18,26;STUTTERUP=0.0678093;STUTTERDOWN=0.183381;STUTTERP=0.755901;EXPTHRESH=18 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:27:0.833584:22,23:21-23,21-23:5,7,0,14:22,3|23,2:5,2|6,1|7,2|8,1|12,1|15,1|17,2|19,2|20,1|23,1:203.602:366.612,131.36:0.505823,0.613702:0,0,1 +chr1 5144394 . taaataaataaa . . PASS END=5144405;RU=taaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00050916;STUTTERDOWN=0.00101832;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:27:0.99998:3,3:3-3,3-3:19,8,0,0:3,19:NULL:149.522:366.612,131.36:0,0:0,1.52514e-05,0.999986 +chr1 5144427 . aaaagaaaagaaaag . . PASS END=5144441;RU=aaaag;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000577555;STUTTERDOWN=0.00462038;STUTTERP=0.893947;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:1:3,3:3-3,3-3:20,9,0,0:3,20:NULL:162.113:366.612,131.36:0,0:0,1.0044e-05,0.999993 +chr1 5146387 . ctctctctctctct . . PASS END=5146400;RU=ct;PERIOD=2;REF=7;GRID=4,10;STUTTERUP=0.0134387;STUTTERDOWN=0.0199787;STUTTERP=0.911279;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:20:0.919069:7,7:7-7,7-7:7,13,0,0:7,7:NULL:143.578:366.612,131.36:0,0:5.6896e-14,0.0473101,0.952768 +chr1 5151445 . ttgttgttgttg . . PASS END=5151456;RU=ttg;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.0012751;STUTTERDOWN=0.0012751;STUTTERP=0.964893;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:41:1:4,4:4-4,4-4:25,16,0,0:4,25:NULL:244.901:366.612,131.36:0,0:0,3.24408e-07,1 +chr1 5152296 . aagtcaagtcaagtc . . PASS END=5152310;RU=aagtc;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000463085;STUTTERDOWN=0.00370463;STUTTERP=0.966669;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:0.999903:3,3:3-3,3-3:17,21,0,0:3,17:NULL:265.343:366.612,131.36:0,0:0,9.4407e-05,0.999909 +chr1 5155085 . ttgttgttgttgttgttg . . PASS END=5155102;RU=ttg;PERIOD=3;REF=6;GRID=2,9;STUTTERUP=0.000483042;STUTTERDOWN=0.00857592;STUTTERP=0.934187;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:46:0.999279:6,6:5-6,5-6:26,17,0,3:5,2|6,24:5,3:300.68:366.612,131.36:0.298675,0.298675:0,0.000723085,0.999279 +chr1 5162575 . tccccctccccctccccc . . PASS END=5162592;RU=tccccc;PERIOD=6;REF=3;GRID=1,6;STUTTERUP=0.000471754;STUTTERDOWN=0.000471754;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:1:3,3:3-3,3-3:20,17,0,0:3,20:NULL:237.625:366.612,131.36:0,0:0,7.16308e-06,0.999994 +chr1 5163622 . tctctctctctctctc tctctctctctctc . PASS END=5163637;RU=tc;PERIOD=2;REF=8;GRID=2,10;STUTTERUP=0.00755799;STUTTERDOWN=0.0454427;STUTTERP=0.879018;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:39:0.901722:7,7:5-7,5-7:21,18,0,0:5,2|6,2|7,17:NULL:276.157:366.612,131.36:0.847446,0.847446:1,2.2429e-06,1.38999e-28 +chr1 5164581 . tgttttgttttgttt . . PASS END=5164595;RU=tgttt;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.00100869;STUTTERDOWN=0.00243047;STUTTERP=0.761825;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:27:0.995517:3,3:3-3,3-3:12,15,0,0:3,12:NULL:184.023:366.612,131.36:0,0:7.00488e-37,0.0035241,0.996483 +chr1 5170810 . ccaccaccacca . . PASS END=5170821;RU=cca;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000874294;STUTTERDOWN=0.00211065;STUTTERP=0.986219;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:1:4,4:4-4,4-4:24,14,0,0:4,24:NULL:226.062:366.612,131.36:0,0:0,2.6812e-07,1 +chr1 5173050 . ttgttgttgttgttgttg . . PASS END=5173067;RU=ttg;PERIOD=3;REF=6;GRID=3,9;STUTTERUP=0.00110301;STUTTERDOWN=0.00979134;STUTTERP=0.94626;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:0.999862:6,6:6-6,6-6:16,15,0,5:6,16:3,1|4,2|5,2:240.565:366.612,131.36:0,0:0,6.14837e-05,0.999941 +chr1 5173130 . tatttatttatttatttatttatttatttatttatt tatttatttatttatttatttatttatttatttatttatttatt . PASS END=5173165;RU=tatt;PERIOD=4;REF=9;GRID=1,14;STUTTERUP=0.0133366;STUTTERDOWN=0.0431571;STUTTERP=0.582533;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:30:0.986903:11,11:4-11,4-11:10,12,0,7:11,10:4,1|5,1|6,1|7,2|10,2:217.158:366.612,131.36:3.47918,3.47918:4.21791e-43,0.00497608,0.995039 +chr1 5181851 . taaataaataaa . . PASS END=5181862;RU=taaa;PERIOD=4;REF=3;GRID=1,7;STUTTERUP=0.000887059;STUTTERDOWN=0.00044353;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:0.998314:3,3:3-4,3-4:13,21,0,0:3,13:NULL:237.575:366.612,131.36:0.442564,0.442564:7.37232e-40,0.00129224,0.99871 +chr1 5195638 . gggtgggtgggt . . PASS END=5195649;RU=gggt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00124679;STUTTERDOWN=0.00124679;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:28:0.976028:3,3:3-3,3-3:9,19,0,0:3,9:NULL:204.429:366.612,131.36:0.0990099,0.0990099:2.21323e-26,0.0157165,0.984315 +chr1 5199281 . aacaacaacaacaacaacaac aac . PASS END=5199301;RU=aac;PERIOD=3;REF=7;GRID=1,103;STUTTERUP=0.0046419;STUTTERDOWN=0.017069;STUTTERP=0.607625;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP .:.:.:.:.:.:.:.:.:.:.:. +chr1 5199415 . tcaattcaattcaat tcaat . PASS END=5199429;RU=tcaat;PERIOD=5;REF=3;GRID=1,103;STUTTERUP=0.000693526;STUTTERDOWN=0.000693526;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP .:.:.:.:.:.:.:.:.:.:.:. +chr1 5203454 . cacacacacacacacacacacacacacacacacacacacacacaca cacacacacacacacacacacacacacacacacacacacacacacacacacaca . PASS END=5203499;RU=ca;PERIOD=2;REF=23;GRID=24,31;STUTTERUP=0.0859234;STUTTERDOWN=0.21177;STUTTERP=0.681432;EXPTHRESH=23 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:19:0.616492:27,27:27-28,27-28:5,10,0,3:27,5:12,1|16,1|20,1:142.65:366.612,131.36:0.475866,0.475866:0,0,1 +chr1 5204415 . aaaacaaaacaaaac . . PASS END=5204429;RU=aaaac;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000385877;STUTTERDOWN=0.00260878;STUTTERP=0.833561;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:46:1:3,3:3-3,3-3:24,22,0,0:3,24:NULL:289.691:366.612,131.36:0,0:0,6.84593e-07,1 +chr1 5206150 . tattattattat . . PASS END=5206161;RU=tat;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00211652;STUTTERDOWN=0.00544883;STUTTERP=0.859673;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:45:1:4,4:4-4,4-4:24,19,0,2:4,24:3,2:280.676:366.612,131.36:0,0:0,4.49774e-07,1 +chr1 5209488 . tttgtttgtttgtttgtttg . . PASS END=5209507;RU=tttg;PERIOD=4;REF=5;GRID=2,8;STUTTERUP=0.000376872;STUTTERDOWN=0.00727846;STUTTERP=0.761193;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:52:1:5,5:5-5,5-5:24,25,0,3:5,24:4,1|5,2:342.299:366.612,131.36:0,0:0,2.93501e-07,1 +chr1 5212542 . aataaataaata . . PASS END=5212553;RU=aata;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000917999;STUTTERDOWN=0.00221616;STUTTERP=0.843423;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:50:1:3,3:3-3,3-3:29,21,0,0:3,29:NULL:302.188:366.612,131.36:0,0:0,6.61937e-09,1 +chr1 5214463 . acacacacacacacacacacacacacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacac . PASS END=5214514;RU=ac;PERIOD=2;REF=26;GRID=19,42;STUTTERUP=0.0688815;STUTTERDOWN=0.378606;STUTTERP=0.576127;EXPTHRESH=26 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:43:0.179791:38,38:22-39,22-39:2,16,0,22:38,2:7,2|8,1|10,1|12,1|13,1|19,1|20,1|21,1|22,3|24,2|25,1|27,1|28,1|29,1|30,1|33,1|35,1|37,1:332.766:366.612,131.36:8.03867,8.03867:0,0.00525894,0.994754 +chr1 5214858 . acaaacaaacaaacaaacaaacaa acaaacaaacaaacaaacaaacaaacaa . PASS END=5214881;RU=acaa;PERIOD=4;REF=6;GRID=4,10;STUTTERUP=0.00409445;STUTTERDOWN=0.00970691;STUTTERP=0.874633;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:40:0.999981:7,7:7-7,7-7:18,16,0,6:7,18:4,1|5,1|6,4:263.817:366.612,131.36:0,0:0,1.96046e-06,1 +chr1 5215016 . aaacaaacaaacaaac . . PASS END=5215031;RU=aaac;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000580086;STUTTERDOWN=0.00560156;STUTTERP=0.837141;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:42:0.999931:4,4:4-4,4-4:17,22,0,3:4,17:3,3:296.386:366.612,131.36:0,0:0,6.34682e-05,0.99994 +chr1 5215414 . tttgtttgtttgtttgtttgtttgtttg tttgtttgtttgtttgtttgtttg . PASS END=5215441;RU=tttg;PERIOD=4;REF=7;GRID=5,11;STUTTERUP=0.00128534;STUTTERDOWN=0.00734316;STUTTERP=0.792989;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:5:0.0337407:6,6:6-8,6-8:0,4,0,0:NULL:NULL:33.8497:366.612,131.36:0.950082,0.950082:0.12587,0.46186,0.412459 +chr1 5215633 . gtttttttgtttttttgttttttt gttttttt . PASS END=5215656;RU=gttttttt;PERIOD=8;REF=3;GRID=1,103;STUTTERUP=0.00150454;STUTTERDOWN=0.0021498;STUTTERP=0.959445;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:8:0.0699749:1,1:1-1,1-1:0,8,0,0:NULL:NULL:71.2298:366.612,131.36:0,0:0.161111,0.542501,0.296497 +chr1 5222650 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=5222685;RU=gt;PERIOD=2;REF=18;GRID=11,28;STUTTERUP=0.0588622;STUTTERDOWN=0.192446;STUTTERP=0.445834;EXPTHRESH=18 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/0:37:0.999975:14,18:14-15,15-25:15,18,0,3:14,8|15,2|18,5:8,1|10,1|13,1:265.085:366.612,131.36:1.09602,1.47222:1.35483e-06,1,1.7173e-11 +chr1 5222686 . gagagagagagagagagagagagagagagagaga gagagagagagagagagagagagagagagagagagagagagagagagagagagagaga . PASS END=5222719;RU=ga;PERIOD=2;REF=17;GRID=14,35;STUTTERUP=0.0335549;STUTTERDOWN=0.127275;STUTTERP=0.549468;EXPTHRESH=17 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:28:0.0157724:29,29:15-32,15-32:0,16,0,9:NULL:8,1|9,2|11,1|12,2|15,1|25,1|28,1:217.563:366.612,131.36:7.10125,7.10125:1.02035e-15,0.221213,0.778826 +chr1 5223713 . tttgtttgtttg . . PASS END=5223724;RU=tttg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.0010571;STUTTERDOWN=0.00150988;STUTTERP=0.959079;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:46:1:3,3:3-3,3-3:25,19,0,2:3,25:2,2:291.821:366.612,131.36:0,0:0,7.77745e-08,1 +chr1 5224486 . ttccttccttccttccttccttccttccttccttcc ttccttccttccttccttccttccttccttccttccttccttccttccttccttccttcc . PASS END=5224521;RU=ttcc;PERIOD=4;REF=9;GRID=1,18;STUTTERUP=0.00274006;STUTTERDOWN=0.0325523;STUTTERP=0.541449;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:32:0.737032:15,15:4-15,4-15:6,15,0,8:15,6:2,1|5,1|8,1|10,1|13,1|14,3:230.197:366.612,131.36:3.75682,3.75682:0,0.0851395,0.914956 +chr1 5225503 . tttatttatttatttattta . . PASS END=5225522;RU=ttta;PERIOD=4;REF=5;GRID=2,8;STUTTERUP=0.00274016;STUTTERDOWN=0.0124355;STUTTERP=0.729287;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:52:1.00001:5,5:5-5,5-5:22,25,0,5:5,22:2,2|3,2|4,1:355.417:366.612,131.36:0,0:0,2.06382e-06,1 +chr1 5225865 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt,gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=5225896;RU=gt;PERIOD=2;REF=16;GRID=16,32;STUTTERUP=0.0560427;STUTTERDOWN=0.208994;STUTTERP=0.630059;EXPTHRESH=16 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:80:0.347947:22,29:21-22,21-29:15,34,0,28:21,6|22,9:5,2|6,1|8,1|9,1|10,1|11,1|12,1|13,2|14,4|15,1|16,3|17,3|18,1|19,1|21,4|29,1:621.824:366.612,131.36:0.236383,3.71225:0,0,1 +chr1 5228543 . tttatttattta . . PASS END=5228554;RU=ttta;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000448962;STUTTERDOWN=0.00216769;STUTTERP=0.841787;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:44:1:3,3:3-3,3-3:28,12,0,4:3,28:2,3|3,1:251.392:366.612,131.36:0,0:0,7.3749e-09,1 +chr1 5232603 . taataataataa . . PASS END=5232614;RU=taa;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000449277;STUTTERDOWN=0.00216921;STUTTERP=0.984306;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:32:1.00001:4,4:4-4,4-4:23,9,0,0:4,23:NULL:168.543:366.612,131.36:0,0:0,1.06949e-06,1 +chr1 5237129 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . . PASS END=5237166;RU=tg;PERIOD=2;REF=19;GRID=15,22;STUTTERUP=0.0591748;STUTTERDOWN=0.131212;STUTTERP=0.698853;EXPTHRESH=19 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:20:0.813959:19,19:18-19,18-19:7,10,0,2:19,7:7,1|11,1:145.291:366.612,131.36:0.374147,0.374147:2.06632e-09,0.114796,0.885306 +chr1 5237829 . ttctttctttctttctttctttctttctttctttctttctttctttctttctttctttctttctttct ttctttctttctttctttctttctttctttctttctttctttctttctttctttctttctttctttctttctttct . PASS END=5237896;RU=ttct;PERIOD=4;REF=17;GRID=1,21;STUTTERUP=0.0317993;STUTTERDOWN=0.0633323;STUTTERP=0.600355;EXPTHRESH=17 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:16:0.0416806:19,19:14-21,14-21:0,8,0,8:NULL:4,1|5,1|6,2|12,1|14,1|17,1|18,1:130.054:366.612,131.36:1.80051,1.80051:3.71072e-16,0.376297,0.623757 +chr1 5248663 . accaccaccacc . . PASS END=5248674;RU=acc;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000602469;STUTTERDOWN=0.00120493;STUTTERP=0.866591;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:56:1:4,4:4-4,4-4:40,16,0,0:4,40:NULL:299.265:366.612,131.36:0,0:0,8.09204e-12,1 +chr1 5256153 . gagcaagagcaagagcaa . . PASS END=5256170;RU=gagcaa;PERIOD=6;REF=3;GRID=1,6;STUTTERUP=0.0131214;STUTTERDOWN=0.00179594;STUTTERP=0.926667;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:27:0.999993:3,3:3-3,3-3:19,8,0,0:3,19:NULL:143.436:366.612,131.36:0,0:2.84919e-36,1.28151e-05,0.999987 +chr1 5258418 . cacacacacacacacacacacacacacacacacacacaca cacacacacacacacacacacacacacacacacacacacacaca,cacacacacacacacacacacacacacacacacacacacacacacaca . PASS END=5258457;RU=ca;PERIOD=2;REF=20;GRID=5,31;STUTTERUP=0.0813038;STUTTERDOWN=0.229074;STUTTERP=0.498964;EXPTHRESH=20 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:64:0.49556:22,24:22-22,8-28:24,16,0,20:21,6|22,18:5,1|10,1|11,1|13,1|14,1|15,1|16,5|17,3|18,1|19,1|20,2|22,1|24,1:437.329:366.612,131.36:0,6.46634:0,4.22087e-09,1 +chr1 5258712 . gtttgtttgtttgtttgttt . . PASS END=5258731;RU=gttt;PERIOD=4;REF=5;GRID=1,8;STUTTERUP=0.00114067;STUTTERDOWN=0.0101258;STUTTERP=0.769145;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:59:1:5,5:2-5,2-5:32,19,0,7:5,32:2,1|3,2|4,4:353.064:366.612,131.36:0.5093,0.5093:0,8.45447e-10,1 +chr1 5259167 . gagagagagagagagaga . . PASS END=5259184;RU=ga;PERIOD=2;REF=9;GRID=5,12;STUTTERUP=0.013888;STUTTERDOWN=0.0674875;STUTTERP=0.89086;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:34:0.997238:9,9:8-9,8-9:22,12,0,0:8,3|9,19:NULL:205.731:366.612,131.36:0.253975,0.253975:1.4656e-32,0.00277942,0.99723 +chr1 5260536 . agagagagagag . . PASS END=5260547;RU=ag;PERIOD=2;REF=6;GRID=3,9;STUTTERUP=0.00487578;STUTTERDOWN=0.00348212;STUTTERP=0.981517;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:42:1:6,6:6-6,6-6:24,15,0,3:6,24:4,1|5,2:257.581:366.612,131.36:0,0:0,3.27837e-07,1 +chr1 5261841 . accctgtgaggggagcacaccctgtgaggggagcacaccctgtgaggggagcac . . PASS END=5261894;RU=accctgtgaggggagcac;PERIOD=18;REF=3;GRID=1,6;STUTTERUP=0.05;STUTTERDOWN=0.05;STUTTERP=0.9;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:40:0.989161:3,3:3-3,3-3:12,25,0,3:3,12:2,3:307.882:366.612,131.36:0.19802,0.19802:1.21564e-13,0.0108002,0.989224 +chr1 5274498 . cacacacacacacacacacacacacacaca . . PASS END=5274527;RU=ca;PERIOD=2;REF=15;GRID=9,19;STUTTERUP=0.0661637;STUTTERDOWN=0.1282;STUTTERP=0.818338;EXPTHRESH=15 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:0.827913:15,15:12-16,12-16:14,11,0,4:14,3|15,11:5,1|10,1|13,2:198.033:366.612,131.36:1.07834,1.07834:8.4421e-11,0.171242,0.828827 +chr1 5275399 . ccaaccaaccaaccaa . . PASS END=5275414;RU=ccaa;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000649646;STUTTERDOWN=0.0018558;STUTTERP=0.941457;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:0.992288:4,4:4-4,4-4:10,26,0,2:4,10:3,2:288.018:366.612,131.36:0.29703,0.29703:1.16967e-32,0.00604591,0.99397 +chr1 5277383 . tctctctctctctctctctctctctctctctctctctctctctctc tctctctctctctctctctctctc,tctctctctctctctctctctctctctctctctctctctctc . PASS END=5277428;RU=tc;PERIOD=2;REF=23;GRID=9,24;STUTTERUP=0.0510786;STUTTERDOWN=0.305161;STUTTERP=0.673503;EXPTHRESH=23 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:30:0.898518:12,21:12-21,20-21:11,10,0,7:12,2|20,4|21,5:5,1|7,1|9,1|10,3|14,1:208.996:366.612,131.36:3.65753,0.35561:1,3.34413e-09,4.59526e-18 +chr1 5287020 . ctttctttcttt . . PASS END=5287031;RU=cttt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000469252;STUTTERDOWN=0.00134048;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:34:0.999962:3,3:3-3,3-3:18,16,0,0:3,18:NULL:226.214:366.612,131.36:0,0:0,4.26436e-05,0.999957 +chr1 5287167 . cactcactcact . . PASS END=5287178;RU=cact;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000534042;STUTTERDOWN=0.00106808;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:30:0.997619:3,3:3-3,3-3:13,17,0,0:3,13:NULL:209.212:366.612,131.36:0,0:2.21685e-42,0.00140441,0.998602 +chr1 5292757 . tatttatttatttatt . . PASS END=5292772;RU=tatt;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.00136424;STUTTERDOWN=0.00605525;STUTTERP=0.999;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:57:1:4,4:4-4,4-4:24,28,0,5:4,24:3,5:381.227:366.612,131.36:0,0:0,2.152e-07,1 +chr1 5293618 . acccacccaccc . . PASS END=5293629;RU=accc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00124042;STUTTERDOWN=0.00124042;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:7:0.286812:3,3:1-4,1-4:2,5,0,0:3,2:NULL:56.0438:366.612,131.36:0.4771,0.4771:6.95321e-07,0.320178,0.679833 +chr1 5296079 . tctctctctctc tctctctctc . PASS END=5296090;RU=tc;PERIOD=2;REF=6;GRID=2,9;STUTTERUP=0.0110614;STUTTERDOWN=0.0227243;STUTTERP=0.872577;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/0:30:0.999768:5,6:5-6,6-6:23,7,0,0:5,6|6,17:NULL:167.987:366.612,131.36:0.323567,0:3.67971e-28,0.999766,0.000235612 +chr1 5297215 . ttattattatta . . PASS END=5297226;RU=tta;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00101619;STUTTERDOWN=0.00343507;STUTTERP=0.840664;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:68:1:4,4:4-4,4-4:30,36,0,2:4,30:3,2:473.448:366.612,131.36:0,0:0,3.80989e-08,1 +chr1 5301831 . aaagaaagaaag . . PASS END=5301842;RU=aaag;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00041617;STUTTERDOWN=0.000832339;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:49:1:3,3:3-3,3-3:29,20,0,0:3,29:NULL:294.546:366.612,131.36:0,0:0,7.70578e-09,1 +chr1 5303346 . tttgtttgtttgtttg . . PASS END=5303361;RU=tttg;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000534591;STUTTERDOWN=0.00427668;STUTTERP=0.966669;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:0.997585:4,4:4-4,4-4:13,20,0,0:4,13:NULL:228.538:366.612,131.36:0,0:1.00053e-42,0.00188801,0.998117 +chr1 5303465 . taggtaggtagg . . PASS END=5303476;RU=tagg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000437018;STUTTERDOWN=0.000437018;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:1:3,3:3-3,3-3:23,8,0,2:3,23:2,2:179.066:366.612,131.36:0,0:0,4.32502e-07,1 +chr1 5304109 . caaagcaaagcaaagcaaagcaaagcaaagcaaagcaaagcaaagcaaag caaagcaaagcaaagcaaagcaaagcaaagcaaagcaaagcaaagcaaagcaaag . PASS END=5304158;RU=caaag;PERIOD=5;REF=10;GRID=8,14;STUTTERUP=0.000650369;STUTTERDOWN=0.0216225;STUTTERP=0.550964;EXPTHRESH=10 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:43:0.990926:11,11:11-11,11-11:10,24,0,9:11,10:4,2|5,1|7,1|8,3|9,1|10,1:325.961:366.612,131.36:0,0:4.2039e-45,0.00453009,0.995484 +chr1 5305886 . acacacacacacacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacac . PASS END=5305925;RU=ac;PERIOD=2;REF=20;GRID=16,39;STUTTERUP=0.063061;STUTTERDOWN=0.255117;STUTTERP=0.695012;EXPTHRESH=20 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/1:54:0.338605:20,37:20-20,19-37:16,21,0,16:19,5|20,11:6,1|8,2|10,3|11,1|12,1|13,2|16,2|17,1|18,1|19,1|36,1:415.777:366.612,131.36:0,8.43581:1.53622e-12,0.00330418,0.996707 +chr1 5306965 . atcatcatcatc . . PASS END=5306976;RU=atc;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000878179;STUTTERDOWN=0.000614833;STUTTERP=0.959079;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:1:4,4:4-4,4-4:29,9,0,0:4,29:NULL:194.503:366.612,131.36:0,0:0,1.60491e-08,1 +chr1 5312273 . tctctctctctctctc . . PASS END=5312288;RU=tc;PERIOD=2;REF=8;GRID=2,12;STUTTERUP=0.00792062;STUTTERDOWN=0.155851;STUTTERP=0.626916;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:0.987404:8,8:6-8,6-8:26,9,0,0:6,4|7,2|8,20:NULL:212.78:366.612,131.36:0.850448,0.850448:1.56833e-41,0.0126277,0.987401 +chr1 5312289 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=5312324;RU=tg;PERIOD=2;REF=18;GRID=13,23;STUTTERUP=0.0313563;STUTTERDOWN=0.296569;STUTTERP=0.498197;EXPTHRESH=18 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/0:43:0.868327:17,18:17-17,17-20:13,14,0,15:16,2|17,9|18,2:5,2|9,1|11,2|12,2|15,4|16,4:320.234:366.612,131.36:0.417958,1.14937:0.120619,0.879405,7.83593e-05 +chr1 5312324 . gagagagagagagagagagagagagagagagaga . . PASS END=5312357;RU=ga;PERIOD=2;REF=17;GRID=14,22;STUTTERUP=0.0192005;STUTTERDOWN=0.125404;STUTTERP=0.409973;EXPTHRESH=17 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:40:0.999867:17,17:17-19,17-19:17,19,0,3:17,17:5,1|8,1|11,1:278.5:366.612,131.36:0.507951,0.507951:3.43283e-35,6.11318e-05,0.999941 +chr1 5318871 . acacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacac . PASS END=5318898;RU=ac;PERIOD=2;REF=14;GRID=14,22;STUTTERUP=0.0464777;STUTTERDOWN=0.146426;STUTTERP=0.821766;EXPTHRESH=14 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:35:0.960449:19,19:17-19,17-19:13,14,0,7:18,2|19,11:7,1|9,1|10,2|12,1|13,1|15,1:251.315:366.612,131.36:0.628225,0.628225:0,0,1 +chr1 5327635 . ctctttccctctttccctctttcc ctctttcc . PASS END=5327658;RU=ctctttcc;PERIOD=8;REF=3;GRID=1,6;STUTTERUP=0.00294351;STUTTERDOWN=0.00588212;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:20:0.325739:1,1:1-3,1-3:0,19,0,0:NULL:NULL:172.932:366.612,131.36:0.978146,0.978146:0.565034,0.384922,0.0501882 +chr1 5333023 . tatatatatatatata tatatatatatatatatatata . PASS END=5333038;RU=ta;PERIOD=2;REF=8;GRID=7,16;STUTTERUP=0.0626307;STUTTERDOWN=0.0935027;STUTTERP=0.848865;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:19:0.441393:11,11:10-13,10-13:9,9,0,0:10,2|11,7:NULL:122.896:366.612,131.36:1.11059,1.11059:1.78662e-29,0.0036561,0.996353 +chr1 5334011 . acacacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacac,acacacacacacacacacacacacacacacacacacacac . PASS END=5334042;RU=ac;PERIOD=2;REF=16;GRID=16,24;STUTTERUP=0.0512797;STUTTERDOWN=0.235399;STUTTERP=0.742016;EXPTHRESH=16 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:33:0.702044:19,20:19-21,19-21:7,12,0,13:19,3|20,4:6,2|7,1|8,4|9,1|12,1|13,2|14,2:248.604:366.612,131.36:0.830386,0.473387:0,0,1 +chr1 5337377 . tttatttattta . . PASS END=5337388;RU=ttta;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000495581;STUTTERDOWN=0.000991161;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:40:1:3,3:3-3,3-3:24,16,0,0:3,24:NULL:237.645:366.612,131.36:0,0:0,6.40429e-07,1 +chr1 5340739 . tatttatttatt . . PASS END=5340750;RU=tatt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000516771;STUTTERDOWN=0.00103354;STUTTERP=0.73234;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:25:0.999984:3,3:3-3,3-3:18,7,0,0:3,18:NULL:134.707:366.612,131.36:0,0:0,1.97523e-05,0.99998 +chr1 5341947 . aaggaaggaaggaaggaaggaaggaagg . . PASS END=5341974;RU=aagg;PERIOD=4;REF=7;GRID=4,10;STUTTERUP=0.00229454;STUTTERDOWN=0.0168709;STUTTERP=0.77222;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:0.99808:7,7:7-7,7-7:13,15,0,3:7,13:2,1|4,1|6,1:218.78:366.612,131.36:0,0:7.99043e-36,0.0014034,0.998602 +chr1 5357169 . gggtgggtgggt . . PASS END=5357180;RU=gggt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.0022373;STUTTERDOWN=0.0022373;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:15:0.608255:3,3:3-3,3-3:4,11,0,0:3,4:NULL:112:366.612,131.36:0.19802,0.19802:2.62201e-11,0.214101,0.785943 +chr1 5365050 . cctccctccctc . . PASS END=5365061;RU=cctc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000598978;STUTTERDOWN=0.00119794;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:53:1:3,3:3-3,3-3:31,22,0,0:3,31:NULL:322.918:366.612,131.36:0,0:0,4.07982e-09,1 +chr1 5368230 . ctcttgcgctcttgcgctcttgcgctcttgcg ctcttgcgctcttgcgctcttgcg . PASS END=5368261;RU=ctcttgcg;PERIOD=8;REF=4;GRID=1,14;STUTTERUP=0.000611106;STUTTERDOWN=0.00290603;STUTTERP=0.839063;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:49:0.882176:3,3:3-11,3-11:20,27,0,2:3,20:2,1|11,1:362.233:366.612,131.36:3.12646,3.12646:0.882095,0.118006,0 +chr1 5368294 . cttgcactcttgcactcttgcact . . PASS END=5368317;RU=cttgcact;PERIOD=8;REF=3;GRID=1,6;STUTTERUP=0.00180538;STUTTERDOWN=0.00128883;STUTTERP=0.847027;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:0.997641:3,3:3-3,3-3:14,25,0,0:3,14:NULL:292.044:366.612,131.36:0,0:2.19494e-38,0.002326,0.997678 +chr1 5369349 . gtttgtttgttt . . PASS END=5369360;RU=gttt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000480263;STUTTERDOWN=0.000480263;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:32:1:3,3:3-3,3-3:19,13,0,0:3,19:NULL:193.077:366.612,131.36:0,0:0,7.50507e-06,0.999994 +chr1 5369470 . atatatatatatatatatatatatatatatatatat atatatatatatatatatatatatat . PASS END=5369505;RU=at;PERIOD=2;REF=18;GRID=10,17;STUTTERUP=0.0988351;STUTTERDOWN=0.0651593;STUTTERP=0.708481;EXPTHRESH=18 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:17:0.65517:13,13:13-14,13-14:5,11,0,0:13,5:NULL:125.134:366.612,131.36:0.44763,0.44763:1,0,0 +chr1 5374204 . tttgtttgtttgtttg . . PASS END=5374219;RU=tttg;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.00104083;STUTTERDOWN=0.00104083;STUTTERP=0.976453;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:30:0.999829:4,4:3-4,3-4:16,13,0,0:4,16:NULL:181.117:366.612,131.36:0.390807,0.390807:0,0.000140681,0.999864 +chr1 5380595 . acacacacacac . . PASS END=5380606;RU=ac;PERIOD=2;REF=6;GRID=3,9;STUTTERUP=0.00429117;STUTTERDOWN=0.0101555;STUTTERP=0.936705;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:23:0.995403:6,6:6-6,6-6:11,12,0,0:6,11:NULL:153.893:366.612,131.36:0,0:6.47033e-27,0.00291211,0.997095 +chr1 5380856 . tctgtctgtctg . . PASS END=5380867;RU=tctg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000401051;STUTTERDOWN=0.00160419;STUTTERP=0.987382;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:48:1:3,3:3-3,3-3:33,15,0,0:3,33:NULL:268.978:366.612,131.36:0,0:0,8.82469e-10,1 +chr1 5380890 . cacacacacacacacacacacacacacacacacacacacacacacacacacaca cacacacacacacacacacacacacacacacacacacacaca,cacacacacacacacacacacacacacacacacacacacacacacacaca . PASS END=5380943;RU=ca;PERIOD=2;REF=27;GRID=17,28;STUTTERUP=0.102568;STUTTERDOWN=0.165361;STUTTERP=0.811942;EXPTHRESH=27 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:55:0.293781:21,25:21-21,21-28:16,16,0,23:20,2|21,14:7,2|8,1|9,2|11,1|12,2|13,1|14,2|16,1|17,1|18,1|19,2|20,4|21,1|23,1|25,1:422.02:366.612,131.36:0,1.90161:0.574979,0.425105,0 +chr1 5382870 . gaggaagaggaagaggaa . . PASS END=5382887;RU=gaggaa;PERIOD=6;REF=3;GRID=1,6;STUTTERUP=0.000844097;STUTTERDOWN=0.00203775;STUTTERP=0.843423;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:45:1.00001:3,3:3-3,3-3:21,18,0,6:3,21:2,6:284.486:366.612,131.36:0,0:0,1.09993e-06,1 +chr1 5384698 . agaaagaaagaaagaa . . PASS END=5384713;RU=agaa;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.00068354;STUTTERDOWN=0.00390524;STUTTERP=0.749297;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:9:0.951299:4,4:4-4,4-4:8,1,0,0:4,8:NULL:42.0356:366.612,131.36:0,0:8.24126e-27,0.0253717,0.974677 +chr1 5384783 . gagagagagagagagagagagagagagagagagagagagagagagagagagagagagagagagagaga gagagagagagagagagagagagagagagagagagagagagagagagagagagagagagagagagagagagaga . PASS END=5384850;RU=ga;PERIOD=2;REF=34;GRID=22,40;STUTTERUP=0.0667891;STUTTERDOWN=0.201259;STUTTERP=0.606804;EXPTHRESH=34 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:14:0.0170297:37,37:25-38,25-38:0,6,0,7:NULL:5,1|15,1|17,1|18,1|21,1|25,1|37,1:109.943:366.612,131.36:4.88194,4.88194:9.74187e-08,0.688895,0.311118 +chr1 5384864 . agaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaa agaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaa . PASS END=5384923;RU=agaa;PERIOD=4;REF=15;GRID=11,17;STUTTERUP=0.00769142;STUTTERDOWN=0.0378094;STUTTERP=0.443125;EXPTHRESH=15 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:24:0.811644:14,14:14-14,14-14:5,12,0,7:14,5:5,1|7,2|10,2|13,1|14,1:181.954:366.612,131.36:0,0:0.884619,0.115484,8.42783e-10 +chr1 5390035 . cctcctcctcct . . PASS END=5390046;RU=cct;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00106309;STUTTERDOWN=0.00179681;STUTTERP=0.949235;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:50:1:4,4:4-4,4-4:30,20,0,0:4,30:NULL:303.92:366.612,131.36:0,0:0,1.00316e-08,1 +chr1 5391563 . tttctttctttc . . PASS END=5391574;RU=tttc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000920478;STUTTERDOWN=0.00311152;STUTTERP=0.940969;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:42:1.00001:3,3:3-3,3-3:20,19,0,3:3,20:2,3:279.261:366.612,131.36:0,0:0,3.85061e-06,1 +chr1 5393656 . tttatttattta . . PASS END=5393667;RU=ttta;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000459543;STUTTERDOWN=0.00131275;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:1:3,3:3-3,3-3:24,13,0,0:3,24:NULL:212.9:366.612,131.36:0,0:0,3.37619e-07,1 +chr1 5400536 . ggggtgggggtgggggtg . . PASS END=5400553;RU=ggggtg;PERIOD=6;REF=3;GRID=1,6;STUTTERUP=0.00194563;STUTTERDOWN=0.00388988;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:32:0.952146:3,3:2-3,2-3:8,22,0,2:3,8:2,2:250.206:366.612,131.36:0.309,0.309:3.00685e-21,0.0377962,0.962271 +chr1 5400652 . taaataaataaataaa . . PASS END=5400667;RU=taaa;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.00102441;STUTTERDOWN=0.00993584;STUTTERP=0.982112;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:0.999912:4,4:4-4,4-4:18,18,0,0:4,18:NULL:240.227:366.612,131.36:0,0:0,8.34338e-05,0.999918 +chr1 5401591 . caaacaaacaaacaaacaaa . . PASS END=5401610;RU=caaa;PERIOD=4;REF=5;GRID=2,8;STUTTERUP=0.00146004;STUTTERDOWN=0.00907414;STUTTERP=0.815822;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:43:1:5,5:5-5,5-5:20,21,0,2:5,20:3,1|4,1:287.227:366.612,131.36:0,0:0,1.04435e-05,0.999993 +chr1 5407272 . aataaataaataaata . . PASS END=5407287;RU=aata;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000246255;STUTTERDOWN=0.00362203;STUTTERP=0.846129;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:52:1:4,4:4-4,4-4:33,17,0,2:4,33:3,2:299.722:366.612,131.36:0,0:0,6.38711e-10,1 +chr1 5411524 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . . PASS END=5411557;RU=gt;PERIOD=2;REF=17;GRID=9,20;STUTTERUP=0.0520819;STUTTERDOWN=0.19251;STUTTERP=0.795626;EXPTHRESH=17 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:65:0.878383:17,17:12-17,12-17:26,17,0,21:16,8|17,18:5,2|7,3|9,2|10,2|12,4|13,4|15,3|16,1:447.231:366.612,131.36:1.11306,1.11306:1.04022e-17,0.121721,0.878381 +chr1 5412318 . gtgtgtgtgtgtgtgtgt . . PASS END=5412335;RU=gt;PERIOD=2;REF=9;GRID=4,13;STUTTERUP=0.0259761;STUTTERDOWN=0.0508707;STUTTERP=0.902778;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:24:0.340536:9,9:7-10,7-10:16,7,0,0:7,2|9,12|10,2:NULL:147.298:366.612,131.36:1.18233,1.18233:5.7347e-20,0.61885,0.381204 +chr1 5412585 . gcaggcaggcag . . PASS END=5412596;RU=gcag;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000381611;STUTTERDOWN=0.000381611;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:42:1:3,3:3-3,3-3:29,11,0,2:3,29:2,2:231.295:366.612,131.36:0,0:0,5.35748e-09,1 +chr1 5414201 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt,gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=5414252;RU=gt;PERIOD=2;REF=26;GRID=17,32;STUTTERUP=0.0775039;STUTTERDOWN=0.255717;STUTTERP=0.680562;EXPTHRESH=26 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:36:0.277101:22,30:21-22,20-32:13,10,0,12:20,3|21,2|22,8:5,1|9,2|10,1|11,1|13,1|14,2|16,1|17,1|21,1|29,1:264.281:366.612,131.36:0.19802,4.38695:0.000455048,0.999546,6.6337e-28 +chr1 5420026 . atgtatgtatgt . . PASS END=5420037;RU=atgt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000914793;STUTTERDOWN=0.000914793;STUTTERP=0.789911;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:1:3,3:3-3,3-3:20,11,0,0:3,20:NULL:182.254:366.612,131.36:0,0:0,6.34021e-06,0.999994 +chr1 5421453 . agaaaagaaaagaaa . . PASS END=5421467;RU=agaaa;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000910741;STUTTERDOWN=0.00219863;STUTTERP=0.986219;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:40:1:3,3:3-3,3-3:25,13,0,2:3,25:2,2:232.041:366.612,131.36:0,0:0,1.245e-07,1 +chr1 5421483 . aacaaacaaacaaaca . . PASS END=5421498;RU=aaca;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.00112719;STUTTERDOWN=0.00381026;STUTTERP=0.940969;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:0.999137:4,4:4-4,4-4:14,12,0,5:4,14:2,2|3,3:205.526:366.612,131.36:0,0:2.63836e-41,0.000376896,0.999628 +chr1 5421960 . tttgtttgtttg . . PASS END=5421971;RU=tttg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000587705;STUTTERDOWN=0.00335771;STUTTERP=0.969616;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:24:0.999768:3,3:3-3,3-3:15,7,0,2:3,15:2,2:142.043:366.612,131.36:0,0:0,9.03633e-05,0.999911 +chr1 5429464 . gggtgggtgggt . . PASS END=5429475;RU=gggt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00190887;STUTTERDOWN=0.000954438;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:26:0.947173:3,3:3-3,3-3:8,18,0,0:3,8:NULL:189.027:366.612,131.36:0.19802,0.19802:4.74538e-22,0.0328576,0.967201 +chr1 5439295 . aaataaataaat . . PASS END=5439306;RU=aaat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000387073;STUTTERDOWN=0.000387073;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:54:1:3,3:3-3,3-3:37,15,0,2:3,37:2,2:300.503:366.612,131.36:0,0:0,4.26324e-11,1 +chr1 5439862 . aaaaacaaaaacaaaaac . . PASS END=5439879;RU=aaaaac;PERIOD=6;REF=3;GRID=1,6;STUTTERUP=0.0011597;STUTTERDOWN=0.000811931;STUTTERP=0.959079;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:55:1:3,3:3-3,3-3:37,18,0,0:3,37:NULL:309.002:366.612,131.36:0,0:0,7.11533e-11,1 +chr1 5439880 . caagcaagcaag . . PASS END=5439891;RU=caag;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000405689;STUTTERDOWN=0.000811377;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:55:1:3,3:3-3,3-3:35,18,0,2:3,35:2,2:316.843:366.612,131.36:0,0:0,1.11968e-10,1 +chr1 5440024 . aaaacaaaacaaaac . . PASS END=5440038;RU=aaaac;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000423121;STUTTERDOWN=0.00169246;STUTTERP=0.987382;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:46:1:3,3:3-3,3-3:30,14,0,2:3,30:2,2:270.182:366.612,131.36:0,0:0,1.14812e-08,1 +chr1 5448684 . gtggtggtggtg . . PASS END=5448695;RU=gtg;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00118203;STUTTERDOWN=0.000413782;STUTTERP=0.941457;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:1.00001:4,4:4-4,4-4:20,13,0,2:4,20:3,2:202.444:366.612,131.36:0,0:0,3.08094e-06,1 +chr1 5448817 . aaacaaacaaacaaacaaacaaac . . PASS END=5448840;RU=aaac;PERIOD=4;REF=6;GRID=3,9;STUTTERUP=0.00132747;STUTTERDOWN=0.0115574;STUTTERP=0.842044;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:24:0.99861:6,6:6-6,6-6:13,8,0,3:6,13:3,1|4,2:144.918:366.612,131.36:0,0:1.36302e-38,0.000751979,0.999249 +chr1 5448857 . aaacaaaacaaaaca . . PASS END=5448871;RU=aaaca;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000513597;STUTTERDOWN=0.0045592;STUTTERP=0.839024;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:17:0.984248:3,3:3-3,3-3:9,8,0,0:3,9:NULL:107.217:366.612,131.36:0,0:1.10938e-30,0.00908823,0.990933 +chr1 5449710 . tttctttctttc . . PASS END=5449721;RU=tttc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000776045;STUTTERDOWN=0.00221688;STUTTERP=0.952743;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:41:1:3,3:3-3,3-3:25,16,0,0:3,25:NULL:243.822:366.612,131.36:0,0:0,1.68455e-07,1 +chr1 5450202 . acacacacacacacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacacacacacacacac . PASS END=5450241;RU=ac;PERIOD=2;REF=20;GRID=22,30;STUTTERUP=0.072874;STUTTERDOWN=0.235864;STUTTERP=0.624576;EXPTHRESH=20 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:54:0.998109:25,25:25-27,25-27:14,20,0,18:25,14:5,3|6,3|7,2|9,1|11,1|14,1|15,1|17,2|18,2|22,1|25,1:392.37:366.612,131.36:0.480581,0.480581:0,0,1 +chr1 5457139 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg,tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=5457182;RU=tg;PERIOD=2;REF=22;GRID=13,24;STUTTERUP=0.0766516;STUTTERDOWN=0.231207;STUTTERP=0.630215;EXPTHRESH=22 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:45:0.986189:19,20:16-21,19-21:11,21,0,10:19,6|20,5:8,1|14,2|15,2|16,1|17,1|18,1|19,2:333.91:366.612,131.36:0.831565,0.667418:0.999903,9.76201e-05,1.34211e-13 +chr1 5457182 . gagagagagagagagagagagaga . . PASS END=5457205;RU=ga;PERIOD=2;REF=12;GRID=4,16;STUTTERUP=0.0265573;STUTTERDOWN=0.0572119;STUTTERP=0.519117;EXPTHRESH=12 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:50:0.877325:12,12:7-13,7-13:24,22,0,2:8,2|12,19|13,3:8,1|12,1:339.915:366.612,131.36:2.23609,2.23609:8.7441e-43,0.00860933,0.991412 +chr1 5458563 . gttggttggttg . . PASS END=5458574;RU=gttg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00049104;STUTTERDOWN=0.00049104;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:34:0.999991:3,3:3-3,3-3:18,14,0,2:3,18:2,2:209.978:366.612,131.36:0,0:0,1.73614e-05,0.999986 +chr1 5467842 . ttgtttgtttgt . . PASS END=5467853;RU=ttgt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000440376;STUTTERDOWN=0.00297722;STUTTERP=0.833561;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:32:1.00001:3,3:3-3,3-3:22,8,0,2:3,22:2,2:179.754:366.612,131.36:0,0:0,9.2688e-07,1 +chr1 5469905 . ttctttctttctttctttctttctttctttctttctttctttctttctttctttctttct ttctttctttctttctttctttctttctttctttctttctttctttctttctttctttctttct . PASS END=5469964;RU=ttct;PERIOD=4;REF=15;GRID=12,20;STUTTERUP=0.0594332;STUTTERDOWN=0.0367383;STUTTERP=0.478991;EXPTHRESH=15 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/1:27:0.779798:15,16:15-15,15-17:9,12,0,5:15,7|16,2:8,1|10,2|13,1|14,1:199.013:366.612,131.36:0.19802,0.57834:9.18276e-12,0.00672041,0.993294 +chr1 5470375 . atttatttatttatttattt . . PASS END=5470394;RU=attt;PERIOD=4;REF=5;GRID=2,8;STUTTERUP=0.00174749;STUTTERDOWN=0.00972579;STUTTERP=0.762128;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:30:0.999856:5,5:5-5,5-5:16,12,0,2:5,16:4,2:185.188:366.612,131.36:0,0:0,6.52832e-05,0.999934 +chr1 5487012 . agaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaaga aga,agaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaaga . PASS END=5487095;RU=aga;PERIOD=3;REF=28;GRID=1,28;STUTTERUP=0.0101854;STUTTERDOWN=0.159974;STUTTERP=0.537643;EXPTHRESH=28 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:22:0.0641902:1,25:1-27,19-27:0,16,0,6:NULL:7,1|15,1|19,1|21,1|24,1|25,1:194.376:366.612,131.36:10.4167,2.80123:0.814845,0.18449,0.000731844 +chr1 5487104 . gaggaggaggaggaggaggaggaggaggaggaggaggaggaggaggaggag gaggaggaggaggaggaggaggaggaggaggaggaggaggaggaggaggaggaggag . PASS END=5487154;RU=gag;PERIOD=3;REF=17;GRID=16,22;STUTTERUP=0.0162012;STUTTERDOWN=0.0959211;STUTTERP=0.588715;EXPTHRESH=17 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:16:0.221203:19,19:16-19,16-19:2,9,0,5:19,2:5,1|7,1|8,1|9,1|10,1:132.591:366.612,131.36:1.14809,1.14809:3.42417e-06,0.223225,0.776813 +chr1 5491577 . tttctttctttctttc . . PASS END=5491592;RU=tttc;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000664068;STUTTERDOWN=0.00320627;STUTTERP=0.984306;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:21:0.999683:4,4:4-4,4-4:15,6,0,0:4,15:NULL:111.491:366.612,131.36:0,0:0,0.00020738,0.999796 +chr1 5495145 . tattattattat . . PASS END=5495156;RU=tat;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000897249;STUTTERDOWN=0.00433212;STUTTERP=0.77435;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:0.999919:4,4:4-4,4-4:17,17,0,2:4,17:3,2:230.211:366.612,131.36:0,0:0,4.36298e-05,0.999957 +chr1 5499413 . aaacaaacaaac . . PASS END=5499424;RU=aaac;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000416267;STUTTERDOWN=0.00118912;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:27:0.999984:3,3:3-3,3-3:18,9,0,0:3,18:NULL:151.645:366.612,131.36:0,0:0,1.95113e-05,0.99998 +chr1 5499767 . atatatatatatatatatatatatatatatatatatatatatatatatatat at . PASS END=5499818;RU=at;PERIOD=2;REF=26;GRID=1,103;STUTTERUP=0.037125;STUTTERDOWN=0.375553;STUTTERP=0.713103;EXPTHRESH=26 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:4:0.00139684:1,1:1-3,1-3:0,4,0,0:NULL:NULL:36.3001:366.612,131.36:0.748295,0.748295:0.364437,0.535353,0.100301 +chr1 5504534 . tatttatttatt . . PASS END=5504545;RU=tatt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000366624;STUTTERDOWN=0.000733247;STUTTERP=0.73234;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:56:1:3,3:3-3,3-3:29,25,0,2:3,29:2,2:358.683:366.612,131.36:0,0:0,1.36141e-08,1 +chr1 5513530 . tctctctctctctctctctctctctctctctctctctc tctctctctctctctctctctctctctctctctctctctctctctc . PASS END=5513567;RU=tc;PERIOD=2;REF=19;GRID=16,27;STUTTERUP=0.0923242;STUTTERDOWN=0.158657;STUTTERP=0.514793;EXPTHRESH=19 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:28:0.31293:23,23:19-24,19-24:3,13,0,9:23,3:4,1|6,1|7,1|9,1|10,1|18,1|20,1|22,1|23,1:206.714:366.612,131.36:2.04637,2.04637:2.11561e-29,0.066714,0.93338 +chr1 5516671 . tctctctctctctc . . PASS END=5516684;RU=tc;PERIOD=2;REF=7;GRID=3,10;STUTTERUP=0.0130417;STUTTERDOWN=0.0393144;STUTTERP=0.851223;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:47:1:7,7:7-7,7-7:33,10,0,3:7,33:6,3:244.379:366.612,131.36:0,0:0,5.01572e-10,1 +chr1 5518233 . acacacacacac . . PASS END=5518244;RU=ac;PERIOD=2;REF=6;GRID=3,9;STUTTERUP=0.00764629;STUTTERDOWN=0.00733124;STUTTERP=0.959369;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:28:1:6,6:6-6,6-6:20,8,0,0:6,20:NULL:155.727:366.612,131.36:0,0:4.54021e-43,8.39984e-06,0.999994 +chr1 5522366 . tttatttattta . . PASS END=5522377;RU=ttta;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000724085;STUTTERDOWN=0.00144817;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:0.998395:3,3:3-3,3-3:13,24,0,0:3,13:NULL:264.156:366.612,131.36:0,0:5.04453e-41,0.00110037,0.998906 +chr1 5526299 . ttatttatttatttatttatttat ttatttatttatttatttatttatttatttatttat . PASS END=5526322;RU=ttat;PERIOD=4;REF=6;GRID=3,12;STUTTERUP=0.00346099;STUTTERDOWN=0.0208901;STUTTERP=0.450591;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/1:23:0.999594:6,9:6-9,9-9:8,13,0,2:6,2|9,6:4,1|5,1:173.311:366.612,131.36:1.17184,0:1.26762e-24,3.43917e-05,0.99997 +chr1 5531371 . aaataaataaataaat . . PASS END=5531386;RU=aaat;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.001256;STUTTERDOWN=0.00502397;STUTTERP=0.887402;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:1.00001:4,4:4-4,4-4:22,11,0,5:4,22:2,5:220.017:366.612,131.36:0,0:0,1.25235e-06,1 +chr1 5532982 . tgtgtgtgtgtgtgtg tgtgtgtg . PASS END=5532997;RU=tg;PERIOD=2;REF=8;GRID=4,10;STUTTERUP=0.0249711;STUTTERDOWN=0.0389324;STUTTERP=0.938424;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:24:0.0437343:4,4:4-8,4-8:0,23,0,0:NULL:NULL:212.091:366.612,131.36:1.29055,1.29055:0.450508,0.449184,0.100457 +chr1 5534046 . atgtatgtatgtatgt . . PASS END=5534061;RU=atgt;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000358779;STUTTERDOWN=0.00318488;STUTTERP=0.981068;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:50:1:4,4:4-4,4-4:29,14,0,6:4,29:3,6:287.447:366.612,131.36:0.0990099,0.0990099:0,5.60014e-09,1 +chr1 5534075 . tatgtatgtatgtatg . . PASS END=5534090;RU=tatg;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000941286;STUTTERDOWN=0.00692191;STUTTERP=0.733927;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:52:1:4,4:4-4,4-4:35,13,0,3:4,35:2,1|3,2:280.629:366.612,131.36:0,0:0,1.11186e-10,1 +chr1 5534127 . tgtgtgtgtgtg . . PASS END=5534138;RU=tg;PERIOD=2;REF=6;GRID=2,9;STUTTERUP=0.00643393;STUTTERDOWN=0.0118291;STUTTERP=0.951605;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:46:1:6,6:6-6,6-6:26,19,0,0:6,26:NULL:275.467:366.612,131.36:0.139319,0.139319:0,3.5554e-07,1 +chr1 5538600 . ttttgttttgttttg . . PASS END=5538614;RU=ttttg;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000426862;STUTTERDOWN=0.000853723;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:30:0.793571:3,3:3-3,3-3:5,25,0,0:3,5:NULL:251.759:366.612,131.36:0.0990099,0.0990099:2.33087e-17,0.156038,0.844041 +chr1 5539245 . agagagagagag . . PASS END=5539256;RU=ag;PERIOD=2;REF=6;GRID=2,9;STUTTERUP=0.00345114;STUTTERDOWN=0.0121674;STUTTERP=0.883495;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:1:6,6:5-6,5-6:24,10,0,2:6,24:4,1|5,1:203.302:366.612,131.36:0.169767,0.169767:0,3.64039e-07,1 +chr1 5541995 . tctatctatcta . . PASS END=5542006;RU=tcta;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000880007;STUTTERDOWN=0.000440004;STUTTERP=0.597956;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:1:3,3:3-3,3-3:19,14,0,0:3,19:NULL:198.958:366.612,131.36:0,0:0,7.97423e-06,0.999994 +chr1 5543920 . aaacaaacaaacaaacaaac . . PASS END=5543939;RU=aaac;PERIOD=4;REF=5;GRID=2,8;STUTTERUP=0.000912838;STUTTERDOWN=0.00308569;STUTTERP=0.744192;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:46:1:5,5:5-5,5-5:27,14,0,5:5,27:3,2|4,3:270.026:366.612,131.36:0,0:0,1.74728e-08,1 +chr1 5548928 . gtgtgcgtgtgcgtgtgcgtgtgcgtgtgcgtgtgc gtgtgcgtgtgcgtgtgcgtgtgcgtgtgc . PASS END=5548963;RU=gtgtgc;PERIOD=6;REF=6;GRID=1,9;STUTTERUP=0.00137332;STUTTERDOWN=0.0228314;STUTTERP=0.450752;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:32:0.996997:5,5:4-6,4-6:12,16,0,2:5,12:3,2:215.759:366.612,131.36:0.563226,0.563226:0.999097,0.000907121,4.83865e-25 +chr1 5568606 . tatatatatatatatatatatatatatatata tatatatatatatatatatatata . PASS END=5568637;RU=ta;PERIOD=2;REF=16;GRID=9,16;STUTTERUP=0.157322;STUTTERDOWN=0.137472;STUTTERP=0.77963;EXPTHRESH=16 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:3:0.191459:12,12:12-13,12-13:2,0,0,0:12,2:NULL:8.72991:366.612,131.36:0.472558,0.472558:0.898586,0.101517,4.30333e-07 +chr1 5568681 . tctctctctctctctctctc tctctctctctctctctc . PASS END=5568700;RU=tc;PERIOD=2;REF=10;GRID=3,13;STUTTERUP=0.0778614;STUTTERDOWN=0.024052;STUTTERP=0.579168;EXPTHRESH=10 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:6:0.167585:9,9:6-10,6-10:2,1,0,0:9,2:NULL:16.2695:366.612,131.36:1.41933,1.41933:0.676238,0.323648,0.000128575 +chr1 5568724 . agagagagagagagagagagagagagag agagagagagagagagagag,agagagagagagagagagagag . PASS END=5568751;RU=ag;PERIOD=2;REF=14;GRID=3,14;STUTTERUP=0.0679009;STUTTERDOWN=0.165633;STUTTERP=0.560655;EXPTHRESH=14 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:9:0.981721:10,11:6-10,6-11:7,1,0,0:10,4|11,3:NULL:42.692:366.612,131.36:1.60988,1.61328:0.999643,0.000360942,2.85432e-12 +chr1 5571339 . aacaacaacaac . . PASS END=5571350;RU=aac;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00190258;STUTTERDOWN=0.00229655;STUTTERP=0.948224;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:20:0.993811:4,4:4-4,4-4:11,9,0,0:4,11:NULL:128.626:366.612,131.36:0,0:1.40082e-30,0.0044127,0.995598 +chr1 5573523 . gaaagaaagaaagaaa . . PASS END=5573538;RU=gaaa;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.00123864;STUTTERDOWN=0.00738088;STUTTERP=0.952254;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:0.99979:4,4:4-4,4-4:15,12,0,2:4,15:3,2:184.59:366.612,131.36:0,0:1.68156e-44,0.000114813,0.999887 +chr1 5573587 . aaagaaagaaag . . PASS END=5573598;RU=aaag;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00045522;STUTTERDOWN=0.00364172;STUTTERP=0.966669;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:0.999662:3,3:3-3,3-3:14,13,0,2:3,14:2,2:192.077:366.612,131.36:0,0:0,0.000165596,0.999835 +chr1 5579717 . acacacacacacacacacacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacacacacacacacacac . PASS END=5579762;RU=ac;PERIOD=2;REF=23;GRID=18,29;STUTTERUP=0.0945428;STUTTERDOWN=0.17619;STUTTERP=0.795361;EXPTHRESH=23 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:26:0.03869:26,26:21-26,21-26:0,16,0,8:NULL:7,1|9,1|16,2|18,1|20,1|23,1|26,1:220.015:366.612,131.36:2.18267,2.18267:3.56267e-15,0.437331,0.562764 +chr1 5581808 . gtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgt . PASS END=5581829;RU=gt;PERIOD=2;REF=11;GRID=9,15;STUTTERUP=0.0340868;STUTTERDOWN=0.0761447;STUTTERP=0.818542;EXPTHRESH=11 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:35:0.999005:12,12:12-12,12-12:14,15,0,6:12,14:5,1|6,1|8,1|9,2|11,1:246.406:366.612,131.36:0,0:7.50395e-39,0.00022835,0.999773 +chr1 5585680 . ctctctctctct ctctctctctctct . PASS END=5585691;RU=ct;PERIOD=2;REF=6;GRID=3,10;STUTTERUP=0.0122584;STUTTERDOWN=0.0139098;STUTTERP=0.854347;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/1:23:0.716874:6,7:6-6,6-7:13,10,0,0:6,11|7,2:NULL:153.498:366.612,131.36:0,0.491073:1.32097e-24,0.000262666,0.999742 +chr1 5589327 . ggtggtggtggtggtggtggtggtggtggt ggtggtggtggtggtggtggtggtggtggtggtggt . PASS END=5589356;RU=ggt;PERIOD=3;REF=10;GRID=9,15;STUTTERUP=0.00341656;STUTTERDOWN=0.028557;STUTTERP=0.721196;EXPTHRESH=10 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:24:0.975048:12,12:12-12,12-12:9,13,0,2:12,9:7,2:169.879:366.612,131.36:0,0:3.58951e-33,0.00724252,0.992775 +chr1 5589376 . tgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=5589399;RU=tg;PERIOD=2;REF=12;GRID=16,26;STUTTERUP=0.0393852;STUTTERDOWN=0.0932214;STUTTERP=0.791335;EXPTHRESH=12 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:17:0.122528:23,23:19-23,19-23:2,12,0,0:23,2:NULL:116.017:366.612,131.36:1.34493,1.34493:0,0,1 +chr1 5589780 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=5589835;RU=tg;PERIOD=2;REF=28;GRID=19,25;STUTTERUP=0.0856912;STUTTERDOWN=0.219837;STUTTERP=0.710113;EXPTHRESH=28 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:25:0.684515:22,22:22-22,22-22:5,9,0,11:22,5:9,2|10,2|12,1|15,3|17,2|20,1:194.5:366.612,131.36:0,0:1,0,0 +chr1 5592598 . tctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctc tctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctc . PASS END=5592667;RU=tc;PERIOD=2;REF=35;GRID=1,37;STUTTERUP=0.0686584;STUTTERDOWN=0.31883;STUTTERP=0.670536;EXPTHRESH=35 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:16:0.0124984:36,36:2-36,2-36:0,10,0,6:NULL:8,1|17,1|22,1|23,1|33,1|34,1:142.041:366.612,131.36:12.4172,12.4172:0.208392,0.695051,0.0966789 +chr1 5593742 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=5593777;RU=gt;PERIOD=2;REF=18;GRID=13,25;STUTTERUP=0.0789385;STUTTERDOWN=0.194848;STUTTERP=0.575965;EXPTHRESH=18 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/1:25:0.887398:18,19:16-22,16-22:6,10,0,5:18,4|19,2:6,1|8,1|9,2|11,1:165.187:366.612,131.36:1.81321,1.54443:3.33702e-07,0.0161178,0.983918 +chr1 5594362 . acagatatcagcacagatatcagcacagatatcagcacagatatcagc . . PASS END=5594409;RU=acagatatcagc;PERIOD=12;REF=4;GRID=1,7;STUTTERUP=0.05;STUTTERDOWN=0.05;STUTTERP=0.9;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:0.99997:4,4:4-4,4-4:19,9,0,7:4,19:2,4|3,3:214.928:366.612,131.36:0,0:2.03387e-23,3.57251e-05,0.999964 +chr1 5594483 . acagatatcagcacagatatcagcacagatatcagc . . PASS END=5594518;RU=acagatatcagc;PERIOD=12;REF=3;GRID=1,6;STUTTERUP=0.05;STUTTERDOWN=0.05;STUTTERP=0.9;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:25:0.992171:3,3:3-3,3-3:10,9,0,6:3,10:2,5|3,1:162.564:366.612,131.36:0,0:1.07008e-20,0.00423133,0.995779 +chr1 5601522 . ctctctctctctctct ctctctctctctctctctctctctctctctctctctct . PASS END=5601537;RU=ct;PERIOD=2;REF=8;GRID=16,22;STUTTERUP=0.0427598;STUTTERDOWN=0.12684;STUTTERP=0.588053;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:16:0.381909:19,19:16-19,16-19:3,10,0,3:19,3:6,1|11,1|18,1:127.14:366.612,131.36:0.550196,0.550196:0,0,1 +chr1 5601538 . cacacacacacacacacacacacacacacacaca cacacacacacacacacacacacacacacacacacacaca . PASS END=5601571;RU=ca;PERIOD=2;REF=17;GRID=20,26;STUTTERUP=0.0529083;STUTTERDOWN=0.109316;STUTTERP=0.615522;EXPTHRESH=17 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:16:0.0438883:20,20:20-23,20-23:0,8,0,7:NULL:4,1|5,1|6,2|9,1|13,2:127.313:366.612,131.36:1.37748,1.37748:0,0,1 +chr1 5605789 . tatatatatata . . PASS END=5605800;RU=ta;PERIOD=2;REF=6;GRID=3,9;STUTTERUP=0.0178747;STUTTERDOWN=0.0167815;STUTTERP=0.884809;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:20:0.999173:6,6:6-6,6-6:14,6,0,0:6,14:NULL:109.551:366.612,131.36:0,0:1.50464e-25,0.000455149,0.999546 +chr1 5607518 . ccctcccctcccctcccctcccctcccctcccctcccctcccctcccctc ccctcccctcccctcccctcccctcccctcccctc . PASS END=5607567;RU=ccctc;PERIOD=5;REF=10;GRID=1,9;STUTTERUP=0.010144;STUTTERDOWN=0.0185065;STUTTERP=0.507146;EXPTHRESH=10 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:6:0.0428456:7,7:2-8,2-8:0,3,0,3:NULL:5,2|6,1:47.4534:366.612,131.36:1.42106,1.42106:1,0,0 +chr1 5609483 . tctttctttctttctttctttctttctttctttctttctttctttctttctt tctttctttctttctttctttctttctttctttctttctttctttctttctttctttctttctt,tctttctttctttctttctttctttctttctttctttctttctttctttctttctttctttctttctttctt . PASS END=5609534;RU=tctt;PERIOD=4;REF=13;GRID=10,21;STUTTERUP=0.00824102;STUTTERDOWN=0.08169;STUTTERP=0.459365;EXPTHRESH=13 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:27:0.457214:16,18:13-16,13-18:8,9,0,9:13,3|16,5:2,1|3,1|4,1|7,2|8,1|13,1|16,1|18,1:204.837:366.612,131.36:1.26965,2.41742:5.45352e-38,3.81258e-08,1 +chr1 5609614 . tctctctctctctctctctctctctc tctctctctctctctctctctctctctctctctctctc,tctctctctctctctctctctctctctctctctctctctctctctctc . PASS END=5609639;RU=tc;PERIOD=2;REF=13;GRID=16,27;STUTTERUP=0.0712192;STUTTERDOWN=0.116004;STUTTERP=0.668867;EXPTHRESH=13 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:13:0.974538:19,24:16-24,19-24:4,6,0,3:19,2|24,2:9,1|12,1|16,1:103.857:366.612,131.36:1.59046,1.91609:0,0,1 +chr1 5612315 . ctggctggctgg . . PASS END=5612326;RU=ctgg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000593642;STUTTERDOWN=0.000593642;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:28:0.998233:3,3:3-3,3-3:13,15,0,0:3,13:NULL:191.934:366.612,131.36:0,0:2.73954e-42,0.00100296,0.998999 +chr1 5612776 . tttatttattta . . PASS END=5612787;RU=ttta;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00107139;STUTTERDOWN=0.000535697;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:30:0.999995:3,3:3-3,3-3:19,11,0,0:3,19:NULL:173.896:366.612,131.36:0,0:0,1.15696e-05,0.999987 +chr1 5614359 . tccctccctccctccc . . PASS END=5614374;RU=tccc;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000443464;STUTTERDOWN=0.00253363;STUTTERP=0.969616;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:26:0.998846:4,4:4-4,4-4:13,11,0,2:4,13:2,1|3,1:165.446:366.612,131.36:0,0:3.50325e-44,0.00055509,0.999447 +chr1 5616757 . aagcaagcaagc . . PASS END=5616768;RU=aagc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000482169;STUTTERDOWN=0.000482169;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:0.999861:3,3:3-3,3-3:16,17,0,0:3,16:NULL:219.518:366.612,131.36:0,0:0,8.99908e-05,0.999911 +chr1 5617140 . acacacacacacacacacacacacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacac . PASS END=5617189;RU=ac;PERIOD=2;REF=25;GRID=20,46;STUTTERUP=0.0726802;STUTTERDOWN=0.243169;STUTTERP=0.675436;EXPTHRESH=25 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/1:30:0.290156:25,43:24-26,23-43:5,6,0,16:25,5:5,1|6,1|8,1|12,2|14,1|20,2|21,2|22,3|23,1|24,1|43,1:206.925:366.612,131.36:0.344122,8.89312:2.08458e-12,2.3267e-06,1 +chr1 5617615 . ttctcttctcttctcttctcttctcttctcttctcttctcttctcttctcttctcttctcttctcttctcttctcttctcttctc . . PASS END=5617699;RU=ttctc;PERIOD=5;REF=17;GRID=14,20;STUTTERUP=0.0141893;STUTTERDOWN=0.010933;STUTTERP=0.561309;EXPTHRESH=17 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:14:0.287728:17,17:14-19,14-19:2,2,0,10:17,2:6,1|7,2|11,1|12,4|16,2:101.018:366.612,131.36:0.856307,0.856307:4.75116e-05,0.26636,0.733597 +chr1 5618977 . cagcagcagcag . . PASS END=5618988;RU=cag;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000417033;STUTTERDOWN=0.00119131;STUTTERP=0.941457;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:41:1:4,4:4-4,4-4:23,18,0,0:4,23:NULL:253.62:366.612,131.36:0,0:0,8.95862e-07,1 +chr1 5620595 . acacacacacacacacacacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacacacacacacacac . PASS END=5620640;RU=ac;PERIOD=2;REF=23;GRID=19,28;STUTTERUP=0.0588975;STUTTERDOWN=0.201513;STUTTERP=0.707127;EXPTHRESH=23 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:28:0.138323:25,25:21-25,21-25:2,14,0,9:25,2:5,1|6,1|7,1|12,1|13,2|15,1|20,1|23,1:216.568:366.612,131.36:0.923821,0.923821:3.11768e-12,0.378233,0.621819 +chr1 5623551 . ttattttattttatt . . PASS END=5623565;RU=ttatt;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000676349;STUTTERDOWN=0.00457255;STUTTERP=0.958596;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:15:0.671791:3,3:1-3,1-3:5,10,0,0:3,5:NULL:113.692:366.612,131.36:0.390054,0.390054:2.78286e-16,0.187197,0.812863 +chr1 5625250 . cacacacacacacacacacacacacacacacacacacacacacacaca cacacacacacacacacacacacacacacacacacacacacaca,cacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacaca . PASS END=5625297;RU=ca;PERIOD=2;REF=24;GRID=17,35;STUTTERUP=0.0962079;STUTTERDOWN=0.230986;STUTTERP=0.610202;EXPTHRESH=24 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:46:0.291461:22,33:22-22,21-35:11,19,0,15:21,2|22,9:8,1|9,3|11,2|16,3|17,1|18,2|19,1|21,1|32,1:360.412:366.612,131.36:0,5.49805:9.90578e-05,0.999903,3.27363e-12 +chr1 5626755 . tatatatatatata ta . PASS END=5626768;RU=ta;PERIOD=2;REF=7;GRID=1,103;STUTTERUP=0.0474001;STUTTERDOWN=0.0311644;STUTTERP=0.88674;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:5:0.00338735:1,1:1-4,1-4:0,5,0,0:NULL:NULL:46.7652:366.612,131.36:0.896026,0.896026:0.0533552,0.4034,0.543409 +chr1 5627434 . acccacccaccc . . PASS END=5627445;RU=accc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00274677;STUTTERDOWN=0.00274677;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:4:0.439336:3,3:3-3,3-3:3,1,0,0:3,3:NULL:21.193:366.612,131.36:0.29703,0.29703:7.97056e-09,0.185254,0.814805 +chr1 5628800 . gtgtgtgtgtgt . . PASS END=5628811;RU=gt;PERIOD=2;REF=6;GRID=3,9;STUTTERUP=0.00948623;STUTTERDOWN=0.0254714;STUTTERP=0.885622;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:45:0.999987:6,6:6-6,6-6:19,26,0,0:6,19:NULL:306.178:366.612,131.36:0,0:2.44924e-39,2.24444e-05,0.999979 +chr1 5634536 . acatacatacat . . PASS END=5634547;RU=acat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.0011814;STUTTERDOWN=0.000590702;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:0.999781:3,3:3-3,3-3:15,18,0,2:3,15:2,2:241.613:366.612,131.36:0,0:5.32493e-44,0.000139803,0.999864 +chr1 5645300 . ccacccacccacccac . . PASS END=5645315;RU=ccac;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000449568;STUTTERDOWN=0.00719304;STUTTERP=0.976744;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:43:1:4,4:4-4,4-4:26,14,0,3:4,26:2,1|3,2:257.308:366.612,131.36:0,0:0,5.39436e-08,1 +chr1 5648208 . tttctttctttc . . PASS END=5648219;RU=tttc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000441018;STUTTERDOWN=0.00125983;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:1.00001:3,3:3-3,3-3:21,17,0,0:3,21:NULL:236.188:366.612,131.36:0,0:0,3.50995e-06,1 +chr1 5658059 . aaccaaccaaccaaccaaccaaccaaccaacc . . PASS END=5658090;RU=aacc;PERIOD=4;REF=8;GRID=5,11;STUTTERUP=0.00122367;STUTTERDOWN=0.0158637;STUTTERP=0.666414;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:0.997758:8,8:8-8,8-8:12,19,0,6:8,12:5,3|6,1|7,2:270.432:366.612,131.36:0,0:4.34303e-37,0.00122251,0.998784 +chr1 5659996 . acacacacacacac . . PASS END=5660009;RU=ac;PERIOD=2;REF=7;GRID=4,10;STUTTERUP=0.00401986;STUTTERDOWN=0.0138774;STUTTERP=0.865227;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:0.999491:7,7:7-7,7-7:15,22,0,2:7,15:5,2:281.623:366.612,131.36:0,0:5.3889e-37,0.000244781,0.999758 +chr1 5667369 . ttgttttgttttgtt . . PASS END=5667383;RU=ttgtt;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000537789;STUTTERDOWN=0.00215113;STUTTERP=0.987382;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:0.999211:3,3:3-3,3-3:14,19,0,0:3,14:NULL:237.415:366.612,131.36:0,0:1.4013e-45,0.00064475,0.999356 +chr1 5668188 . tctctctctctctctctctctctctctctctctctctctctctctc tctctctctctctctctctctctctctctctctc . PASS END=5668233;RU=tc;PERIOD=2;REF=23;GRID=13,20;STUTTERUP=0.0383795;STUTTERDOWN=0.170478;STUTTERP=0.689075;EXPTHRESH=23 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:42:0.973632:17,17:16-17,16-17:16,18,0,8:16,3|17,13:5,2|7,1|8,1|13,1|15,1|16,2:309.774:366.612,131.36:0.345543,0.345543:1,0,0 +chr1 5668714 . acacacacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacacacacacacacacacacac,acacacacacacacacacacacacacacacacacacacacacacacacacacacacacacac . PASS END=5668747;RU=ac;PERIOD=2;REF=17;GRID=25,34;STUTTERUP=0.0524427;STUTTERDOWN=0.151219;STUTTERP=0.710836;EXPTHRESH=17 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:49:0.306761:28,31:28-30,29-32:5,13,0,30:28,3|29,2:4,1|5,1|6,1|7,1|8,2|9,1|10,2|12,1|13,1|14,1|15,1|16,1|17,1|18,5|22,2|23,2|24,1|27,1|28,1|30,1|31,2:394.435:366.612,131.36:0.553571,0.556925:0,0,1 +chr1 5683487 . caaacaaacaaacaaa . . PASS END=5683502;RU=caaa;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000497723;STUTTERDOWN=0.00480623;STUTTERP=0.978866;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:1.00001:4,4:4-4,4-4:21,12,0,4:4,21:3,4:221.239:366.612,131.36:0,0:0,1.81181e-06,1 +chr1 5686946 . actccactccactccactccactcc . . PASS END=5686970;RU=actcc;PERIOD=5;REF=5;GRID=2,8;STUTTERUP=0.000523043;STUTTERDOWN=0.0054942;STUTTERP=0.835759;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:1:5,5:5-5,5-5:20,16,0,3:5,20:3,3:251.76:366.612,131.36:0,0:0,1.09203e-05,0.999993 +chr1 5691957 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=5691994;RU=tg;PERIOD=2;REF=19;GRID=24,32;STUTTERUP=0.037619;STUTTERDOWN=0.159597;STUTTERP=0.55303;EXPTHRESH=19 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:14:0.0317843:25,25:25-29,25-29:0,7,0,5:NULL:4,1|18,1|20,1|22,2:107.25:366.612,131.36:1.14347,1.14347:0,0,1 +chr1 5702366 . gggtgggtgggt . . PASS END=5702377;RU=gggt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00131485;STUTTERDOWN=0.00131485;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:25:0.928342:3,3:3-3,3-3:7,18,0,0:3,7:NULL:186.16:366.612,131.36:0,0:1.29376e-20,0.0464803,0.953593 +chr1 5703039 . tttctttctttc . . PASS END=5703050;RU=tttc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000531719;STUTTERDOWN=0.00472007;STUTTERP=0.981068;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:34:1:3,3:3-3,3-3:26,8,0,0:3,26:NULL:177.97:366.612,131.36:0,0:0,6.52669e-08,1 +chr1 5703348 . tctctctctctc . . PASS END=5703359;RU=tc;PERIOD=2;REF=6;GRID=3,10;STUTTERUP=0.00978999;STUTTERDOWN=0.0191724;STUTTERP=0.977097;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:24:0.999335:6,6:6-7,6-7:14,9,0,0:6,14:NULL:139.208:366.612,131.36:0.323567,0.323567:5.59831e-29,0.000328401,0.999674 +chr1 5705129 . tttatttattta . . PASS END=5705140;RU=ttta;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000498224;STUTTERDOWN=0.000996447;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:0.999745:3,3:3-3,3-3:14,13,0,4:3,14:2,4:207.898:366.612,131.36:0,0:0,0.000127164,0.999873 +chr1 5705229 . cccacccaccca . . PASS END=5705240;RU=ccca;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000461279;STUTTERDOWN=0.000461279;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:1.00001:3,3:3-3,3-3:21,14,0,2:3,21:2,2:230.431:366.612,131.36:0,0:0,2.13014e-06,1 +chr1 5706741 . aaacaaacaaacaaacaaacaaac aaacaaacaaacaaacaaacaaacaaac . PASS END=5706764;RU=aaac;PERIOD=4;REF=6;GRID=3,10;STUTTERUP=0.00128941;STUTTERDOWN=0.0130098;STUTTERP=0.872508;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:26:0.999701:7,7:6-7,6-7:15,10,0,0:7,15:NULL:155.182:366.612,131.36:0.311527,0.311527:0,0.000164888,0.999835 +chr1 5708798 . tttatttattta . . PASS END=5708809;RU=ttta;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000941213;STUTTERDOWN=0.00188241;STUTTERP=0.866591;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:46:1:3,3:3-3,3-3:28,18,0,0:3,28:NULL:273.838:366.612,131.36:0,0:0,2.28799e-08,1 +chr1 5709925 . ttctttctttct ttctttct . PASS END=5709936;RU=ttct;PERIOD=4;REF=3;GRID=1,5;STUTTERUP=0.000449907;STUTTERDOWN=0.000899758;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:35:1:2,2:2-2,2-2:19,16,0,0:2,19:NULL:225.294:366.612,131.36:0,0:0.999993,1.1175e-05,0 +chr1 5710226 . ttgttttgttttgttttgtt . . PASS END=5710245;RU=ttgtt;PERIOD=5;REF=4;GRID=1,7;STUTTERUP=0.000372637;STUTTERDOWN=0.00503852;STUTTERP=0.902196;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:54:1:4,4:2-4,2-4:32,19,0,2:4,32:2,1|3,1:318.661:366.612,131.36:0.507951,0.507951:0,1.20364e-09,1 +chr1 5712340 . aaaacaaaacaaaacaaaacaaaacaaaac aaaacaaaac . PASS END=5712369;RU=aaaac;PERIOD=5;REF=6;GRID=1,5;STUTTERUP=0.00396376;STUTTERDOWN=0.00315915;STUTTERP=0.799737;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:19:0.780734:2,2:2-2,2-2:5,14,0,0:2,5:NULL:149.149:366.612,131.36:0.139319,0.139319:1,0,0 +chr1 5718275 . tttatttattta . . PASS END=5718286;RU=ttta;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000406352;STUTTERDOWN=0.000812703;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:1.00001:3,3:3-3,3-3:21,17,0,0:3,21:NULL:246.484:366.612,131.36:0,0:0,3.01196e-06,1 +chr1 5722194 . tatatatatata tatatatatatata . PASS END=5722205;RU=ta;PERIOD=2;REF=6;GRID=4,10;STUTTERUP=0.0251171;STUTTERDOWN=0.0286283;STUTTERP=0.89539;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:33:0.999787:7,7:7-7,7-7:16,17,0,0:7,16:NULL:216.966:366.612,131.36:0,0:4.4197e-42,7.55325e-05,0.999926 +chr1 5722249 . tttgttttgttttgttttgt . . PASS END=5722268;RU=tttgt;PERIOD=5;REF=4;GRID=1,7;STUTTERUP=0.000450635;STUTTERDOWN=0.00180252;STUTTERP=0.844424;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:0.999984:4,4:4-4,4-4:18,16,0,2:4,18:3,2:229.225:366.612,131.36:0,0:0,2.02604e-05,0.99998 +chr1 5727994 . atacatacatac . . PASS END=5728005;RU=atac;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000437046;STUTTERDOWN=0.00174816;STUTTERP=0.706087;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:1:3,3:3-3,3-3:24,12,0,0:3,24:NULL:199.933:366.612,131.36:0,0:0,2.5561e-07,1 +chr1 5733779 . acccacccaccc . . PASS END=5733790;RU=accc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00109634;STUTTERDOWN=0.00109634;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:42:0.995933:3,3:3-3,3-3:11,31,0,0:3,11:NULL:317.64:366.612,131.36:0,0:2.46417e-33,0.00271117,0.997298 +chr1 5742710 . gggtgggtgggt . . PASS END=5742721;RU=gggt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000917308;STUTTERDOWN=0.00183461;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:40:0.998455:3,3:3-3,3-3:11,27,0,2:3,11:2,2:291.594:366.612,131.36:0,0:2.44778e-34,0.000965837,0.999036 +chr1 5743415 . tttatttattta . . PASS END=5743426;RU=ttta;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000441329;STUTTERDOWN=0.000882656;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:43:1.00001:3,3:3-3,3-3:22,21,0,0:3,22:NULL:279.685:366.612,131.36:0,0:0,2.47098e-06,1 +chr1 5743494 . cccacccacccaccca . . PASS END=5743509;RU=ccca;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.00100516;STUTTERDOWN=0.0105584;STUTTERP=0.977258;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:40:0.987266:4,4:4-4,4-4:10,30,0,0:4,10:NULL:311.546:366.612,131.36:0,0:2.71427e-30,0.0104821,0.989543 +chr1 5749087 . ctcttgctcttgctcttg . . PASS END=5749104;RU=ctcttg;PERIOD=6;REF=3;GRID=1,6;STUTTERUP=0.000548072;STUTTERDOWN=0.0048652;STUTTERP=0.907264;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:45:0.999994:3,3:3-3,3-3:20,23,0,2:3,20:2,2:306.234:366.612,131.36:0,0:0,1.8489e-05,0.999985 +chr1 5759909 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=5759948;RU=gt;PERIOD=2;REF=20;GRID=22,29;STUTTERUP=0.0677747;STUTTERDOWN=0.223374;STUTTERP=0.689023;EXPTHRESH=20 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:39:0.929275:26,26:25-26,25-26:11,14,0,14:25,2|26,9:7,1|11,3|15,2|17,1|18,1|19,1|20,1|22,1|23,1|24,1|25,1:288.672:366.612,131.36:0.195027,0.195027:0,0,1 +chr1 5762305 . agagagagagagagag agagagagagagagagag . PASS END=5762320;RU=ag;PERIOD=2;REF=8;GRID=5,12;STUTTERUP=0.0113018;STUTTERDOWN=0.00915734;STUTTERP=0.816661;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/1:29:0.990522:8,9:8-9,9-9:8,17,0,4:8,2|9,6:4,1|5,1|7,2:232.974:366.612,131.36:0.419363,0.0990099:6.99306e-19,0.000572497,0.999431 +chr1 5769922 . ttgtttgtttgtttgtttgt ttgtttgtttgtttgtttgtttgt . PASS END=5769941;RU=ttgt;PERIOD=4;REF=5;GRID=2,9;STUTTERUP=0.000456529;STUTTERDOWN=0.0355261;STUTTERP=0.886027;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:39:0.999988:6,6:5-6,5-6:19,13,0,6:6,19:3,3|5,3:242.009:366.612,131.36:0.169767,0.169767:0,2.48747e-06,1 +chr1 5772735 . aaataaataaataaat . . PASS END=5772750;RU=aaat;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.00106561;STUTTERDOWN=0.00472972;STUTTERP=0.923971;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:42:0.99989:4,4:4-4,4-4:16,22,0,4:4,16:2,1|3,3:292.378:366.612,131.36:0,0:0,6.38866e-05,0.99994 +chr1 5773613 . ggaggggaggggaggggaggggaggggaggggaggggaggggaggggaggggaggggagg ggaggggaggggaggggaggggaggggaggggagg . PASS END=5773672;RU=ggagg;PERIOD=5;REF=12;GRID=1,10;STUTTERUP=0.05;STUTTERDOWN=0.05;STUTTERP=0.9;EXPTHRESH=12 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:4:0.0340636:7,7:3-7,3-7:0,0,0,4:NULL:2,1|3,1|5,1|7,1:28.2102:366.612,131.36:1.30122,1.30122:1,0,0 +chr1 5774929 . aaaataaaataaaataaaataaaataaaataaaat aaaataaaataaaataaaataaaataaaataaaataaaataaaataaaataaaataaaataaaat,aaaataaaataaaataaaataaaataaaataaaataaaataaaataaaataaaataaaataaaataaaat . PASS END=5774963;RU=aaaat;PERIOD=5;REF=7;GRID=1,17;STUTTERUP=0.0123331;STUTTERDOWN=0.0277507;STUTTERP=0.345585;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:21:0.996759:13,14:4-13,4-14:6,11,0,2:13,4|14,2:2,2:151.098:366.612,131.36:3.55444,4.36098:9.05931e-17,0.00197197,0.998034 +chr1 5775613 . aaacaaacaaacaaac . . PASS END=5775628;RU=aaac;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000408447;STUTTERDOWN=0.00695273;STUTTERP=0.933539;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:0.999805:4,4:4-4,4-4:16,15,0,0:4,16:NULL:202.513:366.612,131.36:0,0:0,0.000142664,0.999858 +chr1 5779912 . aataataataataat . . PASS END=5779926;RU=aat;PERIOD=3;REF=5;GRID=2,8;STUTTERUP=0.00773876;STUTTERDOWN=0.0130796;STUTTERP=0.872504;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:17:0.989972:5,5:5-5,5-5:10,7,0,0:5,10:NULL:100.348:366.612,131.36:0,0:2.77029e-22,0.00627996,0.993737 +chr1 5780434 . cattgtgagcattgtgagcattgtgag . . PASS END=5780460;RU=cattgtgag;PERIOD=9;REF=3;GRID=1,6;STUTTERUP=0.00058281;STUTTERDOWN=0.00281393;STUTTERP=0.841787;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:0.999298:3,3:3-3,3-3:13,17,0,3:3,13:2,3:230.502:366.612,131.36:0,0:6.69821e-43,0.000502598,0.9995 +chr1 5781296 . ttattattatta ttattatta . PASS END=5781307;RU=tta;PERIOD=3;REF=4;GRID=1,6;STUTTERUP=0.00263175;STUTTERDOWN=0.00221257;STUTTERP=0.972501;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:32:0.99987:3,3:3-3,3-3:16,16,0,0:3,16:NULL:215.133:366.612,131.36:0,0:0.999926,7.53605e-05,1.80768e-43 +chr1 5783455 . gtgggtgggtgg gtgggtgggtgggtgggtgggtgggtgg . PASS END=5783466;RU=gtgg;PERIOD=4;REF=3;GRID=4,10;STUTTERUP=0.00832545;STUTTERDOWN=0.00469874;STUTTERP=0.365621;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:11:0.959332:7,7:7-7,7-7:8,3,0,0:7,8:NULL:63.0944:366.612,131.36:0,0:0,0,1 +chr1 5785041 . taaataaataaa . . PASS END=5785052;RU=taaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000588542;STUTTERDOWN=0.000588542;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:27:0.999171:3,3:3-3,3-3:13,10,0,4:3,13:2,4:166.912:366.612,131.36:0,0:1.02295e-42,0.000293774,0.999706 +chr1 5785417 . ttatttatttat . . PASS END=5785428;RU=ttat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000439358;STUTTERDOWN=0.00461514;STUTTERP=0.977258;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:1:3,3:3-3,3-3:26,10,0,0:3,26:NULL:191.362:366.612,131.36:0,0:0,5.39921e-08,1 +chr1 5791745 . cacacacacacaca cacaca,cacacaca . PASS END=5791758;RU=ca;PERIOD=2;REF=7;GRID=1,7;STUTTERUP=0.0486063;STUTTERDOWN=0.0158126;STUTTERP=0.9409;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:33:0.98971:3,4:3-4,3-4:6,27,0,0:3,2|4,4:NULL:277.703:366.612,131.36:0.422855,0.326282:0.999879,0.000123949,6.18505e-28 +chr1 5793084 . aataaataaata . . PASS END=5793095;RU=aata;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00104235;STUTTERDOWN=0.00104235;STUTTERP=0.976453;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:32:0.999877:3,3:3-3,3-3:17,13,0,2:3,17:2,2:202.902:366.612,131.36:0,0:0,6.08471e-05,0.999941 +chr1 5795883 . taaataaataaa . . PASS END=5795894;RU=taaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000427479;STUTTERDOWN=0.000427479;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:1:3,3:3-3,3-3:20,13,0,0:3,20:NULL:200.221:366.612,131.36:0,0:0,4.6765e-06,0.999995 +chr1 5796091 . tttgttttgttttgt . . PASS END=5796105;RU=tttgt;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000479327;STUTTERDOWN=0.000479327;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:25:0.999901:3,3:3-3,3-3:16,9,0,0:3,16:NULL:145.659:366.612,131.36:0,0:0,6.52105e-05,0.999934 +chr1 5796722 . aataaataaata . . PASS END=5796733;RU=aata;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000469869;STUTTERDOWN=0.00268449;STUTTERP=0.666133;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:1.00001:3,3:1-3,1-3:22,13,0,0:3,22:NULL:202.736:366.612,131.36:0.540126,0.540126:0,1.23798e-06,1 +chr1 5797431 . aaacaaacaaacaaacaaacaaac aaacaaacaaacaaacaaac . PASS END=5797454;RU=aaac;PERIOD=4;REF=6;GRID=2,8;STUTTERUP=0.00129013;STUTTERDOWN=0.0122145;STUTTERP=0.861845;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:48:1:5,5:5-5,5-5:35,10,0,3:5,35:2,1|4,2:256.075:366.612,131.36:0,0:1,1.1966e-10,0 +chr1 5799311 . tatatatatatatatatatatatatatatatatatata tatatatatatatatatatatatatatatatatata . PASS END=5799348;RU=ta;PERIOD=2;REF=19;GRID=14,21;STUTTERUP=0.0801087;STUTTERDOWN=0.247423;STUTTERP=0.586756;EXPTHRESH=19 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:9:0.486078:18,18:17-18,17-18:4,4,0,0:18,4:NULL:54.5028:366.612,131.36:0.374147,0.374147:0.76037,0.238382,0.0012729 +chr1 5799404 . taaataaataaa . . PASS END=5799415;RU=taaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00144991;STUTTERDOWN=0.000724958;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:18:0.988207:3,3:3-3,3-3:10,8,0,0:3,10:NULL:113.088:366.612,131.36:0,0:9.73386e-29,0.00654213,0.993474 +chr1 5800120 . ttattattattatta . . PASS END=5800134;RU=tta;PERIOD=3;REF=5;GRID=2,8;STUTTERUP=0.00154816;STUTTERDOWN=0.00309632;STUTTERP=0.920482;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:0.999937:5,5:5-5,5-5:18,11,0,0:5,18:NULL:179.431:366.612,131.36:0,0:0,4.3944e-05,0.999957 +chr1 5803800 . caacaacaacaacaa caacaacaacaacaacaacaacaacaacaacaacaa . PASS END=5803814;RU=caa;PERIOD=3;REF=5;GRID=8,15;STUTTERUP=0.00114912;STUTTERDOWN=0.0184994;STUTTERP=0.785269;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:39:0.999723:12,12:11-12,11-12:15,13,0,10:12,15:4,3|6,2|7,1|8,2|11,2:256.851:366.612,131.36:0.169767,0.169767:0,0,1 +chr1 5813834 . tcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttct tcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttct,tcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttct . PASS END=5813884;RU=tct;PERIOD=3;REF=17;GRID=14,26;STUTTERUP=0.0152699;STUTTERDOWN=0.0674738;STUTTERP=0.542535;EXPTHRESH=17 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:14:0.279533:18,23:17-23,17-23:2,3,0,8:18,2:4,1|7,1|9,1|11,1|12,1|17,1|18,1|23,1:97.0994:366.612,131.36:1.15753,2.37116:1.86078e-27,9.98403e-06,0.999993 +chr1 5813889 . ttcttttcttttcttttcttttcttttcttttcttttcttttctt ttctt . PASS END=5813933;RU=ttctt;PERIOD=5;REF=9;GRID=1,103;STUTTERUP=0.0026402;STUTTERDOWN=0.02522;STUTTERP=0.457747;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP .:.:.:.:.:.:.:.:.:.:.:. +chr1 5819521 . aaacaaacaaacaaacaaac aaacaaacaaacaaacaaacaaac . PASS END=5819540;RU=aaac;PERIOD=4;REF=5;GRID=3,9;STUTTERUP=0.00204913;STUTTERDOWN=0.0145108;STUTTERP=0.881789;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:42:0.998514:6,6:6-6,6-6:14,23,0,5:6,14:2,1|3,1|4,1|5,2:314.068:366.612,131.36:0,0:0,0.000353151,0.999651 +chr1 5829633 . ttccttccttcc . . PASS END=5829644;RU=ttcc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000441236;STUTTERDOWN=0.00126045;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:27:0.998494:3,3:3-3,3-3:13,14,0,0:3,13:NULL:182.139:366.612,131.36:0,0:1.54143e-44,0.000928731,0.999074 +chr1 5831560 . gatagatagatagatagatagatagatagatagatagatagatagatagatagata gata . PASS END=5831615;RU=gata;PERIOD=4;REF=14;GRID=1,103;STUTTERUP=0.00802346;STUTTERDOWN=0.0740321;STUTTERP=0.510627;EXPTHRESH=14 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:10:0.0234766:1,1:1-3,1-3:0,10,0,0:NULL:NULL:87.0303:366.612,131.36:0.339533,0.339533:0.76147,0.231543,0.00702052 +chr1 5832533 . aacaaacaaaca aacaaaca . PASS END=5832544;RU=aaca;PERIOD=4;REF=3;GRID=1,103;STUTTERUP=0.000445626;STUTTERDOWN=0.00089125;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:16:0.0412102:2,2:1-3,1-3:0,16,0,0:NULL:NULL:145.95:366.612,131.36:0.587088,0.587088:0.137906,0.489938,0.372325 +chr1 5833064 . tttgtttgtttgtttgtttgtttgtttg tttgtttgtttgtttgtttgtttg . PASS END=5833091;RU=tttg;PERIOD=4;REF=7;GRID=3,9;STUTTERUP=0.00177984;STUTTERDOWN=0.00895282;STUTTERP=0.683439;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:36:1:6,6:6-6,6-6:26,8,0,2:6,26:3,1|5,1:191.71:366.612,131.36:0,0:1,6.68227e-08,0 +chr1 5836792 . ttttgttttgttttg . . PASS END=5836806;RU=ttttg;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000374493;STUTTERDOWN=0.00506362;STUTTERP=0.902196;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:16:0.0532816:3,3:1-6,1-6:0,14,0,2:NULL:3,2:143.036:366.612,131.36:1.5536,1.5536:2.74641e-16,0.419007,0.581072 +chr1 5843531 . gttgttgttgtt gttgttgtt . PASS END=5843542;RU=gtt;PERIOD=3;REF=4;GRID=1,6;STUTTERUP=0.0028975;STUTTERDOWN=0.00125905;STUTTERP=0.992583;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:20:0.252266:3,3:2-4,2-4:2,17,0,0:3,2:NULL:166.713:366.612,131.36:0.665211,0.665211:0.577122,0.422964,1.17689e-06 +chr1 5844583 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . . PASS END=5844632;RU=gt;PERIOD=2;REF=25;GRID=22,28;STUTTERUP=0.0723067;STUTTERDOWN=0.24854;STUTTERP=0.664633;EXPTHRESH=25 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:12:0.193242:25,25:22-25,22-25:2,10,0,0:25,2:NULL:100.105:366.612,131.36:1.12192,1.12192:0.0045807,0.480536,0.514971 +chr1 5861282 . atatatatatat at . PASS END=5861293;RU=at;PERIOD=2;REF=6;GRID=1,103;STUTTERUP=0.0292654;STUTTERDOWN=0.00799332;STUTTERP=0.872508;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:7:0.00357437:1,1:1-7,1-7:0,7,0,0:NULL:NULL:64.8289:366.612,131.36:2.00328,2.00328:0.0589627,0.398793,0.542412 +chr1 5863544 . gggtgggtgggt gggt . PASS END=5863555;RU=gggt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00267297;STUTTERDOWN=0.00267297;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:1:0.0278135:1,1:3-3,3-3:0,0,0,0:NULL:NULL:-25:366.612,131.36:0,0:0.111169,0.444566,0.444358 +chr1 5864371 . attaattaatta attaattaattaatta . PASS END=5864382;RU=atta;PERIOD=4;REF=3;GRID=1,7;STUTTERUP=0.000990628;STUTTERDOWN=0.0267266;STUTTERP=0.906608;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:32:0.992643:4,4:4-4,4-4:11,21,0,0:4,11:NULL:235.41:366.612,131.36:0,0:1.12104e-44,0.00467797,0.995334 +chr1 5865370 . tctctctctctctc tctc . PASS END=5865383;RU=tc;PERIOD=2;REF=7;GRID=1,103;STUTTERUP=0.00830357;STUTTERDOWN=0.0152671;STUTTERP=0.998646;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:6:0.0027445:2,2:1-4,1-4:0,6,0,0:NULL:NULL:53.8209:366.612,131.36:0.789724,0.789724:0.0679048,0.427125,0.505172 +chr1 5868012 . acacacacacacacacacacacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacacacacacacacacacacacacac . PASS END=5868059;RU=ac;PERIOD=2;REF=24;GRID=27,33;STUTTERUP=0.0640362;STUTTERDOWN=0.284868;STUTTERP=0.712529;EXPTHRESH=24 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:20:0.34883:30,30:27-30,27-30:3,9,0,8:30,3:10,1|11,1|15,1|17,1|18,1|25,1|27,2:157.6:366.612,131.36:0.5093,0.5093:0,0,1 +chr1 5871062 . tattttattttattt . . PASS END=5871076;RU=tattt;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.00101743;STUTTERDOWN=0.00491237;STUTTERP=0.984306;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:6:0.864268:3,3:3-3,3-3:6,0,0,0:3,6:NULL:23.6225:366.612,131.36:0,0:1.2182e-18,0.0541899,0.945893 +chr1 5877999 . gatagatagatagatagatagatagatagatagatagatagata gatagatagatagatagatagatagatagatagatagatagatagata . PASS END=5878042;RU=gata;PERIOD=4;REF=11;GRID=9,16;STUTTERUP=0.00731594;STUTTERDOWN=0.0496832;STUTTERP=0.829235;EXPTHRESH=11 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:22:0.950424:12,12:12-13,12-13:9,10,0,2:12,9:3,2:143.371:366.612,131.36:0.469019,0.469019:2.10753e-26,0.0189762,0.981064 +chr1 5882501 . taaataaataaa . . PASS END=5882512;RU=taaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000701603;STUTTERDOWN=0.00311407;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:1:3,3:3-3,3-3:24,14,0,0:3,24:NULL:227.145:366.612,131.36:0,0:0,7.88834e-07,1 +chr1 5887687 . agaatagaatagaat . . PASS END=5887701;RU=agaat;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000860649;STUTTERDOWN=0.00122928;STUTTERP=0.959079;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:1:3,3:3-3,3-3:21,17,0,0:3,21:NULL:243.932:366.612,131.36:0,0:0,4.85605e-06,0.999995 +chr1 5889757 . acacacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacac,acacacacacacacacacacacacacacacacacacacac . PASS END=5889788;RU=ac;PERIOD=2;REF=16;GRID=15,23;STUTTERUP=0.062493;STUTTERDOWN=0.156986;STUTTERP=0.674193;EXPTHRESH=16 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:46:0.56051:19,20:18-19,18-21:12,21,0,13:18,4|19,8:5,2|6,1|7,3|13,1|14,1|16,1|18,2|20,2:371.436:366.612,131.36:0.298675,0.638748:0,9.94627e-11,1 +chr1 5890307 . acaaaacaaaacaaa . . PASS END=5890321;RU=acaaa;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000540888;STUTTERDOWN=0.00216353;STUTTERP=0.987382;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:0.999566:3,3:3-3,3-3:15,24,0,0:3,15:NULL:282.549:366.612,131.36:0,0:0,0.000391388,0.999613 +chr1 5896268 . tagatagatagatagatagatagataga tagatagatagatagatagatagatagatagatagatagataga . PASS END=5896295;RU=taga;PERIOD=4;REF=7;GRID=4,14;STUTTERUP=0.0598072;STUTTERDOWN=0.0314074;STUTTERP=0.782251;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:22:0.620046:11,11:7-11,7-11:4,11,0,5:11,4:8,3|9,1|11,1:157.745:366.612,131.36:1.2298,1.2298:0,0.0275314,0.972524 +chr1 5896295 . agacagacagacagacagacagacagacagacagac . . PASS END=5896330;RU=agac;PERIOD=4;REF=9;GRID=5,12;STUTTERUP=0.00884478;STUTTERDOWN=0.0834451;STUTTERP=0.798296;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:20:0.568114:9,9:8-9,8-9:4,10,0,5:9,4:5,2|6,1|7,2:145:366.612,131.36:0.484441,0.484441:4.39201e-09,0.215137,0.784907 +chr1 5897769 . atatatatatat atatatatatatat . PASS END=5897780;RU=at;PERIOD=2;REF=6;GRID=1,11;STUTTERUP=0.0865377;STUTTERDOWN=0.089048;STUTTERP=0.730963;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/1:56:1:6,7:6-6,6-8:30,25,0,0:6,16|7,11|8,3:NULL:370.665:366.612,131.36:0,0.263076:2.2259e-32,1.54871e-13,1 +chr1 5897783 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=5897826;RU=tg;PERIOD=2;REF=22;GRID=16,27;STUTTERUP=0.0970126;STUTTERDOWN=0.157355;STUTTERP=0.579071;EXPTHRESH=22 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:54:0.97053:23,23:22-24,22-24:19,23,0,11:22,3|23,14|24,2:4,1|5,1|9,1|10,1|14,1|15,1|19,2|20,1|21,1|22,1:391.072:366.612,131.36:0.701085,0.701085:1.6511e-30,3.98863e-05,0.999963 +chr1 5897969 . acacacacacacacacac acacacacacacacacacac . PASS END=5897986;RU=ac;PERIOD=2;REF=9;GRID=5,13;STUTTERUP=0.013322;STUTTERDOWN=0.0508239;STUTTERP=0.979928;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/1:49:0.471053:9,10:9-9,8-10:17,18,0,14:8,2|9,15:4,1|6,2|7,1|8,7|9,2|10,1:358.011:366.612,131.36:0,0.717122:3.53127e-43,4.02365e-06,0.999995 +chr1 5898251 . ttgttgttgttg . . PASS END=5898262;RU=ttg;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00164931;STUTTERDOWN=0.00557525;STUTTERP=0.907582;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:1:4,4:4-4,4-4:29,10,0,0:4,29:NULL:204.271:366.612,131.36:0,0:0,1.64728e-08,1 +chr1 5899946 . catacatacatacatacatacatacatacatacatacata catacatacatacatacatacatacatacatacata . PASS END=5899985;RU=cata;PERIOD=4;REF=10;GRID=5,12;STUTTERUP=0.0352013;STUTTERDOWN=0.0721805;STUTTERP=0.864358;EXPTHRESH=10 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:35:0.524396:9,9:8-9,8-9:14,12,0,9:8,3|9,11:3,1|5,3|6,1|7,3|8,1:244.737:366.612,131.36:0.481803,0.481803:0.999697,0.000306133,1.72282e-16 +chr1 5899987 . gtatgtatgtat . . PASS END=5899998;RU=gtat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00280811;STUTTERDOWN=0.00237307;STUTTERP=0.906199;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:26:0.999084:3,3:3-3,3-3:13,13,0,0:3,13:NULL:172.571:366.612,131.36:0,0:2.75199e-34,0.000516341,0.999485 +chr1 5902689 . cacacacacacacacacacacacacacaca cacacacacacacacacacacacacacacaca . PASS END=5902718;RU=ca;PERIOD=2;REF=15;GRID=9,19;STUTTERUP=0.0518038;STUTTERDOWN=0.142223;STUTTERP=0.765765;EXPTHRESH=15 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:44:0.872688:16,16:12-16,12-16:6,21,0,15:16,6:6,2|8,1|9,3|10,1|11,2|12,1|14,4|15,1:345.735:366.612,131.36:1.43308,1.43308:1.11668e-19,0.0185593,0.981481 +chr1 5903515 . tgttttgttttgttt . . PASS END=5903529;RU=tgttt;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000456431;STUTTERDOWN=0.00220375;STUTTERP=0.984306;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:34:0.999941:3,3:3-3,3-3:17,17,0,0:3,17:NULL:221.876:366.612,131.36:0,0:0,5.57718e-05,0.999948 +chr1 5907759 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=5907810;RU=gt;PERIOD=2;REF=26;GRID=22,28;STUTTERUP=0.0847173;STUTTERDOWN=0.210187;STUTTERP=0.709139;EXPTHRESH=26 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:43:0.0838707:25,25:23-26,23-26:0,30,0,12:NULL:4,1|8,1|11,1|14,1|15,1|18,2|21,2|23,1|24,1|25,1:364.098:366.612,131.36:0.655263,0.655263:0.251683,0.543114,0.205209 +chr1 5912141 . taaataaataaa . . PASS END=5912152;RU=taaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000345648;STUTTERDOWN=0.000691295;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:1.00001:3,3:3-3,3-3:22,16,0,0:3,22:NULL:237.723:366.612,131.36:0,0:0,3.11145e-06,1 +chr1 5915677 . caccaccaccaccac . . PASS END=5915691;RU=cac;PERIOD=3;REF=5;GRID=2,9;STUTTERUP=0.00191633;STUTTERDOWN=0.0117853;STUTTERP=0.690037;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:93:1:5,5:5-5,5-5:61,27,0,4:5,61:3,2|4,2:522.376:366.612,131.36:0,0:0,2.71225e-18,1 +chr1 5915768 . acacacacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacacac . PASS END=5915801;RU=ac;PERIOD=2;REF=17;GRID=13,24;STUTTERUP=0.0688425;STUTTERDOWN=0.269358;STUTTERP=0.50245;EXPTHRESH=17 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:73:0.780363:20,20:20-21,20-21:34,20,0,18:18,2|19,5|20,22|21,5:4,1|5,1|6,3|9,3|10,1|11,1|12,1|14,1|15,2|16,2|18,2:516.966:366.612,131.36:0.451989,0.451989:0,8.05231e-11,1 +chr1 5918994 . ccctccctccct . . PASS END=5919005;RU=ccct;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000594451;STUTTERDOWN=0.00169813;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:0.999912:3,3:3-3,3-3:16,13,0,0:3,16:NULL:186.507:366.612,131.36:0,0:0,6.56808e-05,0.999934 +chr1 5919625 . atatatatatat . . PASS END=5919636;RU=at;PERIOD=2;REF=6;GRID=3,9;STUTTERUP=0.0221095;STUTTERDOWN=0.00840933;STUTTERP=0.893988;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:0.999156:6,6:6-6,6-6:14,22,0,0:6,14:NULL:260.754:366.612,131.36:0,0:2.20629e-24,0.000583008,0.999422 +chr1 5919950 . gatgatgatgat . . PASS END=5919961;RU=gat;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00322879;STUTTERDOWN=0.00136429;STUTTERP=0.95527;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:0.999713:4,4:4-4,4-4:16,15,0,0:4,16:NULL:207.353:366.612,131.36:0,0:1.2002e-40,0.000204791,0.999797 +chr1 5922252 . atatatatatatatatatatatatatat atatatatatatatatatatatatatatatat,atatatatatatatatatatatatatatatatat . PASS END=5922279;RU=at;PERIOD=2;REF=14;GRID=13,21;STUTTERUP=0.160016;STUTTERDOWN=0.190892;STUTTERP=0.742789;EXPTHRESH=14 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:13:0.646279:16,17:16-18,17-18:6,6,0,0:16,2|17,4:NULL:90.1045:366.612,131.36:0.617841,0.304526:3.00658e-13,0.0144617,0.98557 +chr1 5926025 . tctttctttctt . . PASS END=5926036;RU=tctt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000452772;STUTTERDOWN=0.00362213;STUTTERP=0.966669;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:32:1:3,3:3-3,3-3:20,12,0,0:3,20:NULL:194.3:366.612,131.36:0,0:0,1.13297e-05,0.999993 +chr1 5927629 . gatgaagatgaagatgaagatgaagatgaagatgaagatgaagatgaagatgaagatgaagatgaagatgaa gatgaagatgaagatgaagatgaagatgaagatgaagatgaagatgaagatgaagatgaagatgaa . PASS END=5927700;RU=gatgaa;PERIOD=6;REF=12;GRID=7,14;STUTTERUP=0.00178151;STUTTERDOWN=0.0175601;STUTTERP=0.498828;EXPTHRESH=12 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:92:0.497956:11,11:10-11,10-11:15,43,0,34:10,2|11,13:2,1|3,1|4,2|5,5|6,6|7,6|8,2|9,6|10,5:718.283:366.612,131.36:0.481803,0.481803:0.999993,1.10196e-05,4.5566e-31 +chr1 5927964 . acccacccaccc . . PASS END=5927975;RU=accc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000844772;STUTTERDOWN=0.00168953;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:48:1:3,3:3-3,3-3:24,20,0,4:3,24:2,4:310.166:366.612,131.36:0,0:0,1.91414e-07,1 +chr1 5929823 . tttgtttgtttg . . PASS END=5929834;RU=tttg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000452829;STUTTERDOWN=0.000452829;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:49:1:3,3:3-3,3-3:29,20,0,0:3,29:NULL:296.826:366.612,131.36:0,0:0,9.32122e-09,1 +chr1 5930224 . gttgttgttgttgttgttgttgtt . . PASS END=5930247;RU=gtt;PERIOD=3;REF=8;GRID=5,11;STUTTERUP=0.00126689;STUTTERDOWN=0.0182464;STUTTERP=0.75731;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:43:1:8,8:8-8,8-8:27,12,0,4:8,27:4,2|5,1|7,1:252.24:366.612,131.36:0,0:0,4.44333e-08,1 +chr1 5934390 . tttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcc tttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcctttcc . PASS END=5934474;RU=tttcc;PERIOD=5;REF=17;GRID=11,17;STUTTERUP=0.00854848;STUTTERDOWN=0.0171118;STUTTERP=0.921241;EXPTHRESH=17 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:37:0.301504:14,14:11-14,11-14:2,14,0,21:14,2:3,2|4,2|5,3|6,2|7,2|8,1|9,2|10,3|11,2|12,1|13,1:286.328:366.612,131.36:0.676608,0.676608:0.927216,0.0728785,3.47771e-10 +chr1 5940366 . aattaattaatt . . PASS END=5940377;RU=aatt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000430615;STUTTERDOWN=0.00123011;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:25:0.999654:3,3:3-3,3-3:15,10,0,0:3,15:NULL:147.578:366.612,131.36:0,0:0,0.000189184,0.999812 +chr1 5940451 . tttgttttgttttgt . . PASS END=5940465;RU=tttgt;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000866787;STUTTERDOWN=0.00293002;STUTTERP=0.940969;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:27:0.999994:3,3:3-3,3-3:19,8,0,0:3,19:NULL:147.155:366.612,131.36:0,0:0,1.23806e-05,0.999987 +chr1 5941150 . acacacacacac . . PASS END=5941161;RU=ac;PERIOD=2;REF=6;GRID=3,9;STUTTERUP=0.00732232;STUTTERDOWN=0.0121325;STUTTERP=0.992655;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:1:6,6:6-6,6-6:20,15,0,2:6,20:4,1|5,1:232.608:366.612,131.36:0,0:3.65739e-43,3.9473e-06,0.999995 +chr1 5942017 . acaaaacaaaacaaa . . PASS END=5942031;RU=acaaa;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000445987;STUTTERDOWN=0.00127402;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:1.00001:3,3:3-3,3-3:22,9,0,0:3,22:NULL:166.874:366.612,131.36:0,0:0,1.36527e-06,1 +chr1 5945567 . aaacaaacaaacaaacaaacaaac . . PASS END=5945590;RU=aaac;PERIOD=4;REF=6;GRID=2,9;STUTTERUP=0.00119302;STUTTERDOWN=0.0151446;STUTTERP=0.911994;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:46:0.999936:6,6:5-6,5-6:17,17,0,11:6,17:2,2|3,2|4,4|5,3:307.495:366.612,131.36:0.253975,0.253975:0,3.38207e-05,0.99997 +chr1 5946795 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=5946832;RU=gt;PERIOD=2;REF=19;GRID=18,25;STUTTERUP=0.0704551;STUTTERDOWN=0.208859;STUTTERP=0.715889;EXPTHRESH=19 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:32:0.472493:22,22:21-22,21-22:12,9,0,11:21,4|22,8:6,1|7,1|8,1|11,2|12,1|13,1|14,1|16,1|20,2:231.246:366.612,131.36:0.489073,0.489073:6.16571e-44,7.10627e-05,0.999932 +chr1 5947011 . tccatccatcca . . PASS END=5947022;RU=tcca;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000379604;STUTTERDOWN=0.000759208;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:44:1:3,3:3-3,3-3:27,17,0,0:3,27:NULL:260.132:366.612,131.36:0,0:0,3.17725e-08,1 +chr1 5953047 . tcattcattcattcat . . PASS END=5953062;RU=tcat;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000453506;STUTTERDOWN=0.00952751;STUTTERP=0.974963;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:0.998895:4,4:3-4,3-4:14,21,0,3:4,14:3,3:275.253:366.612,131.36:0.412766,0.412766:0,0.000556861,0.999446 +chr1 5953771 . attttattttatttt . . PASS END=5953785;RU=atttt;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.00180703;STUTTERDOWN=0.000903525;STUTTERP=0.741116;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:1:3,3:3-3,3-3:23,14,0,0:3,23:NULL:215.118:366.612,131.36:0,0:0,7.59821e-07,1 +chr1 5956109 . agagagagagag . . PASS END=5956120;RU=ag;PERIOD=2;REF=6;GRID=3,9;STUTTERUP=0.00502821;STUTTERDOWN=0.0146694;STUTTERP=0.936778;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:0.999051:6,6:6-6,6-6:14,17,0,0:6,14:NULL:213.09:366.612,131.36:0,0:1.35846e-32,0.000674371,0.999331 +chr1 5956842 . ttctttctttct . . PASS END=5956853;RU=ttct;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000476103;STUTTERDOWN=0.00229873;STUTTERP=0.984306;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:47:1:3,3:3-3,3-3:34,13,0,0:3,34:NULL:257.7:366.612,131.36:0,0:0,2.2876e-10,1 +chr1 5958262 . gaaggaaggaaggaaggaag . . PASS END=5958281;RU=gaag;PERIOD=4;REF=5;GRID=2,8;STUTTERUP=0.000884187;STUTTERDOWN=0.008905;STUTTERP=0.943295;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:1.00001:5,5:5-5,5-5:22,15,0,0:5,22:NULL:229.447:366.612,131.36:0,0:0,3.26586e-06,1 +chr1 5963266 . gtttgtttgtttgtttgtttgtttgtttgtttgtttgttt . . PASS END=5963305;RU=gttt;PERIOD=4;REF=10;GRID=7,13;STUTTERUP=0.00275552;STUTTERDOWN=0.0328398;STUTTERP=0.839777;EXPTHRESH=10 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:56:1:10,10:10-10,10-10:28,19,0,9:10,28:3,1|4,1|5,2|6,2|7,1|8,2:366.047:366.612,131.36:0,0:0,8.63647e-08,1 +chr1 5964606 . atatatatatatat atatatatatatatatatatatat,atatatatatatatatatatatatat . PASS END=5964619;RU=at;PERIOD=2;REF=7;GRID=4,17;STUTTERUP=0.0642761;STUTTERDOWN=0.155693;STUTTERP=0.588943;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:39:0.886418:12,13:7-13,7-14:14,23,0,0:10,2|11,2|12,4|13,6:NULL:290.803:366.612,131.36:1.66142,1.61043:1.54621e-36,9.18377e-06,0.999993 +chr1 5964620 . acacacacacacacacacacac acacacacacacacacacacacacacacacacac . PASS END=5964641;RU=ac;PERIOD=2;REF=11;GRID=8,21;STUTTERUP=0.0765166;STUTTERDOWN=0.133235;STUTTERP=0.560336;EXPTHRESH=11 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:43:0.187232:17,17:11-15,11-15:5,29,0,4:17,5:4,1|8,2|9,1:321.414:366.612,131.36:1.56711,1.56711:4.96889e-16,0.413864,0.58621 +chr1 5969864 . ccacccacccacccac . . PASS END=5969879;RU=ccac;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000325807;STUTTERDOWN=0.00744567;STUTTERP=0.977178;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:67:1:4,4:4-4,4-4:33,31,0,3:4,33:2,1|3,2:441.455:366.612,131.36:0,0:0,4.1973e-10,1 +chr1 5971172 . tgtttgtttgtttgtttgtttgtt tgtttgtttgtttgtt . PASS END=5971195;RU=tgtt;PERIOD=4;REF=6;GRID=1,7;STUTTERUP=0.00100859;STUTTERDOWN=0.00882569;STUTTERP=0.798503;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:41:0.999887:4,4:4-4,4-4:16,23,0,2:4,16:2,1|3,1:291.383:366.612,131.36:0,0:0.999985,1.85909e-05,0 +chr1 5973006 . acacacacacac acacacacacacacac . PASS END=5973017;RU=ac;PERIOD=2;REF=6;GRID=4,11;STUTTERUP=0.00923009;STUTTERDOWN=0.0454966;STUTTERP=0.67267;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:34:0.937908:8,8:7-8,7-8:15,17,0,2:7,2|8,13:6,2:237.838:366.612,131.36:0.40582,0.40582:0,8.97946e-05,0.999911 +chr1 5974638 . aaataaataaat . . PASS END=5974649;RU=aaat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000725834;STUTTERDOWN=0.00350449;STUTTERP=0.719903;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:17:0.994209:3,3:3-3,3-3:11,6,0,0:3,11:NULL:97.3759:366.612,131.36:0,0:2.8099e-36,0.00287796,0.997132 +chr1 5974827 . ataataataataataata . . PASS END=5974844;RU=ata;PERIOD=3;REF=6;GRID=1,9;STUTTERUP=0.00791169;STUTTERDOWN=0.031646;STUTTERP=0.863378;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:11:0.949345:6,6:4-6,4-6:8,0,0,2:6,8:3,2:47.1122:366.612,131.36:0.957892,0.957892:8.02138e-18,0.0264945,0.973556 +chr1 5974849 . aaattaaattaaattaaatt aaattaaattaaatt . PASS END=5974868;RU=aaatt;PERIOD=5;REF=4;GRID=1,7;STUTTERUP=0.000984197;STUTTERDOWN=0.00873665;STUTTERP=0.839025;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:3:0.0334915:3,3:3-4,3-4:0,0,0,2:NULL:3,2:14.0982:366.612,131.36:0.44763,0.44763:0.0669411,0.400408,0.532829 +chr1 5976547 . tttgttttgttttgttttgt . . PASS END=5976566;RU=tttgt;PERIOD=5;REF=4;GRID=1,7;STUTTERUP=0.000636861;STUTTERDOWN=0.00254742;STUTTERP=0.844424;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:25:0.997467:4,4:4-4,4-4:12,11,0,2:4,12:3,2:157.502:366.612,131.36:0,0:1.78561e-39,0.0011616,0.998845 +chr1 5978570 . aaagaaagaaag . . PASS END=5978581;RU=aaag;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000449388;STUTTERDOWN=0.00128374;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:47:1:3,3:3-3,3-3:30,15,0,2:3,30:2,2:271.734:366.612,131.36:0,0:0,5.8207e-09,1 +chr1 5981538 . ataataataata . . PASS END=5981549;RU=ata;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00256377;STUTTERDOWN=0.00212397;STUTTERP=0.948224;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:24:0.993889:4,4:4-4,4-4:11,13,0,0:4,11:NULL:163.313:366.612,131.36:0,0:1.29433e-29,0.00370406,0.996307 +chr1 5990630 . tggattatctggattatctggattatc tggattatc . PASS END=5990656;RU=tggattatc;PERIOD=9;REF=3;GRID=1,103;STUTTERUP=0.000421338;STUTTERDOWN=0.00120361;STUTTERP=0.761601;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:19:0.220125:1,1:1-2,1-2:0,19,0,0:NULL:NULL:165.643:366.612,131.36:0.311527,0.311527:0.586116,0.37447,0.0395355 +chr1 5990673 . acacacacacac acacacacacacacacacacacacacacacacacacacac . PASS END=5990684;RU=ac;PERIOD=2;REF=6;GRID=16,23;STUTTERUP=0.0130328;STUTTERDOWN=0.0304194;STUTTERP=0.799802;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:23:0.322577:20,20:19-20,19-20:2,14,0,6:20,2:4,1|8,2|9,1|12,1|20,1:184.95:366.612,131.36:0.661813,0.661813:0,0,1 +chr1 5991174 . aaaacaaaacaaaac aaaac . PASS END=5991188;RU=aaaac;PERIOD=5;REF=3;GRID=1,5;STUTTERUP=0.000903851;STUTTERDOWN=0.00200978;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:11:0.0600654:1,1:1-3,1-3:0,10,0,0:NULL:NULL:92.4002:366.612,131.36:0.485855,0.485855:0.185855,0.498351,0.315903 +chr1 5999275 . gggtgggtgggt gggt . PASS END=5999286;RU=gggt;PERIOD=4;REF=3;GRID=1,103;STUTTERUP=0.0015928;STUTTERDOWN=0.0015928;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:7:0.00981823:1,1:1-2,1-2:0,7,0,0:NULL:NULL:58.3651:366.612,131.36:0.469019,0.469019:0.0380205,0.352752,0.609338 +chr1 6002341 . aaataaataaat aaat . PASS END=6002352;RU=aaat;PERIOD=4;REF=3;GRID=1,103;STUTTERUP=0.000594061;STUTTERDOWN=0.00118775;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:18:0.0846653:1,1:1-1,1-1:0,18,0,0:NULL:NULL:164.799:366.612,131.36:0.139319,0.139319:0.190566,0.5221,0.287427 +chr1 6003957 . tttgtttgtttgtttgtttgtttg tttg,tttgtttg . PASS END=6003980;RU=tttg;PERIOD=4;REF=6;GRID=1,103;STUTTERUP=0.000915846;STUTTERDOWN=0.00522844;STUTTERP=0.96802;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:9:0.0340808:1,2:1-3,1-3:0,9,0,0:NULL:NULL:82.4126:366.612,131.36:0.86417,0.863602:0.273918,0.532388,0.193697 +chr1 6007179 . tgtgtgtgtgtgtg . . PASS END=6007192;RU=tg;PERIOD=2;REF=7;GRID=4,11;STUTTERUP=0.0150802;STUTTERDOWN=0.0182027;STUTTERP=0.934731;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:32:1.00001:7,7:7-7,7-7:21,10,0,0:7,21:NULL:175.581:366.612,131.36:0.0990099,0.0990099:6.33055e-39,4.40377e-06,0.999995 +chr1 6008813 . cacacacacacacacacacacacacacacacacacacacacacacacacaca cacacacacacacacacacacacacacacacacacacacacacacaca . PASS END=6008864;RU=ca;PERIOD=2;REF=26;GRID=18,27;STUTTERUP=0.0646537;STUTTERDOWN=0.233679;STUTTERP=0.806718;EXPTHRESH=26 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:28:0.0685445:24,24:21-24,21-24:0,10,0,16:NULL:7,2|9,1|11,2|12,2|14,1|15,1|16,1|20,2|22,1|23,1|24,2:215.675:366.612,131.36:1.34544,1.34544:0.376805,0.480889,0.142383 +chr1 6010711 . atttatttattt . . PASS END=6010722;RU=attt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000860382;STUTTERDOWN=0.00370672;STUTTERP=0.624684;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:4:0.614864:3,3:3-3,3-3:4,0,0,0:3,4:NULL:15.6359:366.612,131.36:0,0:8.92207e-14,0.153957,0.846123 +chr1 6016751 . catacatacata . . PASS END=6016762;RU=cata;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000583097;STUTTERDOWN=0.000583097;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:34:1:3,3:3-3,3-3:24,10,0,0:3,24:NULL:186.522:366.612,131.36:0,0:0,2.81512e-07,1 +chr1 6022355 . tttgtttgtttgtttgtttgtttgtttgtttg tttg . PASS END=6022386;RU=tttg;PERIOD=4;REF=8;GRID=1,103;STUTTERUP=0.00305899;STUTTERDOWN=0.0112483;STUTTERP=0.852877;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:12:0.0275954:1,1:1-4,1-4:0,12,0,0:NULL:NULL:111.669:366.612,131.36:0.805213,0.805213:0.541162,0.403616,0.0553774 +chr1 6023295 . ttatttatttatttatttatttatttat ttatttatttatttatttat . PASS END=6023322;RU=ttat;PERIOD=4;REF=7;GRID=2,8;STUTTERUP=0.00137576;STUTTERDOWN=0.0127454;STUTTERP=0.63335;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:32:0.999751:5,5:5-5,5-5:16,14,0,2:5,16:4,2:209.297:366.612,131.36:0,0:0.999948,5.54584e-05,1.19573e-41 +chr1 6023967 . tttttgtttttgtttttg . . PASS END=6023984;RU=tttttg;PERIOD=6;REF=3;GRID=1,6;STUTTERUP=0.000488629;STUTTERDOWN=0.00390898;STUTTERP=0.826703;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:22:0.98759:3,3:3-3,3-3:10,12,0,0:3,10:NULL:152.337:366.612,131.36:0,0:3.97564e-34,0.00838731,0.99163 +chr1 6025872 . tttatttatttatttatttatttattta tttatttatttatttatttattta . PASS END=6025899;RU=ttta;PERIOD=4;REF=7;GRID=2,9;STUTTERUP=0.00518887;STUTTERDOWN=0.0257263;STUTTERP=0.788397;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:28:0.975625:6,6:5-6,5-6:10,14,0,3:6,10:2,1|3,1|5,1:200.967:366.612,131.36:0.442564,0.442564:0.993257,0.00675705,8.68775e-18 +chr1 6025930 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=6025961;RU=tg;PERIOD=2;REF=16;GRID=22,29;STUTTERUP=0.0663689;STUTTERDOWN=0.125736;STUTTERP=0.876381;EXPTHRESH=16 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:15:0.0335167:23,23:23-26,23-26:0,13,0,0:NULL:NULL:131.818:366.612,131.36:0.917112,0.917112:0,0,1 +chr1 6033005 . taaataaataaa . . PASS END=6033016;RU=taaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000450843;STUTTERDOWN=0.000450843;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:1.00001:3,3:3-3,3-3:23,12,0,3:3,23:2,3:225.16:366.612,131.36:0,0:0,6.25145e-07,1 +chr1 6033244 . atacatacatacatacatacatacatacatacatac atacatacatacatacatacatac,atacatacatacatacatacatacatac . PASS END=6033279;RU=atac;PERIOD=4;REF=9;GRID=3,10;STUTTERUP=0.0042982;STUTTERDOWN=0.0520259;STUTTERP=0.878454;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:33:0.902238:6,7:6-7,7-7:8,20,0,5:6,2|7,6:2,1|3,2|5,2:264.045:366.612,131.36:0.478946,0.0990099:0.999545,0.000455991,4.64201e-20 +chr1 6033357 . atatatatatatatat . . PASS END=6033372;RU=at;PERIOD=2;REF=8;GRID=5,11;STUTTERUP=0.02937;STUTTERDOWN=0.0451372;STUTTERP=0.845196;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:0.999213:8,8:8-8,8-8:14,15,0,0:8,14:NULL:202.918:366.612,131.36:0,0:7.41025e-23,0.000450359,0.999552 +chr1 6034894 . ggcaggcaggcaggca . . PASS END=6034909;RU=ggca;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000567673;STUTTERDOWN=0.00324327;STUTTERP=0.969616;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:0.990581:4,4:4-4,4-4:11,20,0,0:4,11:NULL:229.918:366.612,131.36:0,0:5.80723e-36,0.00742497,0.992595 +chr1 6041090 . aaaataaaataaaat . . PASS END=6041104;RU=aaaat;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000432756;STUTTERDOWN=0.00173101;STUTTERP=0.987382;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:43:0.999995:3,3:3-3,3-3:20,23,0,0:3,20:NULL:296.664:366.612,131.36:0,0:0,1.48067e-05,0.999987 +chr1 6041134 . tgtttgtttgtttgtttgtttgtttgtt . . PASS END=6041161;RU=tgtt;PERIOD=4;REF=7;GRID=2,10;STUTTERUP=0.000962005;STUTTERDOWN=0.0224524;STUTTERP=0.770213;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:41:0.999963:7,7:5-7,5-7:18,17,0,5:7,18:3,1|5,3|6,1:268.322:366.612,131.36:0.597351,0.597351:0,3.16593e-05,0.999971 +chr1 6041922 . ttggtttggtttggtttggt ttggtttggtttggtttggtttggt . PASS END=6041941;RU=ttggt;PERIOD=5;REF=4;GRID=1,8;STUTTERUP=0.00114511;STUTTERDOWN=0.0101569;STUTTERP=0.681618;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:42:0.999293:5,5:3-5,3-5:13,22,0,6:5,13:2,1|4,4|5,1:295.978:366.612,131.36:0.863148,0.863148:0,6.90972e-05,0.999933 +chr1 6041960 . tttgtttttgtttttgtt . . PASS END=6041977;RU=tttgtt;PERIOD=6;REF=3;GRID=1,6;STUTTERUP=0.000389942;STUTTERDOWN=0.00222784;STUTTERP=0.969616;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:34:0.999493:3,3:3-3,3-3:14,20,0,0:3,14:NULL:236.201:366.612,131.36:0,0:0,0.000392877,0.999607 +chr1 6042004 . tttgttttgttttgttttgttttgttttgttttgt . . PASS END=6042038;RU=tttgt;PERIOD=5;REF=7;GRID=4,10;STUTTERUP=0.000795621;STUTTERDOWN=0.009482;STUTTERP=0.681419;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:17:0.161982:7,7:4-7,4-7:2,15,0,0:7,2:NULL:150.298:366.612,131.36:1.38953,1.38953:8.51861e-07,0.69187,0.308144 +chr1 6048614 . aaacaaacaaac . . PASS END=6048625;RU=aaac;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000482928;STUTTERDOWN=0.00137955;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:47:1:3,3:3-3,3-3:38,7,0,2:3,38:2,2:231.003:366.612,131.36:0,0:0,1.21015e-11,1 +chr1 6051144 . gtttgtttgtttgtttgtttgtttgttt gtttgtttgtttgtttgtttgtttgtttgtttgttt . PASS END=6051171;RU=gttt;PERIOD=4;REF=7;GRID=6,12;STUTTERUP=0.00410198;STUTTERDOWN=0.0291204;STUTTERP=0.862158;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:20:0.978832:9,9:9-9,9-9:9,9,0,2:9,9:2,1|8,1:134.067:366.612,131.36:0,0:7.00649e-45,0.00358442,0.996428 +chr1 6056382 . cctcctcctcctcct . . PASS END=6056396;RU=cct;PERIOD=3;REF=5;GRID=2,8;STUTTERUP=0.00165382;STUTTERDOWN=0.00719614;STUTTERP=0.755336;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:0.998765:5,5:5-5,5-5:13,23,0,0:5,13:NULL:259.972:366.612,131.36:0,0:3.85917e-38,0.00100599,0.998998 +chr1 6056414 . tttgtttgtttgtttgtttgtttgtttg . . PASS END=6056441;RU=tttg;PERIOD=4;REF=7;GRID=4,10;STUTTERUP=0.00160744;STUTTERDOWN=0.0145898;STUTTERP=0.653978;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:0.990886:7,7:7-7,7-7:10,17,0,2:7,10:5,2:214.125:366.612,131.36:0,0:6.78826e-30,0.00684723,0.993167 +chr1 6059464 . aaaaacaaaaacaaaaac . . PASS END=6059481;RU=aaaaac;PERIOD=6;REF=3;GRID=1,6;STUTTERUP=0.000347928;STUTTERDOWN=0.00235222;STUTTERP=0.833561;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:58:1:3,3:3-3,3-3:33,25,0,0:3,33:NULL:365.524:366.612,131.36:0,0:0,3.01269e-09,1 +chr1 6059973 . aaataaataaat . . PASS END=6059984;RU=aaat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000483516;STUTTERDOWN=0.00138123;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:46:1:3,3:3-3,3-3:23,21,0,2:3,23:2,2:303.124:366.612,131.36:0,0:0,3.97391e-07,1 +chr1 6061243 . agagagagagag agagagag . PASS END=6061254;RU=ag;PERIOD=2;REF=6;GRID=1,7;STUTTERUP=0.00449748;STUTTERDOWN=0.00756111;STUTTERP=0.838338;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:20:1:4,4:4-4,4-4:20,0,0,0:4,20:NULL:77.6389:366.612,131.36:0,0:1,3.85916e-06,0 +chr1 6062647 . gtgggtgggtgg . . PASS END=6062658;RU=gtgg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00049518;STUTTERDOWN=0.000990358;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:49:1:3,3:3-3,3-3:19,28,0,2:3,19:2,2:337.593:366.612,131.36:0,0:0,6.14054e-06,0.999995 +chr1 6062751 . taaataaataaa . . PASS END=6062762;RU=taaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000439234;STUTTERDOWN=0.000878467;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:28:0.999991:3,3:3-3,3-3:18,10,0,0:3,18:NULL:161.93:366.612,131.36:0,0:0,1.2184e-05,0.999987 +chr1 6066036 . ctctgtctctgtctctgt ctctgtctctgt . PASS END=6066053;RU=ctctgt;PERIOD=6;REF=3;GRID=1,5;STUTTERUP=0.000450093;STUTTERDOWN=0.00611038;STUTTERP=0.902366;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:29:0.99997:2,2:2-2,2-2:17,12,0,0:2,17:NULL:176.013:366.612,131.36:0,0:0.999979,2.31339e-05,5.9961e-40 +chr1 6072915 . aataataataataataataataataataataataataat aataataataataataataataataat,aataataataataataataataataataat . PASS END=6072953;RU=aat;PERIOD=3;REF=13;GRID=1,11;STUTTERUP=0.048408;STUTTERDOWN=0.0551013;STUTTERP=0.67274;EXPTHRESH=13 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:4:0.0671286:9,10:5-11,5-11:0,2,0,2:NULL:8,2:35.2296:366.612,131.36:1.43267,1.53245:1,0,0 +chr1 6077184 . gagagagagagagagagagagagagagagagagagagagagaga gagagagagagagagagagagagagagagagagagagagagagagaga,gagagagagagagagagagagagagagagagagagagagagagagagaga . PASS END=6077227;RU=ga;PERIOD=2;REF=22;GRID=17,28;STUTTERUP=0.039837;STUTTERDOWN=0.281303;STUTTERP=0.707788;EXPTHRESH=22 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:22:0.892419:24,25:20-24,20-25:7,13,0,0:24,5|25,2:NULL:158.487:366.612,131.36:1.70567,2.21109:5.40504e-17,0.00942569,0.990596 +chr1 6080857 . aaacaaacaaacaaacaaac aaacaaacaaacaaac . PASS END=6080876;RU=aaac;PERIOD=4;REF=5;GRID=1,7;STUTTERUP=0.000566212;STUTTERDOWN=0.00961137;STUTTERP=0.896315;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:35:0.999992:4,4:4-4,4-4:18,14,0,3:4,18:2,1|3,2:220.417:366.612,131.36:0,0:0.999987,1.36199e-05,1.52107e-38 +chr1 6083873 . aataaataaata aataaata . PASS END=6083884;RU=aata;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000616084;STUTTERDOWN=0.00246431;STUTTERP=0.987382;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/0:32:0.774856:2,3:2-2,2-3:20,10,0,2:2,18|3,2:2,2:202.804:366.612,131.36:0,0.497026:0.225216,0.774819,1.26257e-42 +chr1 6084220 . atttatttattt attt . PASS END=6084231;RU=attt;PERIOD=4;REF=3;GRID=1,103;STUTTERUP=0.00326359;STUTTERDOWN=0.00228491;STUTTERP=0.959079;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:15:0.138181:1,1:1-1,1-1:0,15,0,0:NULL:NULL:149.469:366.612,131.36:0,0:0.260032,0.543367,0.196608 +chr1 6085465 . taataataataataa taataataataa . PASS END=6085479;RU=taa;PERIOD=3;REF=5;GRID=1,7;STUTTERUP=0.00308708;STUTTERDOWN=0.0076497;STUTTERP=0.763541;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:16:0.98907:4,4:4-4,4-4:10,6,0,0:4,10:NULL:93.322:366.612,131.36:0,0:0.995439,0.00457339,2.73967e-23 +chr1 6085756 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=6085801;RU=tg;PERIOD=2;REF=23;GRID=13,20;STUTTERUP=0.0618974;STUTTERDOWN=0.177363;STUTTERP=0.757477;EXPTHRESH=23 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:25:0.750683:17,17:16-17,16-17:8,12,0,5:16,2|17,6:7,1|14,2|16,1|17,1:195.426:366.612,131.36:0.35561,0.35561:1,0,0 +chr1 6086268 . tctctctctctctctctctctctctctctctc tctctctctctctctctctctctctctctctctctctctctctctc . PASS END=6086299;RU=tc;PERIOD=2;REF=16;GRID=1,24;STUTTERUP=0.0342398;STUTTERDOWN=0.221881;STUTTERP=0.65104;EXPTHRESH=16 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:7:0.0130102:23,23:1-23,1-23:0,5,0,2:NULL:15,1|21,1:63.6069:366.612,131.36:8.93866,8.93866:1.83284e-08,0.60832,0.391743 +chr1 6087008 . tatttatttatt . . PASS END=6087019;RU=tatt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000610122;STUTTERDOWN=0.000610122;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:21:0.998042:3,3:3-3,3-3:12,9,0,0:3,12:NULL:131.045:366.612,131.36:0,0:2.22887e-39,0.00113631,0.998868 +chr1 6092499 . tgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=6092524;RU=tg;PERIOD=2;REF=13;GRID=11,19;STUTTERUP=0.0511601;STUTTERDOWN=0.121647;STUTTERP=0.793766;EXPTHRESH=13 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:36:0.997822:16,16:15-16,15-16:18,14,0,3:15,2|16,16:7,1|9,1|11,1:246.975:366.612,131.36:0.258566,0.258566:0,2.54159e-05,0.999978 +chr1 6093013 . cacacacacacaca . . PASS END=6093026;RU=ca;PERIOD=2;REF=7;GRID=4,10;STUTTERUP=0.041446;STUTTERDOWN=0.0067867;STUTTERP=0.960129;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:13:0.396531:7,7:5-7,5-7:3,10,0,0:7,3:NULL:100.647:366.612,131.36:0.404368,0.404368:7.27447e-05,0.406649,0.593349 +chr1 6098593 . ctagaactagaactagaa . . PASS END=6098610;RU=ctagaa;PERIOD=6;REF=3;GRID=1,6;STUTTERUP=0.000497971;STUTTERDOWN=0.00099594;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:0.999992:3,3:3-3,3-3:18,11,0,0:3,18:NULL:172.134:366.612,131.36:0,0:0,1.78548e-05,0.999986 +chr1 6099223 . ttggttggttgg . . PASS END=6099234;RU=ttgg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000705663;STUTTERDOWN=0.00201582;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:6:0.623441:3,3:3-3,3-3:4,2,0,0:3,4:NULL:32.203:366.612,131.36:0,0:1.71507e-13,0.160163,0.839912 +chr1 6099488 . cccacccaccca . . PASS END=6099499;RU=ccca;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000361738;STUTTERDOWN=0.00174655;STUTTERP=0.984306;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:1.00001:3,3:3-3,3-3:22,11,0,0:3,22:NULL:182.584:366.612,131.36:0,0:0,1.09776e-06,1 +chr1 6099665 . ttgtttgtttgtttgtttgtttgt ttgtttgtttgtttgtttgtttgtttgt . PASS END=6099688;RU=ttgt;PERIOD=4;REF=6;GRID=2,9;STUTTERUP=0.000850878;STUTTERDOWN=0.01902;STUTTERP=0.827841;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:21:0.0649898:7,7:4-7,4-7:0,15,0,5:NULL:4,3|5,1|6,1:172.593:366.612,131.36:0.866209,0.866209:8.74432e-09,0.541024,0.459089 +chr1 6102505 . caacaacaacaa . . PASS END=6102516;RU=caa;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000500816;STUTTERDOWN=0.00100163;STUTTERP=0.999;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:0.999901:4,4:4-4,4-4:17,12,0,0:4,17:NULL:173.782:366.612,131.36:0,0:0,7.15075e-05,0.999932 +chr1 6107421 . aaataaataaat . . PASS END=6107432;RU=aaat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000991395;STUTTERDOWN=0.00141603;STUTTERP=0.959079;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:26:1:3,3:3-3,3-3:20,6,0,0:3,20:NULL:130.232:366.612,131.36:0,0:0,5.2435e-06,0.999995 +chr1 6108219 . cacacacacacacacacacacacacacacacacacaca ca . PASS END=6108256;RU=ca;PERIOD=2;REF=19;GRID=1,103;STUTTERUP=0.0886658;STUTTERDOWN=0.200564;STUTTERP=0.740247;EXPTHRESH=19 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP .:.:.:.:.:.:.:.:.:.:.:. +chr1 6108461 . agagagagagagagag ag . PASS END=6108476;RU=ag;PERIOD=2;REF=8;GRID=1,103;STUTTERUP=0.00711584;STUTTERDOWN=0.059371;STUTTERP=0.86692;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP .:.:.:.:.:.:.:.:.:.:.:. +chr1 6109390 . cacccacccacc cacccacccacccacc . PASS END=6109401;RU=cacc;PERIOD=4;REF=3;GRID=1,103;STUTTERUP=0.00179757;STUTTERDOWN=0.0014098;STUTTERP=0.779616;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/1:21:0.0564412:3,4:2-6,2-6:0,21,0,0:NULL:NULL:186.57:366.612,131.36:0.979147,0.985832:0.0502075,0.369433,0.580497 +chr1 6109799 . aaataaataaat aaataaat . PASS END=6109810;RU=aaat;PERIOD=4;REF=3;GRID=1,103;STUTTERUP=0.000721485;STUTTERDOWN=0.00174175;STUTTERP=0.986219;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:8:0.0229253:2,2:1-4,1-4:0,8,0,0:NULL:NULL:79.1816:366.612,131.36:0.723518,0.723518:0.0860922,0.471438,0.442637 +chr1 6109840 . caacaacaacaa caacaa . PASS END=6109851;RU=caa;PERIOD=3;REF=4;GRID=1,103;STUTTERUP=0.000412463;STUTTERDOWN=0.00117826;STUTTERP=0.941457;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:10:0.0171646:2,2:1-3,1-3:0,10,0,0:NULL:NULL:95.4701:366.612,131.36:0.673267,0.673267:0.125553,0.493881,0.380755 +chr1 6110101 . aaataaataaat aaat . PASS END=6110112;RU=aaat;PERIOD=4;REF=3;GRID=1,103;STUTTERUP=0.000987721;STUTTERDOWN=0.000987721;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:29:0.114961:1,1:1-3,1-3:0,29,0,0:NULL:NULL:273.872:366.612,131.36:0.984041,0.984041:0.305634,0.506291,0.188084 +chr1 6114158 . aataaataaata . . PASS END=6114169;RU=aata;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00489112;STUTTERDOWN=0.0041336;STUTTERP=0.96831;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:13:0.808815:3,3:3-3,3-3:5,8,0,0:3,5:NULL:94.8619:366.612,131.36:0,0:1.67371e-12,0.0870317,0.913069 +chr1 6118166 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=6118197;RU=tg;PERIOD=2;REF=16;GRID=19,27;STUTTERUP=0.035591;STUTTERDOWN=0.101791;STUTTERP=0.865873;EXPTHRESH=16 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:42:0.999744:24,24:22-24,22-24:16,10,0,15:24,16:6,2|7,2|8,1|9,1|12,1|14,1|17,2|19,1|20,1|21,1|23,1|24,1:287.608:366.612,131.36:0.507951,0.507951:0,0,1 +chr1 6118512 . ttcaattcaattcaattcaa ttcaattcaattcaattcaattcaa . PASS END=6118531;RU=ttcaa;PERIOD=5;REF=4;GRID=2,8;STUTTERUP=0.00276295;STUTTERDOWN=0.00554016;STUTTERP=0.681663;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:37:0.999993:5,5:5-5,5-5:19,13,0,5:5,19:3,1|4,4:231.825:366.612,131.36:0,0:0,1.00077e-06,1 +chr1 6122082 . aaaacaaaacaaaac aaaacaaaacaaaacaaaacaaaac . PASS END=6122096;RU=aaaac;PERIOD=5;REF=3;GRID=2,8;STUTTERUP=0.00132947;STUTTERDOWN=0.00141823;STUTTERP=0.815097;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:24:0.994947:5,5:5-5,5-5:11,13,0,0:5,11:NULL:162.863:366.612,131.36:0,0:0,0.00154822,0.998458 +chr1 6124347 . taaataaataaataaataaa taaa,taaataaa . PASS END=6124366;RU=taaa;PERIOD=4;REF=5;GRID=1,103;STUTTERUP=0.00178931;STUTTERDOWN=0.0111199;STUTTERP=0.969441;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:20:0.0780755:1,2:1-5,1-5:0,20,0,0:NULL:NULL:195.895:366.612,131.36:1.2691,1.27057:0.497749,0.429319,0.072985 +chr1 6126323 . aatcaatcaatcaatcaatcaatcaatcaatc aatcaatcaatcaatcaatcaatc . PASS END=6126354;RU=aatc;PERIOD=4;REF=8;GRID=3,9;STUTTERUP=0.00495518;STUTTERDOWN=0.0115773;STUTTERP=0.784229;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:30:0.997795:6,6:6-6,6-6:13,14,0,3:6,13:3,3:197.893:366.612,131.36:0,0:0.999574,0.00043049,1.30887e-36 +chr1 6130083 . aaatcaaatcaaatc . . PASS END=6130097;RU=aaatc;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.00048551;STUTTERDOWN=0.00430987;STUTTERP=0.907271;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:0.998496:3,3:3-3,3-3:13,18,0,0:3,13:NULL:224.981:366.612,131.36:0,0:7.42688e-44,0.00115319,0.998853 +chr1 6131636 . atagatagatagatagatagatagatagatagatagatag . . PASS END=6131675;RU=atag;PERIOD=4;REF=10;GRID=7,13;STUTTERUP=0.0094316;STUTTERDOWN=0.0339552;STUTTERP=0.40761;EXPTHRESH=10 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:10:0.704011:10,10:10-10,10-10:5,5,0,0:10,5:NULL:66.1764:366.612,131.36:0.29703,0.29703:3.54997e-12,0.179667,0.820398 +chr1 6132801 . ttggttggttggttgg . . PASS END=6132816;RU=ttgg;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.00044902;STUTTERDOWN=0.00179606;STUTTERP=0.987382;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:24:0.948458:4,4:4-4,4-4:8,16,0,0:4,8:NULL:178.262:366.612,131.36:0,0:5.35741e-27,0.0393248,0.960742 +chr1 6133624 . aaataaataaat . . PASS END=6133635;RU=aaat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000791419;STUTTERDOWN=0.00158284;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:18:0.962477:3,3:3-3,3-3:8,10,0,0:3,8:NULL:121.6:366.612,131.36:0,0:2.95185e-25,0.0196238,0.980413 +chr1 6134579 . aaataaaataaaata . . PASS END=6134593;RU=aaata;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000536763;STUTTERDOWN=0.00153333;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:25:0.993759:3,3:3-3,3-3:11,14,0,0:3,11:NULL:174.422:366.612,131.36:0,0:1.87619e-36,0.00370717,0.996301 +chr1 6134731 . tctctctctctctctctctctctctctctctctctctctctctctctctctc tctctctctctctctctctctctctctctctctctctctctctctc . PASS END=6134782;RU=tc;PERIOD=2;REF=26;GRID=1,26;STUTTERUP=0.0666158;STUTTERDOWN=0.137565;STUTTERP=0.621284;EXPTHRESH=26 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:19:0.0170447:23,23:1-24,1-24:0,13,0,6:NULL:7,2|12,2|19,1|23,1:173.358:366.612,131.36:7.47154,7.47154:0.845741,0.152508,0.0018332 +chr1 6136631 . agagagagagagagagagagagagagagag agagagagagagagagagagagagagagagagagagagag . PASS END=6136660;RU=ag;PERIOD=2;REF=15;GRID=16,23;STUTTERUP=0.0679187;STUTTERDOWN=0.200341;STUTTERP=0.717366;EXPTHRESH=15 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:19:0.482195:20,20:16-20,16-20:4,14,0,0:20,4:NULL:151.317:366.612,131.36:0.913899,0.913899:0,0,1 +chr1 6137129 . tattattattat . . PASS END=6137140;RU=tat;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00237881;STUTTERDOWN=0.00339773;STUTTERP=0.763045;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:1:4,4:4-4,4-4:26,12,0,0:4,26:NULL:216.068:366.612,131.36:0,0:0,1.37565e-07,1 +chr1 6137380 . ttgtttgtttgt ttgt . PASS END=6137391;RU=ttgt;PERIOD=4;REF=3;GRID=1,103;STUTTERUP=0.00116523;STUTTERDOWN=0.00116523;STUTTERP=0.964893;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:23:0.138668:1,1:1-2,1-2:0,23,0,0:NULL:NULL:210.404:366.612,131.36:0.323567,0.323567:0.373728,0.491082,0.135269 +chr1 6137986 . tgcatgcatgca . . PASS END=6137997;RU=tgca;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000411184;STUTTERDOWN=0.000411184;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:43:1:3,3:3-3,3-3:24,19,0,0:3,24:NULL:281.014:366.612,131.36:0,0:0,3.39933e-07,1 +chr1 6142183 . aaacaaacaaacaaac aaacaaacaaac . PASS END=6142198;RU=aaac;PERIOD=4;REF=4;GRID=1,6;STUTTERUP=0.00427924;STUTTERDOWN=0.00140822;STUTTERP=0.948212;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:20:0.968282:3,3:3-3,3-3:8,12,0,0:3,8:NULL:141.244:366.612,131.36:0,0:0.98703,0.0129976,3.1702e-24 +chr1 6144901 . gagagagagagagagagagaga gagagagagagagaga . PASS END=6144922;RU=ga;PERIOD=2;REF=11;GRID=4,11;STUTTERUP=0.0266766;STUTTERDOWN=0.0963222;STUTTERP=0.685628;EXPTHRESH=11 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:11:0.983341:8,8:7-8,7-8:10,0,0,0:8,10:NULL:40.7144:366.612,131.36:0.236383,0.236383:0.997944,0.00205975,2.92473e-22 +chr1 6153283 . aaacaaacaaacaaacaaacaaac . . PASS END=6153306;RU=aaac;PERIOD=4;REF=6;GRID=3,9;STUTTERUP=0.000696274;STUTTERDOWN=0.0128926;STUTTERP=0.849998;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:24:0.965536:6,6:6-6,6-6:9,15,0,0:6,9:NULL:174.808:366.612,131.36:0,0:2.75578e-29,0.0260199,0.974032 +chr1 6153696 . aactaactaact . . PASS END=6153707;RU=aact;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000643507;STUTTERDOWN=0.000643507;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:30:0.999994:3,3:3-3,3-3:19,11,0,0:3,19:NULL:177.198:366.612,131.36:0,0:0,1.20556e-05,0.999987 +chr1 6156105 . ggtggtggtggt . . PASS END=6156116;RU=ggt;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00115246;STUTTERDOWN=0.000806865;STUTTERP=0.820218;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:0.999945:4,4:4-4,4-4:18,13,0,0:4,18:NULL:194.984:366.612,131.36:0,0:0,3.71032e-05,0.999964 +chr1 6156235 . aaacaaacaaacaaacaaac aaacaaacaaacaaacaaacaaac . PASS END=6156254;RU=aaac;PERIOD=4;REF=5;GRID=3,9;STUTTERUP=0.00132684;STUTTERDOWN=0.025219;STUTTERP=0.976003;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:41:0.999629:6,6:6-6,6-6:14,23,0,4:6,14:2,1|3,1|4,1|5,1:299.189:366.612,131.36:0,0:0,0.00013068,0.999872 +chr1 6157851 . agagagagagagagagagagagagagagagagagagagag agagagagagagagagagagagagagagagagagagagagagagagag,agagagagagagagagagagagagagagagagagagagagagagagagag . PASS END=6157890;RU=ag;PERIOD=2;REF=20;GRID=20,28;STUTTERUP=0.0436302;STUTTERDOWN=0.249022;STUTTERP=0.580207;EXPTHRESH=20 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:22:0.620061:24,25:24-24,24-25:7,8,0,6:24,7:4,1|6,1|9,1|13,1|21,1|25,1:166.354:366.612,131.36:0,0.525965:0,0,1 +chr1 6158692 . agcagcagcagc . . PASS END=6158703;RU=agc;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000340475;STUTTERDOWN=0.000340475;STUTTERP=0.953462;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:49:1:4,4:4-4,4-4:30,19,0,0:4,30:NULL:296.539:366.612,131.36:0,0:0,1.30628e-08,1 +chr1 6158961 . gtggtggtggtg . . PASS END=6158972;RU=gtg;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000769545;STUTTERDOWN=0.000538776;STUTTERP=0.959079;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:48:1:4,4:4-4,4-4:31,17,0,0:4,31:NULL:274.702:366.612,131.36:0,0:0,4.15691e-09,1 +chr1 6160096 . tacatacataca . . PASS END=6160107;RU=taca;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000430992;STUTTERDOWN=0.00123119;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:41:1.00001:3,3:3-3,3-3:22,17,0,2:3,22:2,2:257.513:366.612,131.36:0,0:0,1.07318e-06,1 +chr1 6160598 . aataaataaata . . PASS END=6160609;RU=aata;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000435245;STUTTERDOWN=0.00210146;STUTTERP=0.841787;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:41:0.999995:3,3:2-3,2-3:19,21,0,0:3,19:NULL:274.628:366.612,131.36:0.323567,0.323567:0,1.31913e-05,0.999987 +chr1 6162049 . ccaccaccacca . . PASS END=6162060;RU=cca;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.0034724;STUTTERDOWN=0.00143845;STUTTERP=0.986235;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:10:0.988354:4,4:4-4,4-4:10,0,0,0:4,10:NULL:39.0933:366.612,131.36:0,0:3.00169e-25,0.00586113,0.994152 +chr1 6163104 . tttgtttgtttg . . PASS END=6163115;RU=tttg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000433525;STUTTERDOWN=0.00123842;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:1:3,3:3-3,3-3:27,12,0,0:3,27:NULL:220.902:366.612,131.36:0,0:0,8.27155e-08,1 +chr1 6178405 . ataaaataaaataaa . . PASS END=6178419;RU=ataaa;PERIOD=5;REF=3;GRID=1,7;STUTTERUP=0.00105861;STUTTERDOWN=0.00105861;STUTTERP=0.976453;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:1.00001:3,3:3-4,3-4:21,15,0,0:3,21:NULL:219.077:366.612,131.36:0.236383,0.236383:0,3.03743e-06,1 +chr1 6178663 . gacctgacctgacct . . PASS END=6178677;RU=gacct;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000443894;STUTTERDOWN=0.000887787;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:60:1:3,3:3-3,3-3:28,32,0,0:3,28:NULL:404.545:366.612,131.36:0,0:0,2.97062e-08,1 +chr1 6180765 . taaataaataaa . . PASS END=6180776;RU=taaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000628641;STUTTERDOWN=0.00251454;STUTTERP=0.987382;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:32:0.999829:3,3:3-3,3-3:15,17,0,0:3,15:NULL:211.521:366.612,131.36:0,0:0,0.000125374,0.999879 +chr1 6188010 . tttaatttaatttaa . . PASS END=6188024;RU=tttaa;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000607801;STUTTERDOWN=0.00173627;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:21:0.838321:3,3:3-3,3-3:6,15,0,0:3,6:NULL:164.825:366.612,131.36:0,0:1.6313e-19,0.108224,0.891874 +chr1 6190661 . aaataaataaat . . PASS END=6190672;RU=aaat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00103714;STUTTERDOWN=0.000518572;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:1.00001:3,3:3-3,3-3:21,17,0,0:3,21:NULL:238.529:366.612,131.36:0,0:0,3.31534e-06,1 +chr1 6191823 . aacaaacaaaca . . PASS END=6191834;RU=aaca;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000460757;STUTTERDOWN=0.000921513;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:50:1.00001:3,3:3-3,3-3:22,24,0,4:3,22:2,4:329.783:366.612,131.36:0,0:0,5.95576e-07,1 +chr1 6193268 . caacaacaacaacaa . . PASS END=6193282;RU=caa;PERIOD=3;REF=5;GRID=1,8;STUTTERUP=0.000777699;STUTTERDOWN=0.00345182;STUTTERP=0.766345;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:50:1:5,5:5-5,5-5:26,23,0,0:5,26:NULL:318.943:366.612,131.36:0.0990099,0.0990099:0,2.14392e-07,1 +chr1 6194222 . aacaaaaacaaaaacaaaaacaaa aacaaaaacaaaaacaaa . PASS END=6194245;RU=aacaaa;PERIOD=6;REF=4;GRID=1,6;STUTTERUP=0.00125438;STUTTERDOWN=0.00298209;STUTTERP=0.88445;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:35:1:3,3:3-3,3-3:20,15,0,0:3,20:NULL:217.53:366.612,131.36:0,0:1,2.13012e-06,0 +chr1 6196714 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt,gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=6196751;RU=gt;PERIOD=2;REF=19;GRID=17,25;STUTTERUP=0.0678652;STUTTERDOWN=0.21565;STUTTERP=0.827137;EXPTHRESH=19 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:42:0.596831:21,22:20-21,20-22:14,10,0,18:20,4|21,7|22,3:5,1|6,2|8,2|9,1|10,1|11,4|12,1|15,4|16,1|19,1:308.486:366.612,131.36:0.374147,0.769225:3.65542e-38,7.91182e-05,0.999925 +chr1 6197125 . gtttgtttgtttgttt gtttgtttgttt . PASS END=6197140;RU=gttt;PERIOD=4;REF=4;GRID=1,6;STUTTERUP=0.0344537;STUTTERDOWN=0.00367291;STUTTERP=0.976988;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:54:1:3,3:3-3,3-3:29,25,0,0:3,29:NULL:343.468:366.612,131.36:0,0:1,5.40311e-09,0 +chr1 6197608 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=6197647;RU=tg;PERIOD=2;REF=20;GRID=1,37;STUTTERUP=0.0858211;STUTTERDOWN=0.19488;STUTTERP=0.71856;EXPTHRESH=20 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:23:0.0197949:34,34:15-37,15-37:0,12,0,11:NULL:9,1|12,1|13,2|15,2|19,1|28,1|29,1|30,1|34,1:197.621:366.612,131.36:6.74231,6.74231:3.45815e-30,0.143738,0.856344 +chr1 6197805 . ctgcctctgcctctgcct ctgcctctgcct . PASS END=6197822;RU=ctgcct;PERIOD=6;REF=3;GRID=1,5;STUTTERUP=0.000351258;STUTTERDOWN=0.00169595;STUTTERP=0.841787;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:46:1:2,2:2-2,2-2:44,2,0,0:2,44:NULL:191.074:366.612,131.36:0,0:1,2.87214e-13,0 +chr1 6198434 . cacacacacacaca . . PASS END=6198447;RU=ca;PERIOD=2;REF=7;GRID=3,10;STUTTERUP=0.016186;STUTTERDOWN=0.0226642;STUTTERP=0.967532;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:0.997258:7,7:6-7,6-7:13,15,0,0:7,13:NULL:190.885:366.612,131.36:0.236383,0.236383:5.4547e-24,0.0019861,0.998019 +chr1 6199733 . ttatttatttat . . PASS END=6199744;RU=ttat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000456608;STUTTERDOWN=0.000913214;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:0.99552:3,3:3-3,3-3:12,24,0,0:3,12:NULL:279.333:366.612,131.36:0,0:1.2305e-39,0.00393815,0.996073 +chr1 6203219 . aaacaaacaaac . . PASS END=6203230;RU=aaac;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000420722;STUTTERDOWN=0.00203134;STUTTERP=0.841787;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:40:0.999833:3,3:3-3,3-3:16,24,0,0:3,16:NULL:278.446:366.612,131.36:0,0:0,0.000147499,0.999856 +chr1 6207701 . gtttgtttgttt . . PASS END=6207712;RU=gttt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00102991;STUTTERDOWN=0.00205981;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:26:0.999763:3,3:3-3,3-3:15,11,0,0:3,15:NULL:161.819:366.612,131.36:0,0:2.8026e-45,0.000127729,0.999873 +chr1 6208513 . gttgttgttgtt . . PASS END=6208524;RU=gtt;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000848434;STUTTERDOWN=0.00169685;STUTTERP=0.866591;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:37:1:4,4:4-4,4-4:25,12,0,0:4,25:NULL:201.525:366.612,131.36:0,0:0,2.75179e-07,1 +chr1 6208671 . ttatttttatttttattt ttattt . PASS END=6208688;RU=ttattt;PERIOD=6;REF=3;GRID=1,103;STUTTERUP=0.000551735;STUTTERDOWN=0.0022069;STUTTERP=0.987384;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:14:0.0737831:1,1:1-3,1-3:0,14,0,0:NULL:NULL:125.31:366.612,131.36:0.515232,0.515232:0.232985,0.519698,0.247355 +chr1 6210401 . tttgtttgtttg . . PASS END=6210412;RU=tttg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00087709;STUTTERDOWN=0.00592969;STUTTERP=0.891787;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:1.00001:3,3:3-3,3-3:22,11,0,0:3,22:NULL:188.78:366.612,131.36:0,0:0,1.50332e-06,1 +chr1 6219473 . gtttgtttgtttgttt . . PASS END=6219488;RU=gttt;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000489938;STUTTERDOWN=0.00236553;STUTTERP=0.984306;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:0.999952:4,4:4-4,4-4:17,15,0,3:4,17:2,1|3,2:231.814:366.612,131.36:0,0:0,2.74888e-05,0.999972 +chr1 6219491 . atttatttattt . . PASS END=6219502;RU=attt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000441437;STUTTERDOWN=0.000441437;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:43:1.00001:3,3:3-3,3-3:20,21,0,2:3,20:2,2:293.52:366.612,131.36:0,0:0,2.06476e-06,1 +chr1 6224070 . gtgtgtgtgtgt . . PASS END=6224081;RU=gt;PERIOD=2;REF=6;GRID=3,9;STUTTERUP=0.00370289;STUTTERDOWN=0.00680801;STUTTERP=0.955932;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:1.00001:6,6:6-6,6-6:21,13,0,2:6,21:4,1|5,1:220.392:366.612,131.36:0,0:0,3.66464e-06,1 +chr1 6226500 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=6226537;RU=gt;PERIOD=2;REF=19;GRID=30,36;STUTTERUP=0.0504922;STUTTERDOWN=0.217756;STUTTERP=0.712615;EXPTHRESH=19 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:12:0.0298444:35,35:33-36,33-36:0,9,0,2:NULL:29,1|31,1:100.568:366.612,131.36:0.877118,0.877118:0,0,1 +chr1 6226712 . tttgtttgtttgtttg tttgtttgtttgtttgtttgtttgtttgtttg . PASS END=6226727;RU=tttg;PERIOD=4;REF=4;GRID=5,11;STUTTERUP=0.000867804;STUTTERDOWN=0.00341802;STUTTERP=0.790273;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:32:0.999816:8,8:8-8,8-8:16,11,0,5:8,16:2,1|4,4:204.676:366.612,131.36:0,0:0,0,1 +chr1 6227414 . ttgtttgtttgt . . PASS END=6227425;RU=ttgt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00101475;STUTTERDOWN=0.00142089;STUTTERP=0.990318;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:45:1:3,3:3-3,3-3:23,22,0,0:3,23:NULL:289.964:366.612,131.36:0,0:0,3.1637e-07,1 +chr1 6228918 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=6228955;RU=tg;PERIOD=2;REF=19;GRID=9,18;STUTTERUP=0.0822019;STUTTERDOWN=0.135464;STUTTERP=0.801198;EXPTHRESH=19 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:41:0.953211:14,14:12-14,12-14:25,14,0,2:12,2|13,4|14,17|15,2:11,1|14,1:272.748:366.612,131.36:0.495643,0.495643:1,0,0 +chr1 6229792 . caaaacaaaacaaaacaaaacaaaa caaaacaaaacaaaacaaaa . PASS END=6229816;RU=caaaa;PERIOD=5;REF=5;GRID=1,7;STUTTERUP=0.00109786;STUTTERDOWN=0.00372598;STUTTERP=0.871276;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:34:0.999971:4,4:4-4,4-4:18,16,0,0:4,18:NULL:223.227:366.612,131.36:0,0:0.999993,1.01201e-05,0 +chr1 6231061 . gtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=6231082;RU=gt;PERIOD=2;REF=11;GRID=1,16;STUTTERUP=0.0518464;STUTTERDOWN=0.0638179;STUTTERP=0.73947;EXPTHRESH=11 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:33:0.0552115:13,13:6-15,6-15:0,24,0,9:NULL:5,2|7,1|8,2|10,1|11,2|13,1:297.205:366.612,131.36:2.34668,2.34668:8.57626e-23,0.273988,0.726012 +chr1 6232825 . tttgtttgtttg tttgtttg . PASS END=6232836;RU=tttg;PERIOD=4;REF=3;GRID=1,5;STUTTERUP=0.0016084;STUTTERDOWN=0.00112661;STUTTERP=0.685825;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:36:1.00001:2,2:2-2,2-2:18,16,0,2:2,18:2,2:229.027:366.612,131.36:0,0:0.999993,9.95117e-06,0 +chr1 6232863 . tttgtttgtttg . . PASS END=6232874;RU=tttg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000857083;STUTTERDOWN=0.00122419;STUTTERP=0.959079;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:47:1:3,3:3-3,3-3:23,24,0,0:3,23:NULL:305.213:366.612,131.36:0,0:0,8.45102e-07,1 +chr1 6232977 . ctgcctctgcctctgcct ctgcctctgcctctgcctctgcct . PASS END=6232994;RU=ctgcct;PERIOD=6;REF=3;GRID=1,7;STUTTERUP=0.00224947;STUTTERDOWN=0.00224469;STUTTERP=0.8912;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:41:1:4,4:4-4,4-4:25,16,0,0:4,25:NULL:248.419:366.612,131.36:0,0:0,2.33065e-07,1 +chr1 6233703 . aaaacaaaacaaaacaaaac . . PASS END=6233722;RU=aaaac;PERIOD=5;REF=4;GRID=1,7;STUTTERUP=0.00188852;STUTTERDOWN=0.000658803;STUTTERP=0.945898;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:0.995376:4,4:4-4,4-4:12,25,0,2:4,12:2,2:292.579:366.612,131.36:0,0:1.19963e-32,0.003873,0.996135 +chr1 6236385 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgt . PASS END=6236434;RU=gt;PERIOD=2;REF=25;GRID=8,15;STUTTERUP=0.0588982;STUTTERDOWN=0.215778;STUTTERP=0.749882;EXPTHRESH=25 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:35:0.98567:12,12:12-12,12-12:13,19,0,3:11,2|12,11:9,1|11,2:261.163:366.612,131.36:0.0990099,0.0990099:1,0,0 +chr1 6238596 . attattattatt attattattattatt . PASS END=6238607;RU=att;PERIOD=3;REF=4;GRID=1,8;STUTTERUP=0.00349645;STUTTERDOWN=0.0266261;STUTTERP=0.936125;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:32:0.999236:5,5:4-5,4-5:15,16,0,0:5,15:NULL:213.502:366.612,131.36:0.270063,0.270063:0,0.000479854,0.999523 +chr1 6239066 . tttgtttgtttg tttgtttgtttgtttg . PASS END=6239077;RU=tttg;PERIOD=4;REF=3;GRID=1,7;STUTTERUP=0.00203864;STUTTERDOWN=0.000689502;STUTTERP=0.9981;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:12:0.271396:4,4:1-4,1-4:2,10,0,0:4,2:NULL:98.8609:366.612,131.36:0.634282,0.634282:1.00093e-11,0.342876,0.657149 +chr1 6240390 . gtgcgtgcgtgc gtgc . PASS END=6240401;RU=gtgc;PERIOD=4;REF=3;GRID=1,103;STUTTERUP=0.000482826;STUTTERDOWN=0.000965651;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:22:0.0746064:1,1:1-4,1-4:0,22,0,0:NULL:NULL:201.478:366.612,131.36:0.92647,0.92647:0.230102,0.516179,0.253757 +chr1 6247906 . tgttgttgttgttgt . . PASS END=6247920;RU=tgt;PERIOD=3;REF=5;GRID=2,8;STUTTERUP=0.00129995;STUTTERDOWN=0.00519977;STUTTERP=0.749924;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:47:1.00001:5,5:5-5,5-5:22,25,0,0:5,22:NULL:313.808:366.612,131.36:0,0:0,3.09887e-06,1 +chr1 6250708 . ttgttgttgttgttgttg . . PASS END=6250725;RU=ttg;PERIOD=3;REF=6;GRID=3,9;STUTTERUP=0.00229644;STUTTERDOWN=0.0128622;STUTTERP=0.782267;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:41:1.00001:6,6:6-6,6-6:22,15,0,4:6,22:4,1|5,3:261.781:366.612,131.36:0,0:0,6.02088e-07,1 +chr1 6250858 . tatgtatgtatgtatg . . PASS END=6250873;RU=tatg;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.00220998;STUTTERDOWN=0.0159145;STUTTERP=0.980173;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:47:1:4,4:4-4,4-4:24,21,0,2:4,24:3,2:303.256:366.612,131.36:0,0:0,3.88591e-07,1 +chr1 6251852 . aaataaataaat . . PASS END=6251863;RU=aaat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00046488;STUTTERDOWN=0.0018595;STUTTERP=0.987382;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:40:1:3,3:3-3,3-3:21,19,0,0:3,21:NULL:250.565:366.612,131.36:0,0:0,4.20457e-06,0.999995 +chr1 6252245 . atatatatatatatat . . PASS END=6252260;RU=at;PERIOD=2;REF=8;GRID=3,11;STUTTERUP=0.049518;STUTTERDOWN=0.091282;STUTTERP=0.620291;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:19:0.428225:8,8:6-8,6-8:4,13,0,0:8,4:NULL:133.525:366.612,131.36:0.788482,0.788482:2.39144e-06,0.441308,0.558798 +chr1 6252276 . atatatatatatatatatatatatatatatatatatatat atatatatat . PASS END=6252315;RU=at;PERIOD=2;REF=20;GRID=1,8;STUTTERUP=0.080048;STUTTERDOWN=0.0897111;STUTTERP=0.846234;EXPTHRESH=20 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:15:0.834081:5,5:3-5,3-5:6,8,0,0:5,6:NULL:95.4925:366.612,131.36:0.945117,0.945117:1,0,0 +chr1 6260354 . taaataaataaa . . PASS END=6260365;RU=taaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000398155;STUTTERDOWN=0.00192238;STUTTERP=0.984306;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:40:1:3,3:3-3,3-3:28,12,0,0:3,28:NULL:217.602:366.612,131.36:0,0:0,2.08516e-08,1 +chr1 6266174 . ttgttttgttttgttttgttttgtt ttgttttgttttgttttgtt . PASS END=6266198;RU=ttgtt;PERIOD=5;REF=5;GRID=1,7;STUTTERUP=0.00874703;STUTTERDOWN=0.00258505;STUTTERP=0.871794;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:30:0.997192:4,4:4-4,4-4:11,16,0,3:4,11:3,3:209.654:366.612,131.36:0,0:0.99877,0.00123274,1.72179e-30 +chr1 6267793 . tgtttgtttgtt . . PASS END=6267804;RU=tgtt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000863983;STUTTERDOWN=0.00208575;STUTTERP=0.986219;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:21:0.997751:3,3:3-3,3-3:12,9,0,0:3,12:NULL:130.684:366.612,131.36:0,0:1.30609e-37,0.00086217,0.999142 +chr1 6269522 . gttgttgttgtt . . PASS END=6269533;RU=gtt;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00166613;STUTTERDOWN=0.00118989;STUTTERP=0.990318;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:25:0.999964:4,4:4-4,4-4:18,7,0,0:4,18:NULL:136.356:366.612,131.36:0,0:0,2.879e-05,0.999972 +chr1 6269576 . gataggataggatag . . PASS END=6269590;RU=gatag;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000858967;STUTTERDOWN=0.00207365;STUTTERP=0.843423;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:28:1:3,3:3-3,3-3:19,9,0,0:3,19:NULL:156.249:366.612,131.36:0,0:0,8.75009e-06,0.999994 +chr1 6271401 . tcatcatcatca . . PASS END=6271412;RU=tca;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000927893;STUTTERDOWN=0.000927893;STUTTERP=0.789911;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:0.999995:4,4:4-4,4-4:20,13,0,0:4,20:NULL:199.249:366.612,131.36:0,0:0,1.43347e-05,0.999987 +chr1 6273501 . ttcattcattca . . PASS END=6273512;RU=ttca;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00084378;STUTTERDOWN=0.00084378;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:13:0.998792:3,3:3-3,3-3:13,0,0,0:3,13:NULL:50.7793:366.612,131.36:0,0:9.47236e-41,0.000490454,0.999514 +chr1 6273618 . acccacccaccc . . PASS END=6273629;RU=accc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00233426;STUTTERDOWN=0.00233426;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:7:0.76159:3,3:3-3,3-3:5,2,0,0:3,5:NULL:36.5433:366.612,131.36:0,0:5.11652e-14,0.0983203,0.901783 +chr1 6274375 . ttgtttgtttgtttgtttgt . . PASS END=6274394;RU=ttgt;PERIOD=4;REF=5;GRID=2,8;STUTTERUP=0.00108015;STUTTERDOWN=0.0113462;STUTTERP=0.942584;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:32:1.00001:5,5:5-5,5-5:21,7,0,4:5,21:3,2|4,2:171.617:366.612,131.36:0,0:0,1.3935e-06,1 +chr1 6276992 . atgatgatgatg . . PASS END=6277003;RU=atg;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000401679;STUTTERDOWN=0.0016067;STUTTERP=0.987382;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:0.999956:4,4:4-4,4-4:18,21,0,0:4,18:NULL:258.046:366.612,131.36:0,0:0,4.97124e-05,0.999949 +chr1 6277038 . agcagcagcagc . . PASS END=6277049;RU=agc;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000414448;STUTTERDOWN=0.000828894;STUTTERP=0.999;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:44:0.999636:4,4:4-4,4-4:15,29,0,0:4,15:NULL:321.087:366.612,131.36:0,0:0,0.00034579,0.999658 +chr1 6285646 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt,gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=6285691;RU=gt;PERIOD=2;REF=23;GRID=21,29;STUTTERUP=0.0751432;STUTTERDOWN=0.244802;STUTTERP=0.726704;EXPTHRESH=23 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:36:0.931843:25,26:24-25,25-26:10,12,0,14:24,2|25,5|26,3:12,1|13,1|15,3|16,2|19,2|20,1|22,2|25,2:276.338:366.612,131.36:0.240494,0.459304:3.22746e-34,0.000101141,0.999902 +chr1 6290853 . tccttccttcct . . PASS END=6290864;RU=tcct;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000439997;STUTTERDOWN=0.000879992;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:0.999831:3,3:3-3,3-3:17,16,0,0:3,17:NULL:214.565:366.612,131.36:0,0:0,0.000103485,0.999896 +chr1 6293821 . ctccctccctcc . . PASS END=6293832;RU=ctcc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000418736;STUTTERDOWN=0.000418736;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:30:1:3,3:3-3,3-3:20,10,0,0:3,20:NULL:170.023:366.612,131.36:0,0:0,4.76004e-06,0.999995 +chr1 6301879 . aataaataaata . . PASS END=6301890;RU=aata;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00038155;STUTTERDOWN=0.00108995;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:44:1:3,3:3-3,3-3:25,19,0,0:3,25:NULL:268.841:366.612,131.36:0,0:0,2.64398e-07,1 +chr1 6303590 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=6303631;RU=gt;PERIOD=2;REF=21;GRID=19,28;STUTTERUP=0.0671933;STUTTERDOWN=0.220662;STUTTERP=0.756953;EXPTHRESH=21 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:44:0.937064:25,25:22-25,22-25:14,11,0,18:24,3|25,11:5,1|9,2|10,1|12,2|13,2|14,3|15,1|16,1|18,1|20,1|21,1|22,1|23,1:316.407:366.612,131.36:0.915721,0.915721:0,3.48342e-05,0.999964 +chr1 6311549 . ggtggtggtggt . . PASS END=6311560;RU=ggt;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000545161;STUTTERDOWN=0.000545161;STUTTERP=0.953462;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:25:0.998851:4,4:4-4,4-4:14,11,0,0:4,14:NULL:160.95:366.612,131.36:0,0:0,0.000681921,0.999323 +chr1 6312247 . tccctccctccctccctccctccctccctccctccctccctccctccc . . PASS END=6312294;RU=tccc;PERIOD=4;REF=12;GRID=10,16;STUTTERUP=0.00753249;STUTTERDOWN=0.0609091;STUTTERP=0.905407;EXPTHRESH=12 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:26:0.0916072:12,12:11-13,11-13:0,16,0,9:NULL:3,1|4,1|6,1|8,1|9,2|10,1|11,2:209.337:366.612,131.36:0.790097,0.790097:0.120643,0.4686,0.410951 +chr1 6312789 . tctctctctctctctctctctctctctctctctctctctctctctctctctctctc tctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctc,tctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctc . PASS END=6312844;RU=tc;PERIOD=2;REF=28;GRID=28,35;STUTTERUP=0.0715492;STUTTERDOWN=0.303438;STUTTERP=0.69633;EXPTHRESH=28 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:36:0.30309:31,32:28-33,28-33:2,16,0,17:31,2:6,1|12,2|13,1|14,3|16,2|19,1|20,2|21,1|22,2|26,1|32,1:298.451:366.612,131.36:0.815616,0.844549:0,0,1 +chr1 6317256 . aaaaacaaaaacaaaaac . . PASS END=6317273;RU=aaaaac;PERIOD=6;REF=3;GRID=1,6;STUTTERUP=0.000475035;STUTTERDOWN=0.002714;STUTTERP=0.969616;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:1.00001:3,3:3-3,3-3:22,11,0,0:3,22:NULL:191.254:366.612,131.36:0,0:0,2.07463e-06,1 +chr1 6324793 . ttatttatttat . . PASS END=6324804;RU=ttat;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000439326;STUTTERDOWN=0.00125499;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:40:1:3,3:3-3,3-3:26,14,0,0:3,26:NULL:237.826:366.612,131.36:0,0:0,7.68292e-08,1 +chr1 6326106 . ctgctgctgctg . . PASS END=6326117;RU=ctg;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00108673;STUTTERDOWN=0.00217345;STUTTERP=0.920482;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:43:1:4,4:4-4,4-4:25,18,0,0:4,25:NULL:261.316:366.612,131.36:0,0:0,2.9682e-07,1 +chr1 6328025 . tccctctccctctccctctccctctccctctccctctccctctccctctccctctccctctccctctccctctccctctccctc tccctctccctctccctctccctctccctc . PASS END=6328108;RU=tccctc;PERIOD=6;REF=14;GRID=1,17;STUTTERUP=0.0561183;STUTTERDOWN=0.0121959;STUTTERP=0.990438;EXPTHRESH=14 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/0:24:0.323834:5,14:3-13,11-15:2,10,0,11:5,2:2,1|3,1|4,2|5,1|6,1|10,1|11,1|12,1|13,1|14,1:178.554:366.612,131.36:1.80051,1.17184:8.72804e-09,1,2.80873e-36 +chr1 6329503 . tgtgtgtgtgtgtgtgtgtgtg . . PASS END=6329524;RU=tg;PERIOD=2;REF=11;GRID=6,15;STUTTERUP=0.0317983;STUTTERDOWN=0.0749561;STUTTERP=0.7936;EXPTHRESH=11 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:45:0.999981:11,11:10-12,10-12:19,18,0,5:11,19:4,1|9,1|10,3:279.328:366.612,131.36:0.385249,0.385249:1.54556e-29,1.48909e-05,0.999986 +chr1 6330314 . tgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=6330337;RU=tg;PERIOD=2;REF=12;GRID=17,24;STUTTERUP=0.0496454;STUTTERDOWN=0.140516;STUTTERP=0.85344;EXPTHRESH=12 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:38:0.717376:21,21:19-21,19-21:6,18,0,13:21,6:8,2|11,1|12,2|13,3|16,2|18,1|19,2:296.872:366.612,131.36:0.481599,0.481599:0,0,1 +chr1 6332594 . ttttgttttgttttgttttgttttgttttgttttgttttg ttttgttttgttttgttttgttttgttttgttttgttttgttttg . PASS END=6332633;RU=ttttg;PERIOD=5;REF=8;GRID=6,12;STUTTERUP=0.000697479;STUTTERDOWN=0.0221617;STUTTERP=0.483596;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:56:1.00001:9,9:9-9,9-9:21,18,0,17:9,21:2,1|3,1|4,4|5,3|6,2|7,2|8,4:375.193:366.612,131.36:0,0:0,1.36888e-07,1 +chr1 6332921 . tgttttgttttgttttgttt tgttttgttttgttttgttttgttt . PASS END=6332940;RU=tgttt;PERIOD=5;REF=4;GRID=2,8;STUTTERUP=0.000518883;STUTTERDOWN=0.00693612;STUTTERP=0.835253;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:35:0.999962:5,5:5-5,5-5:18,17,0,0:5,18:NULL:235.869:366.612,131.36:0,0:0,3.68095e-05,0.999964 +chr1 6341827 . tttatttatttatttattta . . PASS END=6341846;RU=ttta;PERIOD=4;REF=5;GRID=2,8;STUTTERUP=0.00241884;STUTTERDOWN=0.0205873;STUTTERP=0.75254;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:0.999931:5,5:5-5,5-5:17,13,0,3:5,17:2,1|3,1|4,1:208.003:366.612,131.36:0,0:0,4.02341e-05,0.999963 +chr1 6345062 . tattattattattattattattattattat . . PASS END=6345091;RU=tat;PERIOD=3;REF=10;GRID=6,13;STUTTERUP=0.0256785;STUTTERDOWN=0.0790381;STUTTERP=0.766988;EXPTHRESH=10 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:24:0.583909:10,10:9-10,9-10:10,10,0,4:9,2|10,8:5,1|7,1|8,2:173.1:366.612,131.36:0.492866,0.492866:1.20285e-11,0.412318,0.587755 +chr1 6347126 . atttatttattt . . PASS END=6347137;RU=attt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00151954;STUTTERDOWN=0.00183419;STUTTERP=0.948224;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:60:1:3,3:3-3,3-3:30,30,0,0:3,30:NULL:385.253:366.612,131.36:0,0:0,5.45747e-09,1 +chr1 6348865 . ttgttgttgttgttg . . PASS END=6348879;RU=ttg;PERIOD=3;REF=5;GRID=2,8;STUTTERUP=0.00162699;STUTTERDOWN=0.00891257;STUTTERP=0.839517;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:34:1.00001:5,5:5-5,5-5:20,12,0,2:5,20:4,1|5,1:200.063:366.612,131.36:0,0:0,2.3945e-06,1 +chr1 6354453 . tctctctctctctctctctctctctctctctctctctctctctctctctc tctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctc,tctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctc . PASS END=6354502;RU=tc;PERIOD=2;REF=25;GRID=25,39;STUTTERUP=0.0651813;STUTTERDOWN=0.253175;STUTTERP=0.540114;EXPTHRESH=25 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:21:0.260449:31,37:28-31,28-38:2,10,0,8:31,2:7,1|8,1|12,1|19,1|28,1|29,1|32,1|36,1:170.006:366.612,131.36:1.55707,3.13366:0,0,1 +chr1 6354954 . agagagagagagagagagagagagagag agagagagagagagagagagagagagagagagagagagagagagagagagagagagag,agagagagagagagagagagagagagagagagagagagagagagagagagagagagagagagagagagagag . PASS END=6354981;RU=ag;PERIOD=2;REF=14;GRID=1,39;STUTTERUP=0.0331246;STUTTERDOWN=0.129497;STUTTERP=0.856813;EXPTHRESH=14 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:35:0.0666914:29,36:23-36,27-37:0,18,0,17:NULL:5,1|7,1|8,1|14,1|16,1|17,1|19,1|22,3|23,1|26,1|27,2|28,1|29,1|36,1:297.47:366.612,131.36:4.02078,3.49958:0,0.00311768,0.99689 +chr1 6355000 . aggcaggcaggc . . PASS END=6355011;RU=aggc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000536876;STUTTERDOWN=0.00107375;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:30:1:3,3:3-3,3-3:19,11,0,0:3,19:NULL:170.882:366.612,131.36:0,0:0,6.52171e-06,0.999994 +chr1 6357634 . gagagagagagagagagagagagagagagagagagagagagagagagagagagagaga ga . PASS END=6357691;RU=ga;PERIOD=2;REF=29;GRID=1,103;STUTTERUP=0.0635976;STUTTERDOWN=0.213736;STUTTERP=0.744414;EXPTHRESH=29 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:13:0.00843527:1,1:1-8,1-8:0,13,0,0:NULL:NULL:117.297:366.612,131.36:2.03936,2.03936:0.854868,0.142426,0.00279405 +chr1 6359367 . ctgctgctgctg . . PASS END=6359378;RU=ctg;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000345456;STUTTERDOWN=0.00394736;STUTTERP=0.902756;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:64:1:4,4:4-4,4-4:37,27,0,0:4,37:NULL:395.923:366.612,131.36:0,0:0,2.29575e-10,1 +chr1 6368193 . catcatcatcat . . PASS END=6368204;RU=cat;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000389546;STUTTERDOWN=0.000779091;STUTTERP=0.999;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:25:0.999976:4,4:4-4,4-4:18,7,0,0:4,18:NULL:145.628:366.612,131.36:0,0:0,3.0766e-05,0.999971 +chr1 6368347 . tttatttatttatttattta ttta,tttattta . PASS END=6368366;RU=ttta;PERIOD=4;REF=5;GRID=1,103;STUTTERUP=0.00183464;STUTTERDOWN=0.00885807;STUTTERP=0.915698;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:19:0.165475:1,2:1-4,1-4:0,19,0,0:NULL:NULL:196.82:366.612,131.36:0.868696,0.813208:0.728826,0.258439,0.0127586 +chr1 6371007 . aggtaggtaggt . . PASS END=6371018;RU=aggt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00037881;STUTTERDOWN=0.00037881;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:50:1:3,3:3-3,3-3:27,20,0,3:3,27:2,3:310.643:366.612,131.36:0,0:0,5.70152e-08,1 +chr1 6371335 . atatatatatatatatatatatatatatatatatatatatatatatat atatatatatatatatat . PASS END=6371382;RU=at;PERIOD=2;REF=24;GRID=5,13;STUTTERUP=0.0977058;STUTTERDOWN=0.140533;STUTTERP=0.725147;EXPTHRESH=24 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:26:0.578901:9,9:8-10,8-10:9,13,0,3:8,2|9,7:5,1|6,1|7,1:185.232:366.612,131.36:0.598171,0.598171:1,0,0 +chr1 6379206 . aaacaaacaaac . . PASS END=6379217;RU=aaac;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000351262;STUTTERDOWN=0.000351262;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:38:1:3,3:3-3,3-3:19,15,0,4:3,19:2,4:244.686:366.612,131.36:0,0:0,6.60564e-06,0.999994 +chr1 6379384 . tgttttgttttgttt . . PASS END=6379398;RU=tgttt;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.00042541;STUTTERDOWN=0.000850819;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:0.999979:3,3:3-3,3-3:18,13,0,0:3,18:NULL:193.535:366.612,131.36:0,0:0,2.71137e-05,0.999972 +chr1 6386715 . gccagccagcca . . PASS END=6386726;RU=gcca;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000414348;STUTTERDOWN=0.000414348;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:44:1:3,3:3-3,3-3:25,17,0,2:3,25:2,2:277.144:366.612,131.36:0,0:0,7.65198e-08,1 +chr1 6389231 . tgagaatgagaatgagaa . . PASS END=6389248;RU=tgagaa;PERIOD=6;REF=3;GRID=1,6;STUTTERUP=0.000402525;STUTTERDOWN=0.00229973;STUTTERP=0.969616;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:51:1:3,3:3-3,3-3:33,16,0,2:3,33:2,2:292.834:366.612,131.36:0,0:0,4.11387e-10,1 +chr1 6390202 . tatatatatatatatatatata tatatatatatatatatata . PASS END=6390223;RU=ta;PERIOD=2;REF=11;GRID=6,13;STUTTERUP=0.0926136;STUTTERDOWN=0.0649578;STUTTERP=0.875225;EXPTHRESH=11 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:27:0.999128:10,10:9-10,9-10:15,11,0,0:10,15:NULL:167.229:366.612,131.36:0.195027,0.195027:0.999789,0.000212479,1.24383e-18 +chr1 6390677 . acatacatacatacatacatacatacatacat acatacatacatacatacatacatacatacatacat . PASS END=6390708;RU=acat;PERIOD=4;REF=8;GRID=5,12;STUTTERUP=0.0120144;STUTTERDOWN=0.0302523;STUTTERP=0.739298;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/1:56:0.786703:8,9:8-9,9-9:12,20,0,24:8,2|9,10:2,1|3,2|4,3|5,4|6,6|7,3|8,5:412.331:366.612,131.36:0.491073,0:0,2.75677e-05,0.999972 +chr1 6391128 . tctgtctgtctgtctgtctgtctgtctgtctg . . PASS END=6391159;RU=tctg;PERIOD=4;REF=8;GRID=5,11;STUTTERUP=0.00163551;STUTTERDOWN=0.017566;STUTTERP=0.746013;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:54:0.99995:8,8:8-8,8-8:17,26,0,11:8,17:2,1|3,1|4,2|5,2|6,2|7,3:385.269:366.612,131.36:0,0:0,3.36673e-05,0.99997 +chr1 6391479 . caaacaaacaaa . . PASS END=6391490;RU=caaa;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00078485;STUTTERDOWN=0.000392426;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:51:1:3,3:3-3,3-3:23,25,0,3:3,23:2,3:351.872:366.612,131.36:0,0:0,2.91798e-07,1 +chr1 6394101 . aaaacaaaacaaaac . . PASS END=6394115;RU=aaaac;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000388255;STUTTERDOWN=0.00374899;STUTTERP=0.97887;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:0.999747:3,3:3-3,3-3:16,17,0,0:3,16:NULL:215.353:366.612,131.36:0,0:0,0.000173326,0.999827 +chr1 6403250 . tgtttgtttgtt . . PASS END=6403261;RU=tgtt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000508048;STUTTERDOWN=0.00145131;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:21:0.996921:3,3:3-3,3-3:12,9,0,0:3,12:NULL:130.745:366.612,131.36:0,0:7.23095e-40,0.00189695,0.998109 +chr1 6410410 . ccacccccacccccaccc . . PASS END=6410427;RU=ccaccc;PERIOD=6;REF=3;GRID=1,6;STUTTERUP=0.000669776;STUTTERDOWN=0.00133955;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:53:0.999998:3,3:3-3,3-3:21,28,0,4:3,21:2,4:369.966:366.612,131.36:0,0:0,4.48486e-06,0.999995 +chr1 6411672 . ccaccaccacca ccaccaccaccacca . PASS END=6411683;RU=cca;PERIOD=3;REF=4;GRID=2,8;STUTTERUP=0.00467823;STUTTERDOWN=0.00282347;STUTTERP=0.999;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:26:0.933194:5,5:5-5,5-5:7,19,0,0:5,7:NULL:196.656:366.612,131.36:0,0:7.30312e-38,0.0317498,0.968307 +chr1 6412880 . tatgtatgtatg . . PASS END=6412891;RU=tatg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00067385;STUTTERDOWN=0.000336925;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:42:1:3,3:3-3,3-3:27,15,0,0:3,27:NULL:243.736:366.612,131.36:0,0:0,6.45001e-08,1 +chr1 6415172 . tatatatatatatatatatata tatatatatatatatatatatata,tatatatatatatatatatatatatatatatatata . PASS END=6415193;RU=ta;PERIOD=2;REF=11;GRID=9,21;STUTTERUP=0.0535111;STUTTERDOWN=0.0961993;STUTTERP=0.504953;EXPTHRESH=11 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:11:0.231832:12,18:12-18,12-18:2,5,0,2:12,2:6,1|17,1:72.2046:366.612,131.36:1.68794,1.37135:3.04941e-11,0.000441063,0.999561 +chr1 6417480 . agctggagaagctggagaagctggagaagctggaga . . PASS END=6417515;RU=agctggaga;PERIOD=9;REF=4;GRID=1,7;STUTTERUP=0.000604178;STUTTERDOWN=0.00483336;STUTTERP=0.966669;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:42:0.999987:4,4:4-4,4-4:19,20,0,3:4,19:2,1|3,2:285.284:366.612,131.36:0,0:0,2.44925e-05,0.999978 +chr1 6419181 . ttcctttcctttcct . . PASS END=6419195;RU=ttcct;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000429615;STUTTERDOWN=0.00207428;STUTTERP=0.984306;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:44:1:3,3:3-3,3-3:24,18,0,2:3,24:2,2:278.409:366.612,131.36:0,0:0,3.33255e-07,1 +chr1 6419368 . tctctttctctttctctttctctt . . PASS END=6419391;RU=tctctt;PERIOD=6;REF=4;GRID=1,7;STUTTERUP=0.00253877;STUTTERDOWN=0.00929691;STUTTERP=0.765845;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:0.999994:4,4:4-4,4-4:20,18,0,0:4,20:NULL:245.529:366.612,131.36:0.139319,0.139319:0,1.87967e-05,0.999985 +chr1 6419434 . ctcctcctcctcctcctcctc ctcctcctcctcctcctc . PASS END=6419454;RU=ctc;PERIOD=3;REF=7;GRID=3,9;STUTTERUP=0.0241456;STUTTERDOWN=0.0151605;STUTTERP=0.899791;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:49:1:6,6:6-6,6-6:26,18,0,5:6,26:3,2|4,2|5,1:306.28:366.612,131.36:0,0:1,9.48715e-08,0 +chr1 6424394 . ttgttgttgttg . . PASS END=6424405;RU=ttg;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000528467;STUTTERDOWN=0.00211385;STUTTERP=0.987382;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:0.999994:4,4:4-4,4-4:19,12,0,0:4,19:NULL:180:366.612,131.36:0,0:0,1.33005e-05,0.999987 +chr1 6427092 . atatatatatatatatatatatatat at . PASS END=6427117;RU=at;PERIOD=2;REF=13;GRID=1,103;STUTTERUP=0.103737;STUTTERDOWN=0.220545;STUTTERP=0.634261;EXPTHRESH=13 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:11:0.0172122:1,1:1-3,1-3:0,11,0,0:NULL:NULL:99.9566:366.612,131.36:0.48807,0.48807:0.560778,0.398671,0.0406984 +chr1 6427177 . atttatttatttattt atttattt . PASS END=6427192;RU=attt;PERIOD=4;REF=4;GRID=1,103;STUTTERUP=0.00208703;STUTTERDOWN=0.00767434;STUTTERP=0.897626;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:11:0.0306123:2,2:1-3,1-3:0,11,0,0:NULL:NULL:101.966:366.612,131.36:0.732539,0.732539:0.248395,0.537449,0.214171 +chr1 6441337 . gccgccgccgccgcc gccgccgccgcc . PASS END=6441351;RU=gcc;PERIOD=3;REF=5;GRID=1,7;STUTTERUP=0.000573729;STUTTERDOWN=0.00302492;STUTTERP=0.982038;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:61:1:4,4:4-4,4-4:32,29,0,0:4,32:NULL:391.05:366.612,131.36:0,0:1,5.48193e-10,0 +chr1 6441476 . gccggccggccg . . PASS END=6441487;RU=gccg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000226938;STUTTERDOWN=0.000453875;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:63:1:3,3:3-3,3-3:34,26,0,3:3,34:2,3:391.166:366.612,131.36:0,0:0,2.98874e-10,1 +chr1 6442029 . aacaacaacaacaacaacaacaacaacaacaacaac aacaacaacaacaacaacaacaacaacaacaacaacaac . PASS END=6442064;RU=aac;PERIOD=3;REF=12;GRID=10,16;STUTTERUP=0.00530602;STUTTERDOWN=0.0309581;STUTTERP=0.683408;EXPTHRESH=12 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:24:0.868709:13,13:13-13,13-13:6,18,0,0:13,6:NULL:198.809:366.612,131.36:0,0:2.86275e-18,0.0676645,0.932431 +chr1 6442239 . taagattgtaagattgtaagattg . . PASS END=6442262;RU=taagattg;PERIOD=8;REF=3;GRID=1,6;STUTTERUP=0.000372861;STUTTERDOWN=0.00106513;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:44:1:3,3:3-3,3-3:24,20,0,0:3,24:NULL:278.112:366.612,131.36:0,0:0,1.08989e-06,1 +chr1 6443834 . gttggttggttg . . PASS END=6443845;RU=gttg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000430686;STUTTERDOWN=0.00123031;STUTTERP=0.761601;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:1.00001:3,3:3-3,3-3:22,14,0,0:3,22:NULL:216.65:366.612,131.36:0,0:0,1.78562e-06,1 +chr1 6444502 . ctgctgctgctg . . PASS END=6444513;RU=ctg;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000414068;STUTTERDOWN=0.000414068;STUTTERP=0.953462;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:36:1:4,4:4-4,4-4:21,15,0,0:4,21:NULL:220.241:366.612,131.36:0,0:0,5.32636e-06,0.999995 +chr1 6445953 . tattttattttattttattttattt tattttattttattt . PASS END=6445977;RU=tattt;PERIOD=5;REF=5;GRID=1,6;STUTTERUP=0.0124138;STUTTERDOWN=0.00419761;STUTTERP=0.519592;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:15:0.986539:3,3:3-3,3-3:10,5,0,0:3,10:NULL:89.0863:366.612,131.36:0,0:0.996391,0.00361845,7.5186e-31 +chr1 6450086 . tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg tgtgtgtgtgtgtgtgtgtgtgtgtgtgtg,tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg . PASS END=6450121;RU=tg;PERIOD=2;REF=18;GRID=12,36;STUTTERUP=0.0442342;STUTTERDOWN=0.182262;STUTTERP=0.684334;EXPTHRESH=18 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:15:0.251893:15,33:15-20,19-36:5,7,0,2:15,3|19,2:13,1|33,1:116.95:366.612,131.36:2.13292,6.6362:8.74514e-06,0.971979,0.0280665 +chr1 6453097 . tttgtttgtttg . . PASS END=6453108;RU=tttg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000439203;STUTTERDOWN=0.000439203;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:0.999862:3,3:3-3,3-3:16,13,0,0:3,16:NULL:180.898:366.612,131.36:0,0:0,0.000100186,0.999903 +chr1 6454520 . atcatcatcatcatc . . PASS END=6454534;RU=atc;PERIOD=3;REF=5;GRID=2,8;STUTTERUP=0.00225783;STUTTERDOWN=0.0083024;STUTTERP=0.973539;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:55:1:5,5:5-5,5-5:28,24,0,3:5,28:4,3:348.08:366.612,131.36:0,0:0,1.93185e-08,1 +chr1 6455399 . agaaaagaaaagaaa . . PASS END=6455413;RU=agaaa;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000500395;STUTTERDOWN=0.00142945;STUTTERP=0.941457;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:0.996704:3,3:3-3,3-3:11,18,0,0:3,11:NULL:208.198:366.612,131.36:0,0:5.81437e-37,0.00226207,0.997745 +chr1 6456272 . acacacacacacacacacacac acacacacacacacacacacacac . PASS END=6456293;RU=ac;PERIOD=2;REF=11;GRID=9,15;STUTTERUP=0.0372379;STUTTERDOWN=0.0809789;STUTTERP=0.876172;EXPTHRESH=11 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:54:1:12,12:12-12,12-12:24,20,0,10:12,24:5,3|9,1|11,6:355.119:366.612,131.36:0,0:0,4.39573e-09,1 +chr1 6456451 . gtggtggtggtggtg . . PASS END=6456465;RU=gtg;PERIOD=3;REF=5;GRID=2,8;STUTTERUP=0.00131067;STUTTERDOWN=0.0068839;STUTTERP=0.911119;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:50:1:5,5:5-5,5-5:30,15,0,5:5,30:4,5:290.961:366.612,131.36:0,0:0,1.93579e-09,1 +chr1 6459379 . aaaacaaaacaaaacaaaac . . PASS END=6459398;RU=aaaac;PERIOD=5;REF=4;GRID=1,7;STUTTERUP=0.000464472;STUTTERDOWN=0.00185787;STUTTERP=0.844424;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:21:0.999802:4,4:4-4,4-4:16,5,0,0:4,16:NULL:110.009:366.612,131.36:0,0:0,0.000120563,0.99988 +chr1 6461977 . ttttcttttcttttc . . PASS END=6461991;RU=ttttc;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000537307;STUTTERDOWN=0.00518847;STUTTERP=0.905234;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:28:0.999407:3,3:3-3,3-3:14,12,0,2:3,14:2,2:180.461:366.612,131.36:0,0:0,0.000331563,0.999673 +chr1 6467447 . agaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaa . . PASS END=6467494;RU=agaa;PERIOD=4;REF=12;GRID=9,15;STUTTERUP=0.00784974;STUTTERDOWN=0.0462585;STUTTERP=0.501743;EXPTHRESH=12 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:26:0.865652:12,12:12-12,12-12:5,14,0,7:12,5:5,2|8,2|10,1|11,2:202.893:366.612,131.36:0,0:7.7543e-13,0.0593063,0.940778 +chr1 6467698 . cccttcccttccctt . . PASS END=6467712;RU=ccctt;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000482251;STUTTERDOWN=0.00192898;STUTTERP=0.987382;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:39:0.999956:3,3:3-3,3-3:17,19,0,3:3,17:2,3:261.031:366.612,131.36:0,0:0,3.89303e-05,0.999963 +chr1 6467732 . tgtgtgtgtgtgtg . . PASS END=6467745;RU=tg;PERIOD=2;REF=7;GRID=3,10;STUTTERUP=0.0115902;STUTTERDOWN=0.0204314;STUTTERP=0.914438;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:48:0.999988:7,7:6-7,6-7:19,24,0,4:7,19:5,1|6,3:323.777:366.612,131.36:0.169767,0.169767:1.22758e-37,8.88063e-06,0.999994 +chr1 6470121 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=6470162;RU=gt;PERIOD=2;REF=21;GRID=20,28;STUTTERUP=0.0918404;STUTTERDOWN=0.210777;STUTTERP=0.764628;EXPTHRESH=21 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:52:0.419116:25,25:24-25,24-25:12,20,0,19:24,4|25,8:6,1|7,1|8,1|9,2|10,1|11,1|13,1|15,1|16,3|17,1|20,1|21,1|22,2|24,2:396.669:366.612,131.36:0.491073,0.491073:0,1.55313e-05,0.999986 +chr1 6474556 . ttgttgttgttg . . PASS END=6474567;RU=ttg;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.000447729;STUTTERDOWN=0.0017909;STUTTERP=0.987382;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:46:1.00001:4,4:4-4,4-4:22,24,0,0:4,22:NULL:309.116:366.612,131.36:0,0:0,2.64898e-06,1 +chr1 6479132 . acacacacacacacacacacacacacacacacacacacac acacacacacacacacacacacacacacacacacacacacac . PASS END=6479171;RU=ac;PERIOD=2;REF=20;GRID=15,24;STUTTERUP=0.0928519;STUTTERDOWN=0.177749;STUTTERP=0.781585;EXPTHRESH=20 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:33:0.818742:21,21:18-21,18-21:7,18,0,6:21,7:6,1|7,1|9,1|12,1|18,2:244.382:366.612,131.36:1.43581,1.43581:9.04679e-12,0.0961955,0.903909 +chr1 6481961 . aataaataaata . . PASS END=6481972;RU=aata;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000535883;STUTTERDOWN=0.00258736;STUTTERP=0.472189;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:24:0.999864:3,3:3-3,3-3:16,8,0,0:3,16:NULL:135.705:366.612,131.36:0,0:0,6.6863e-05,0.999934 +chr1 6485320 . aatttaatttaattt . . PASS END=6485334;RU=aattt;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.00153351;STUTTERDOWN=0.000536825;STUTTERP=0.761601;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:28:0.998443:3,3:3-3,3-3:13,15,0,0:3,13:NULL:191.214:366.612,131.36:0,0:3.21756e-38,0.00108093,0.998922 +chr1 6485835 . tctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctc tctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctc . PASS END=6485900;RU=tc;PERIOD=2;REF=33;GRID=27,35;STUTTERUP=0.0430699;STUTTERDOWN=0.255365;STUTTERP=0.657205;EXPTHRESH=33 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:33:0.296222:31,31:30-32,30-32:2,17,0,12:31,2:6,1|7,1|11,1|13,2|20,1|22,1|23,1|26,1|27,1|29,1|30,1:262.25:366.612,131.36:0.696174,0.696174:0.758903,0.240269,0.000848255 +chr1 6486465 . ataataataataataata ataataataataata . PASS END=6486482;RU=ata;PERIOD=3;REF=6;GRID=2,8;STUTTERUP=0.0307661;STUTTERDOWN=0.0181953;STUTTERP=0.920322;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:37:1.00001:5,5:5-5,5-5:22,15,0,0:5,22:NULL:226.929:366.612,131.36:0,0:1,1.61118e-06,1.10998e-39 +chr1 6486709 . gaggtagaggtagaggta . . PASS END=6486726;RU=gaggta;PERIOD=6;REF=3;GRID=1,6;STUTTERUP=0.00129224;STUTTERDOWN=0.00218412;STUTTERP=0.645932;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:82:1:3,3:3-3,3-3:31,51,0,0:3,31:NULL:573.653:366.612,131.36:0,0:0,2.10299e-08,1 +chr1 6489307 . aaccaaccaaccaaccaaccaaccaaccaacc aaccaaccaaccaaccaaccaaccaaccaaccaaccaaccaaccaaccaacc . PASS END=6489338;RU=aacc;PERIOD=4;REF=8;GRID=10,16;STUTTERUP=0.00928806;STUTTERDOWN=0.00597795;STUTTERP=0.531186;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:11:0.25467:13,13:11-13,11-13:2,7,0,2:13,2:4,1|9,1:89.9995:366.612,131.36:0.634282,0.634282:0,0,1 +chr1 6497659 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt,gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=6497698;RU=gt;PERIOD=2;REF=20;GRID=16,28;STUTTERUP=0.0680456;STUTTERDOWN=0.214525;STUTTERP=0.715541;EXPTHRESH=20 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:52:0.427282:22,25:22-22,19-26:10,26,0,13:22,10:5,1|6,1|11,2|12,2|14,1|15,2|18,3|25,1:396.318:366.612,131.36:0.29703,1.7353:6.86936e-27,4.79342e-07,1 +chr1 6507213 . ggcaggcaggca . . PASS END=6507224;RU=ggca;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000360682;STUTTERDOWN=0.00206067;STUTTERP=0.829224;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:74:0.999988:3,3:3-3,3-3:20,54,0,0:3,20:NULL:564.517:366.612,131.36:0,0:0,2.21705e-05,0.999979 +chr1 6507332 . cacacacacacacaca cacacacacaca . PASS END=6507347;RU=ca;PERIOD=2;REF=8;GRID=3,9;STUTTERUP=0.0329713;STUTTERDOWN=0.0119427;STUTTERP=0.939122;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:31:0.238502:6,6:3-6,3-6:2,29,0,0:6,2:NULL:276.117:366.612,131.36:1.17884,1.17884:0.890963,0.109137,2.63841e-08 +chr1 6507470 . gttgttgttgtt . . PASS END=6507481;RU=gtt;PERIOD=3;REF=4;GRID=1,8;STUTTERUP=0.00099452;STUTTERDOWN=0.00470734;STUTTERP=0.764467;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:68:1:4,4:4-4,4-4:40,22,0,4:4,40:3,4:391.267:366.612,131.36:0,0:0,2.86979e-12,1 +chr1 6509128 . aagaaagaaaga . . PASS END=6509139;RU=aaga;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000399345;STUTTERDOWN=0.00228156;STUTTERP=0.969616;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:50:1:3,3:3-3,3-3:27,23,0,0:3,27:NULL:320.759:366.612,131.36:0,0:0,5.62015e-08,1 +chr1 6509313 . gtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=6509338;RU=gt;PERIOD=2;REF=13;GRID=10,20;STUTTERUP=0.0555038;STUTTERDOWN=0.175441;STUTTERP=0.741738;EXPTHRESH=13 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:49:0.997491:17,17:13-17,13-17:17,15,0,15:16,2|17,15:5,1|6,4|7,1|8,1|12,1|13,1|14,1|16,5:333.024:366.612,131.36:0.974229,0.974229:0,6.11081e-07,1 +chr1 6509599 . aaaagaaaagaaaag . . PASS END=6509613;RU=aaaag;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000459561;STUTTERDOWN=0.00482736;STUTTERP=0.903747;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:35:0.999935:3,3:3-3,3-3:16,15,0,4:3,16:2,4:228.976:366.612,131.36:0,0:0,4.68756e-05,0.999956 +chr1 6513189 . acaagtacaagtacaagt acaagt . PASS END=6513206;RU=acaagt;PERIOD=6;REF=3;GRID=1,103;STUTTERUP=0.000877571;STUTTERDOWN=0.00175514;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:14:0.0778033:1,1:1-3,1-3:0,14,0,0:NULL:NULL:127.912:366.612,131.36:0.916684,0.916684:0.198352,0.51361,0.288123 +chr1 6519516 . acacacacacacacacacacacacacacacacacacacac acacacacacacacacacac,acacacacacacacacacacacacacacacacac . PASS END=6519555;RU=ac;PERIOD=2;REF=20;GRID=6,17;STUTTERUP=0.0530982;STUTTERDOWN=0.235346;STUTTERP=0.645906;EXPTHRESH=20 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:39:0.326169:10,17:10-10,10-17:11,24,0,4:9,2|10,9:9,1|10,1|14,2:315.968:366.612,131.36:0,2.45293:1,0,0 +chr1 6519558 . gtgtgtgtgtgtgtgtgt gtgtgtgt . PASS END=6519575;RU=gt;PERIOD=2;REF=9;GRID=1,8;STUTTERUP=0.0225574;STUTTERDOWN=0.0878681;STUTTERP=0.572595;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:33:0.935555:4,4:4-5,4-5:8,24,0,0:4,8:NULL:254.948:366.612,131.36:0.469019,0.469019:1,0,0 +chr1 6520061 . aaaacaaaacaaaacaaaacaaaacaaaacaaaac aaaacaaaacaaaacaaaacaaaac . PASS END=6520095;RU=aaaac;PERIOD=5;REF=7;GRID=2,10;STUTTERUP=0.00428164;STUTTERDOWN=0.0173243;STUTTERP=0.587462;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/0:40:0.348329:5,7:5-5,5-8:22,10,0,8:5,22:3,3|5,1|7,4:251.551:366.612,131.36:0,0.516183:1.00958e-24,1,0 +chr1 6520115 . aaccaaccaacc . . PASS END=6520126;RU=aacc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000418854;STUTTERDOWN=0.000837707;STUTTERP=0.597956;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:15:0.842359:3,3:3-3,3-3:6,9,0,0:3,6:NULL:104.041:366.612,131.36:0,0:8.02858e-22,0.0840801,0.916017 +chr1 6525229 . aaacaaacaaacaaacaaacaaacaaacaaacaaac aaacaaacaaacaaacaaacaaacaaac . PASS END=6525264;RU=aaac;PERIOD=4;REF=9;GRID=4,10;STUTTERUP=0.00459794;STUTTERDOWN=0.0222731;STUTTERP=0.602057;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:44:1:7,7:7-7,7-7:27,13,0,4:7,27:3,1|6,3:259.229:366.612,131.36:0,0:1,2.10771e-08,0 +chr1 6525468 . tgtgtgtgtgtgtgtg . . PASS END=6525483;RU=tg;PERIOD=2;REF=8;GRID=4,11;STUTTERUP=0.0157266;STUTTERDOWN=0.0380107;STUTTERP=0.899662;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:41:0.999729:8,8:8-8,8-8:15,20,0,5:8,15:6,4|7,1:286.139:366.612,131.36:0.0990099,0.0990099:4.7596e-28,0.000115341,0.999887 +chr1 6530019 . aattaattaatt . . PASS END=6530030;RU=aatt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00061157;STUTTERDOWN=0.00122314;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:28:0.92595:3,3:3-3,3-3:7,21,0,0:3,7:NULL:218.027:366.612,131.36:0,0:4.4995e-23,0.050793,0.949288 +chr1 6540303 . caaaaacaaaaacaaaaa . . PASS END=6540320;RU=caaaaa;PERIOD=6;REF=3;GRID=1,6;STUTTERUP=0.000447826;STUTTERDOWN=0.0021622;STUTTERP=0.984306;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:45:1:3,3:3-3,3-3:23,19,0,3:3,23:2,3:280.557:366.612,131.36:0,0:0,2.94168e-07,1 +chr1 6542023 . gttttgttttgtttt gtttt . PASS END=6542037;RU=gtttt;PERIOD=5;REF=3;GRID=1,7;STUTTERUP=0.000733379;STUTTERDOWN=0.0040474;STUTTERP=0.667787;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:13:0.0706208:1,1:1-4,1-4:0,12,0,0:NULL:NULL:111.332:366.612,131.36:1.20962,1.20962:0.24805,0.510238,0.241734 +chr1 6542152 . ttccttccttccttccttccttccttccttccttccttccttccttcc ttccttccttccttccttccttccttccttccttccttccttcc . PASS END=6542199;RU=ttcc;PERIOD=4;REF=12;GRID=8,15;STUTTERUP=0.00455139;STUTTERDOWN=0.0176796;STUTTERP=0.577091;EXPTHRESH=12 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/0:39:0.998437:11,12:11-11,9-12:7,20,0,12:11,5|12,2:2,1|3,2|4,2|5,4|6,2|8,1:306.906:366.612,131.36:0,0.705267:0.00121235,0.998792,2.93932e-09 +chr1 6549122 . tatatatatatatatatatatatatatatatatatatatatata tatatatatatatatatatatatatatatatatatata . PASS END=6549165;RU=ta;PERIOD=2;REF=22;GRID=16,22;STUTTERUP=0.128454;STUTTERDOWN=0.330264;STUTTERP=0.590544;EXPTHRESH=22 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:17:0.17645:19,19:17-19,17-19:2,11,0,4:19,2:4,1|5,1|8,1|17,1:144.179:366.612,131.36:0.542842,0.542842:0.871083,0.128396,0.000618529 +chr1 6555095 . gttgttgttgtt . . PASS END=6555106;RU=gtt;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00145678;STUTTERDOWN=0.00175843;STUTTERP=0.87689;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:44:1:4,4:4-4,4-4:24,20,0,0:4,24:NULL:282.923:366.612,131.36:0,0:0,1.12807e-06,1 +chr1 6557207 . ttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttc ttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttc . PASS END=6557281;RU=ttc;PERIOD=3;REF=25;GRID=1,30;STUTTERUP=0.0319551;STUTTERDOWN=0.210872;STUTTERP=0.635073;EXPTHRESH=25 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:21:0.0444653:28,28:1-28,1-28:0,13,0,8:NULL:6,1|11,1|14,1|16,1|24,1|25,1|27,2:178.898:366.612,131.36:6.79896,6.79896:2.57014e-23,0.496631,0.503384 +chr1 6558796 . gggtgggtgggt . . PASS END=6558807;RU=gggt;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.00123549;STUTTERDOWN=0.00247098;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:22:0.992568:3,3:3-3,3-3:10,12,0,0:3,10:NULL:147.84:366.612,131.36:0,0:1.03052e-29,0.00436478,0.995644 +chr1 6573728 . tgtttgtttgtttgtt . . PASS END=6573743;RU=tgtt;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000497201;STUTTERDOWN=0.00480119;STUTTERP=0.905234;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:43:1:4,4:4-4,4-4:29,14,0,0:4,29:NULL:246.303:366.612,131.36:0,0:0,1.95774e-08,1 +chr1 6574488 . tatttatttatttatttatttatttatt tatttatttatttatttatttatttatttatttatt . PASS END=6574515;RU=tatt;PERIOD=4;REF=7;GRID=5,12;STUTTERUP=0.00567387;STUTTERDOWN=0.0246882;STUTTERP=0.71796;EXPTHRESH=7 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:31:0.999898:9,9:9-9,9-9:16,11,0,3:9,16:7,1|8,2:194.239:366.612,131.36:0.0990099,0.0990099:0,9.4853e-06,0.999993 +chr1 6575450 . tttatttatttattta . . PASS END=6575465;RU=ttta;PERIOD=4;REF=4;GRID=1,7;STUTTERUP=0.000981603;STUTTERDOWN=0.00280408;STUTTERP=0.766147;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:34:1:4,4:4-4,4-4:26,8,0,0:4,26:NULL:175.847:366.612,131.36:0,0:0,1.47876e-07,1 +chr1 6579057 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgt . PASS END=6579090;RU=gt;PERIOD=2;REF=17;GRID=6,14;STUTTERUP=0.0484244;STUTTERDOWN=0.147421;STUTTERP=0.790648;EXPTHRESH=17 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:53:1:10,10:10-10,10-10:32,16,0,4:9,2|10,30:5,1|8,1|9,2:311.614:366.612,131.36:0,0:1,0,0 +chr1 6581899 . agagagagagagagagagagagagagagagagagag . . PASS END=6581934;RU=ag;PERIOD=2;REF=18;GRID=1,20;STUTTERUP=0.0655147;STUTTERDOWN=0.176282;STUTTERP=0.797037;EXPTHRESH=18 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:12:0.0409144:18,18:16-19,16-19:0,5,0,7:NULL:5,2|8,1|14,1|15,1|16,1|17,1:102.022:366.612,131.36:2.04575,2.04575:0.143728,0.552506,0.303883 +chr1 6582216 . ttttgttttgttttg . . PASS END=6582230;RU=ttttg;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000490339;STUTTERDOWN=0.00236746;STUTTERP=0.984306;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:21:0.999709:3,3:3-3,3-3:15,6,0,0:3,15:NULL:115.111:366.612,131.36:0,0:0,0.000175043,0.999827 +chr1 6589837 . aatgaatgaatg . . PASS END=6589848;RU=aatg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000891512;STUTTERDOWN=0.00356601;STUTTERP=0.993276;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:1:3,3:2-3,2-3:25,7,0,0:3,25:NULL:162.414:366.612,131.36:0.169767,0.169767:0,1.1825e-07,1 +chr1 6589908 . agtcagtcagtc . . PASS END=6589919;RU=agtc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000537343;STUTTERDOWN=0.00107469;STUTTERP=0.999;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:0.999868:3,3:3-3,3-3:16,17,0,0:3,16:NULL:212.311:366.612,131.36:0,0:0,7.16104e-05,0.999932 +chr1 6591632 . ttcctttcctttcctttcctttcctttcctttcctttcctttcctttcct ttcctttcctttcctttcctttcctttcctttcct . PASS END=6591681;RU=ttcct;PERIOD=5;REF=10;GRID=4,13;STUTTERUP=0.00639156;STUTTERDOWN=0.0476609;STUTTERP=0.369045;EXPTHRESH=10 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/0:20:1:7,10:7-7,10-10:9,7,0,4:7,5|10,4:3,2|5,1|6,1:133.243:366.612,131.36:0.29703,0:8.67611e-10,1,2.09003e-09 +chr1 6591950 . tcctttcctttcctttcctt . . PASS END=6591969;RU=tcctt;PERIOD=5;REF=4;GRID=1,7;STUTTERUP=0.00131246;STUTTERDOWN=0.00916065;STUTTERP=0.848496;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:6:0.576692:4,4:4-4,4-4:4,2,0,0:4,4:NULL:32.3285:366.612,131.36:0.29703,0.29703:1.45405e-12,0.214419,0.785623 +chr1 6598126 . tgtgtgtgtgtgtgtgtgtgtg . . PASS END=6598147;RU=tg;PERIOD=2;REF=11;GRID=7,14;STUTTERUP=0.0280775;STUTTERDOWN=0.0773088;STUTTERP=0.869976;EXPTHRESH=11 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:32:0.999831:11,11:11-11,11-11:17,12,0,2:11,17:6,1|8,1:193.141:366.612,131.36:0,0:6.30627e-27,0.000104113,0.999896 +chr1 6601383 . tgtgtgtgtgtg . . PASS END=6601394;RU=tg;PERIOD=2;REF=6;GRID=2,9;STUTTERUP=0.00639803;STUTTERDOWN=0.00181474;STUTTERP=0.791864;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:34:0.999591:6,6:5-6,5-6:15,18,0,0:6,15:NULL:219.972:366.612,131.36:0.437216,0.437216:4.48063e-35,0.000300498,0.999704 +chr1 6601485 . agggagggaggg . . PASS END=6601496;RU=aggg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000329421;STUTTERDOWN=0.000329421;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:1.00001:3,3:3-3,3-3:23,10,0,0:3,23:NULL:177.924:366.612,131.36:0,0:0,5.48719e-07,1 +chr1 6602519 . ttattattattattattattattatta ttattattattattattattattattattattatta . PASS END=6602545;RU=tta;PERIOD=3;REF=9;GRID=1,14;STUTTERUP=0.023953;STUTTERDOWN=0.0774305;STUTTERP=0.524687;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:14:0.0356188:12,12:1-12,1-12:0,9,0,5:NULL:4,1|5,1|6,1|10,1|11,1:119.866:366.612,131.36:3.31696,3.31696:1.68215e-15,0.498435,0.501573 +chr1 6626511 . acccacccaccc . . PASS END=6626522;RU=accc;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000699207;STUTTERDOWN=0.000699207;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:32:0.999187:3,3:3-3,3-3:13,19,0,0:3,13:NULL:223.009:366.612,131.36:0,0:4.38747e-42,0.000474992,0.999529 +chr1 6633217 . gtgtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=6633244;RU=gt;PERIOD=2;REF=14;GRID=10,19;STUTTERUP=0.0821246;STUTTERDOWN=0.171548;STUTTERP=0.783886;EXPTHRESH=14 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:48:0.878848:15,15:13-16,13-16:17,19,0,12:13,2|15,12|16,3:5,3|6,4|9,1|10,1|14,3:359.766:366.612,131.36:0.751302,0.751302:1.4013e-44,0.00210048,0.997905 +chr1 6635223 . aggaaggaaggaaggaaggaagga aggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaagga . PASS END=6635246;RU=agga;PERIOD=4;REF=6;GRID=8,15;STUTTERUP=0.000748388;STUTTERDOWN=0.0231239;STUTTERP=0.544394;EXPTHRESH=6 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:50:0.868967:12,12:9-12,9-12:8,29,0,12:12,8:4,3|6,2|7,2|8,1|9,3|10,1:399.905:366.612,131.36:0.727436,0.727436:0,0,1 +chr1 6637761 . aaaacaaaacaaaac . . PASS END=6637775;RU=aaaac;PERIOD=5;REF=3;GRID=1,6;STUTTERUP=0.000380092;STUTTERDOWN=0.00217157;STUTTERP=0.721063;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:33:1.00001:3,3:3-3,3-3:21,12,0,0:3,21:NULL:189.748:366.612,131.36:0,0:0,2.94786e-06,1 +chr1 6639022 . ctctctctctctctctctctctctctct ctctctctctctctctctctctctctctctct,ctctctctctctctctctctctctctctctctct . PASS END=6639049;RU=ct;PERIOD=2;REF=14;GRID=12,20;STUTTERUP=0.0704341;STUTTERDOWN=0.168677;STUTTERP=0.654623;EXPTHRESH=14 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:54:0.99161:16,17:16-16,16-17:18,28,0,8:15,2|16,14|17,2:5,2|6,2|7,1|9,1|11,1|17,1:407.064:366.612,131.36:0,0.437216:2.0971e-39,2.13905e-10,1 +chr1 6650989 . acacacacacacacacac . . PASS END=6651006;RU=ac;PERIOD=2;REF=9;GRID=5,13;STUTTERUP=0.0186073;STUTTERDOWN=0.0566844;STUTTERP=0.910802;EXPTHRESH=9 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:49:1:9,9:9-9,9-9:20,20,0,7:9,20:5,1|7,2|8,4:316.391:366.612,131.36:0.0990099,0.0990099:1.13195e-34,6.36215e-06,0.999994 +chr1 6652069 . aataaataaataaataaataaataaataaata aataaataaataaataaataaataaata,aataaataaataaataaataaataaataaataaata . PASS END=6652100;RU=aata;PERIOD=4;REF=8;GRID=4,12;STUTTERUP=0.00680226;STUTTERDOWN=0.0323544;STUTTERP=0.757122;EXPTHRESH=8 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/2:36:0.99999:7,9:7-7,7-9:21,13,0,2:7,15|8,2|9,4:5,1|8,1:250.151:366.612,131.36:0,0.45372:1.27709e-14,1,2.06024e-20 +chr1 6653054 . tttgtttgtttgtttgtttg tttgtttgtttgtttgtttgtttg . PASS END=6653073;RU=tttg;PERIOD=4;REF=5;GRID=3,9;STUTTERUP=0.000839468;STUTTERDOWN=0.00885705;STUTTERP=0.838197;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:45:1.00001:6,6:6-6,6-6:21,18,0,6:6,21:2,1|4,2|5,3:290.798:366.612,131.36:0,0:0,3.94884e-07,1 +chr1 6660614 . tgtttgtttgtttgtttgtt . . PASS END=6660633;RU=tgtt;PERIOD=4;REF=5;GRID=2,8;STUTTERUP=0.000501964;STUTTERDOWN=0.00930428;STUTTERP=0.807341;EXPTHRESH=5 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:29:0.999553:5,5:5-5,5-5:14,13,0,2:5,14:2,1|3,1:191.696:366.612,131.36:0,0:0,0.00022762,0.999774 +chr1 6661173 . gttttgttttgtttt gttttgttttgttttgtttt . PASS END=6661187;RU=gtttt;PERIOD=5;REF=3;GRID=1,7;STUTTERUP=0.000648047;STUTTERDOWN=0.00554822;STUTTERP=0.693638;EXPTHRESH=3 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:20:0.995835:4,4:4-4,4-4:12,8,0,0:4,12:NULL:121.767:366.612,131.36:0,0:0,0.00236118,0.997647 +chr1 6662622 . gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt . PASS END=6662661;RU=gt;PERIOD=2;REF=20;GRID=12,19;STUTTERUP=0.0631601;STUTTERDOWN=0.12976;STUTTERP=0.781228;EXPTHRESH=20 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 1/1:17:0.997073:16,16:16-16,16-16:13,3,0,0:16,13:NULL:80.8523:366.612,131.36:0.0990099,0.0990099:1,0,0 +chr1 6663558 . ctgctgctgctg . . PASS END=6663569;RU=ctg;PERIOD=3;REF=4;GRID=1,7;STUTTERUP=0.00240249;STUTTERDOWN=0.00466994;STUTTERP=0.973954;EXPTHRESH=4 GT:DP:Q:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:6:0.577703:4,4:4-4,4-4:4,2,0,0:4,4:NULL:35.0695:366.612,131.36:0,0:2.88725e-11,0.234658,0.765367 diff --git a/tests/data/test_gangstr_noqual.vcf b/tests/data/test_gangstr_noqual.vcf new file mode 100644 index 0000000..358491d --- /dev/null +++ b/tests/data/test_gangstr_noqual.vcf @@ -0,0 +1,46 @@ +##fileformat=VCFv4.1 +##FILTER= +##command=GangSTR-2.4.2.12-9da7 --bam /scratch/bams/drive3/4512-JFI-0366_BXD196_phased_possorted_bam.bam --regions /scratch/regions/0705_mm10.bed --ref /scratch/ref/mm10.fa --str-info /scratch/strinfo/100519_mm10_strinfo_wo_stutt_recalc_many_samples.bed --chrom chr1 --trim-to-readlength 128 --drop-dupes --out result/4512-JFI-0366_BXD196/res_chr1 +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##bcftools_filterVersion=1.6-49-ga2ffda9-dirty+htslib-1.7-1-gaf40c73 +##bcftools_filterCommand=filter -r chr1:3000000-10000000 /storage/mikhail/100919_BXD_all_drive1_drive3_rep_stutt_model/result/4512-JFI-0366_BXD196/res_chr1.vcf.gz; Date=Sun Nov 24 18:06:49 2019 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BXD196_0366 +chr1 3004986 . tctgtctgtctg . . PASS END=3004997;RU=tctg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000632591;STUTTERDOWN=0.000632591;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:3,3:3-3,3-3:17,12,0,2:3,17:2,2:193.56:366.612,131.36:0,0:0,5.1188e-05,0.999949 diff --git a/tests/data/test_hipstr.vcf b/tests/data/test_hipstr.vcf new file mode 100644 index 0000000..27ad789 --- /dev/null +++ b/tests/data/test_hipstr.vcf @@ -0,0 +1,1300 @@ +##fileformat=VCFv4.1 +##command=HipSTR-v0.5 --bams /storage/gtex-data/wgs/SRR2163846.bam --fasta /storage/resources/Homo_sapiens_assembly19.fasta --regions /storage/resources/GRCh37.hipstr_reference.bed --min-reads 5 --str-vcf /storage/vcfs/SRR2163846.vcf.gz --def-stutter-model --log /storage/vcfs/SRR2163846.log.txt +##reference=/storage/resources/Homo_sapiens_assembly19.fasta +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT GTEX-R55C-0003 +1 16717 STR_2 GGTGGTGGTGGGGGCGGTGGGGGTGGTG GGTGGTGGTGGGGGCGGTGGTGGTGCTG . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=16717;END=16744;PERIOD=3;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=121;DSNP=0;DSTUTTER=3;DFLANKINDEL=15 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:121:0:3:15:96.95|24.05:0|0:29.31:-15.66:93:0.0:-23|1;0|64;1|2;9|5:0|52;9|2 +1 26454 STR_3 GTGTGTGTGTGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=26454;END=26465;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=49;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:49:0:0:2:24.50|24.50:0|0:.:0.0:.:0.0:0|38:0|38 +1 28589 STR_4 TTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=28589;END=28603;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 30863 STR_5 TCTCCCTCTCTCTCTCTCTCTCTCTCTCTCATTTCTCTCTATCTCATTTCTCTCTCTCTCGCTATCTCATTTTTCTCTCTCTCTCTTTCTCTCCTCT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=30863;END=30959;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 31720 STR_6 AAAAAAAAAAAAAA AAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=31720;END=31733;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=70;DSNP=0;DSTUTTER=6;DFLANKINDEL=8 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:70:0:6:8:32.60|37.40:0|0:15.0:-0.3:54:0.0:-3|1;-2|2;-1|27;0|19;1|2:-3|1;-2|2;-1|25;0|17;1|3 +1 33450 STR_7 AAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=33450;END=33464;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=9;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:9:0:1:1:4.50|4.50:0|0:.:0.0:.:0.0:-23|1;0|3:0|2 +1 33520 STR_8 GTTTTTTTTTCTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=33521;END=33541;PERIOD=5;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 35484 STR_9 ATAAAAAATAAATAAATAAATAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=35484;END=35507;PERIOD=4;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 36352 STR_10 AAAAAAAAAAAAA AAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=36352;END=36364;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=37;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:37:0:1:2:18.07|18.93:0|0:9.61:0.0:27:-0.36:-1|12;0|9;23|1:-1|10;0|8 +1 39909 STR_11 AAATAAATAAATAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=39909;END=39923;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=42;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:42:0:0:3:21.00|21.00:0|0:.:0.0:.:0.0:-7|1;-5|1;0|27:0|27 +1 43797 STR_12 AAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=43797;END=43812;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 44836 STR_13 AAATAAATAAATAAATAAATAAATAAATAAATTAAATAAAT AAATAAATAAATAAATAAATAAATAAATAAATAAAATAAAT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=44836;END=44876;PERIOD=4;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=14;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:14:0:0:2:8.50|5.50:0|0:3.22:-0.34:7:0.0:0|6:0|5 +1 46403 STR_14 TTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=46403;END=46416;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 49510 STR_15 AAAAAGAAAAAGAAAAAAAGAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=49510;END=49534;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 50482 STR_16 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=50482;END=50513;PERIOD=2;AN=0;REFAC=0;NSKIP=1;NFILT=0;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 50571 STR_17 TTTCCTTTCCTTTCCTTGCTCTTCTTTCTCTCCTATTGCTTTCCTTTCATTTCCTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=50571;END=50626;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=39;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:39:0:0:1:19.50|19.50:0|0:.:0.0:.:0.0:0|19;44|1:0|19 +1 51865 STR_18 AAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=51865;END=51877;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 61863 STR_21 TTTTTTTTCTTTTTTTTT TTTTTTTTCTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1;START=61863;END=61880;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=14;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|1:0.93:0.46:14:0:0:1:3.62|10.38:0|0:1.12:-1.18:11:0.0:0|2;1|4:0|2;1|4 +1 62232 STR_22 ACACACATACACACACACACACACA ACACACATACACACACACACACA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-2;START=62232;END=62256;PERIOD=2;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=12;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:-2|-2:0.98:0.98:12:0:0:1:6.00|6.00:0|0:1.79:0.0:.:0.0:-2|9:-2|9 +1 71176 STR_24 AAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=71176;END=71186;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=20;DSNP=0;DSTUTTER=1;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:20:0:1:0:10.00|10.00:0|0:.:0.0:.:0.0:0|15;1|1:0|14;1|1 +1 71847 STR_25 TTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=71847;END=71861;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=11;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:11:0:0:0:5.50|5.50:0|0:.:0.0:.:0.0:0|7:0|7 +1 92664 STR_33 AAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=92664;END=92677;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 93726 STR_34 CGGTTTTTTTGTTTTTGTTTTTGTTTTTAGACG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=93731;END=93753;PERIOD=6;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 94810 STR_35 TTTTCTTTTCTTTTCTTTTTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=94810;END=94847;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 94997 STR_36 TTTTTTTTTATTTTTTATTTTTT . . . 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INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=150454;END=150489;PERIOD=5;AN=0;REFAC=0;NSKIP=1;NFILT=0;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 151317 STR_65 TTTCTTTCTTTCTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=151317;END=151331;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=46;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:46:0:0:1:23.00|23.00:0|0:.:0.0:.:0.0:0|31:0|31 +1 151480 STR_66 TTTTATTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=151480;END=151497;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 155855 STR_67 AAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=155855;END=155869;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 155996 STR_68 TTTTATTTTATTTTATTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=155996;END=156014;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=45;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:45:0:0:1:22.50|22.50:0|0:.:0.0:.:0.0:-11|1;0|26:0|26 +1 156280 STR_69 TTTTTTTTTTTT TTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=3;START=156280;END=156291;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=47;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|3:1.0:0.5:47:0:0:2:36.45|10.55:0|0:5.91:-4.89:36:0.0:0|30;3|4:0|29;3|3 +1 157108 STR_70 AAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=157108;END=157121;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=33;DSNP=0;DSTUTTER=3;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:33:0:3:0:16.50|16.50:0|0:.:0.0:.:0.0:-1|2;0|18:-1|2;0|17 +1 158998 STR_71 ACACACACAAACACACACACACACACACACACACC ACACACACAAACACACACACACACACACACACA,ACACACACAAACACACACACACACACACACACACACACC . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-2,4;START=158998;END=159031;PERIOD=2;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=40;DSNP=0;DSTUTTER=1;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:-2|4:1.0:0.5:40:0:1:0:21.05|18.95:0|0:25.19:-0.14:31:0.0:-2|14;0|1;4|9:-2|15;4|9 +1 160472 STR_72 TTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=160472;END=160487;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=51;DSNP=0;DSTUTTER=3;DFLANKINDEL=7 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:51:0:3:7:25.50|25.50:0|0:.:0.0:.:0.0:-2|1;-1|1;0|34:-2|1;-1|1;0|29 +1 162181 STR_73 AAGGAAGGAAAGAAAAAAGGAAGGGAGGAGGGAAGGAGGGAAAAAGGGAAGGAGGGAAGGAAAGGAAGGAAGGGAAAGAAGGAAAGGAAGGAAGG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=162181;END=162275;PERIOD=4;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 162288 STR_74 GAGGGAAGGAGGAAGGGAGGGAAGGAGGGAGGGAGGGAGAGAGAGAGGGAGGGAGGG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=162288;END=162344;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=46;DSNP=0;DSTUTTER=0;DFLANKINDEL=6 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:46:0:0:6:23.00|23.00:0|0:.:0.0:.:0.0:0|13:0|10 +1 162355 STR_75 AAAGGGAAGAGAAGGGAAAGGAGGAAGAAAAGGAAAGGAAAGGAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=162355;END=162399;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=43;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:43:0:0:2:21.50|21.50:0|0:.:0.0:.:0.0:0|23:0|23 +1 164130 STR_77 AAAACAAAACAAAACAAAACAAAAT AAAACAAAACAAAACAAAACAAAAC . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=164130;END=164153;PERIOD=5;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=37;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:37:0:0:2:29.98|7.02:0|0:5.42:-4.47:31:-0.22:-17|1;-3|1;0|19:0|19 +1 164674 STR_78 AAAAAAAAAAAAAAAAAAAAAAT AAAAAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-4;START=164674;END=164695;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=3;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-4:1.0:0.5:35:0:3:5:27.41|7.59:0|0:6.8:-4.06:26:0.0:-25|1;-5|1;-4|1;-1|1;0|8:-4|1;-2|1;-1|1;0|5 +1 165288 STR_79 AAAAAAAAAAAAAAAAAAAAAAAC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=165288;END=165310;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 167135 STR_80 TTTATTTATTTATTTATTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=167135;END=167153;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=64;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:64:0:0:3:32.00|32.00:0|0:.:0.0:.:0.0:-5|1;0|42;2|1:0|41 +1 168770 STR_81 AAAAACAAAAACAAAAACA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=168770;END=168788;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=27;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:27:0:0:2:13.50|13.50:0|0:.:0.0:.:0.0:0|14;2|1:0|15 +1 169658 STR_82 AAAACAAAACAAAACAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=169658;END=169676;PERIOD=5;AN=0;REFAC=0;NSKIP=1;NFILT=0;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 169860 STR_83 TTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=169860;END=169872;PERIOD=1;AN=0;REFAC=0;NSKIP=1;NFILT=0;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 170935 STR_84 GTTTTGTTTTGTTTTGTTTT GTTTGGTTTTGTTTTGTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=170935;END=170954;PERIOD=5;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=42;DSNP=0;DSTUTTER=0;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:42:0:0:5:33.48|8.52:0|0:17.92:-4.38:37:0.0:-1|1;0|32:0|32 +1 174800 STR_85 AAAAAAAAAAAAAAGAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=174800;END=174820;PERIOD=1;AN=0;REFAC=0;NSKIP=1;NFILT=0;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 175039 STR_86 CACAGCACACACACAC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=175039;END=175054;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=44;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:44:0:0:2:22.00|22.00:0|0:.:0.0:.:0.0:-11|1;0|38:0|38 +1 175449 STR_87 AAAAAAAAAACAGAAAAAGAAAAAGAAAAA AAAAAAAAACAGAAAAAGAAAAAGAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=175449;END=175478;PERIOD=6;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=34;DSNP=0;DSTUTTER=1;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:34:0:1:4:18.01|15.99:0|0:76.87:-0.08:20:-0.19:-15|1;-10|1;-6|1;-1|6;0|8:-1|6;0|7 +1 176203 STR_88 AAAACAAAACAAAACAAAACAAAACAAAAAAC AAAACAAAACAAAACAAAACAAAACAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=176203;END=176231;PERIOD=5;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=19;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:19:0:0:2:12.50|6.50:0|0:9.32:-0.84:12:-0.29:0|12:0|12 +1 229805 STR_89 TAAATAAATAAATAAATAAAT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=229805;END=229825;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=22;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:22:0:0:1:11.00|11.00:0|0:.:0.0:.:0.0:0|15:0|14 +1 232435 STR_90 TTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=232435;END=232445;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=30;DSNP=0;DSTUTTER=3;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:30:0:3:0:15.00|15.00:0|0:.:0.0:.:0.0:-9|1;-1|1;0|20;1|1:-1|1;0|18;1|1 +1 237529 STR_91 AAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=237529;END=237544;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 238991 STR_92 AAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=238991;END=239005;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 240059 STR_93 TTTTTGTTTTTGTTTTTGTTTTT TTTTTGTTTTTGTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=240059;END=240081;PERIOD=6;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=47;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:47:0:0:1:36.90|10.10:0|0:11.45:-4.84:39:-1.11:0|27:0|27 +1 241330 STR_94 TTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=241330;END=241345;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 243368 STR_95 GTGTGTGTGCGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=243368;END=243384;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=47;DSNP=0;DSTUTTER=0;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:47:0:0:4:23.50|23.50:0|0:.:0.0:.:0.0:-22|1;0|32:0|29 +1 247653 STR_96 AAAAAAAAAAAAA AAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=247653;END=247665;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=44;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:0.92:0.46:44:0:2:2:29.81|14.19:0|0:1.07:-2.64:29:-0.21:-1|5;0|20;31|1:-1|5;0|16 +1 247992 STR_97 AAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=247992;END=248006;PERIOD=1;AN=0;REFAC=0;NSKIP=1;NFILT=0;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 249573 STR_98 AAAAGTAAAATAAAATAAAATAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=249573;END=249597;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=100;DSNP=0;DSTUTTER=0;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:100:0:0:5:59.91|40.09:0|0:.:0.0:.:0.0:-25|1;-17|1;-2|1;0|49:0|49 +1 250478 STR_99 ACACACACACACACACACACACATACACACACAC ACACACACACACACACACACACACACACACACATACACACACAC . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=10;START=250478;END=250511;PERIOD=2;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=52;DSNP=0;DSTUTTER=6;DFLANKINDEL=6 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|10:1.0:0.5:52:0:6:6:29.67|22.33:0|0:54.01:-0.58:29:-2.46:-13|1;-8|2;0|13;6|3;10|3:0|11;6|3;10|3 +1 251924 STR_100 ATATATATATAGATATATA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=251924;END=251942;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=58;DSNP=0;DSTUTTER=0;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:58:0:0:5:29.00|29.00:0|0:.:0.0:.:0.0:-9|1;0|43:0|41 +1 253244 STR_101 CTCTCTCTTTTCTCTCTCTCTCT CTCTCTTTTCTCTCTCTCTCT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-2;START=253244;END=253266;PERIOD=2;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=99;DSNP=0;DSTUTTER=0;DFLANKINDEL=6 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-2:1.0:0.5:99:0:0:6:68.68|30.32:0|0:17.18:-4.56:85:-0.09:-17|1;-9|1;-2|18;0|49;11|1:-2|18;0|46 +1 254861 STR_102 AAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=254861;END=254882;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 255886 STR_103 TGTGTGTATGCGTGTGTGTGTGTATGTGTGTGTGTGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=255886;END=255929;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 256097 STR_104 ATATATATACATATATA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=256097;END=256113;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=29;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:29:0:0:2:14.50|14.50:0|0:.:0.0:.:0.0:0|25:0|24 +1 257251 STR_105 AAAAAAAAAAGAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=257251;END=257265;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=33;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:33:0:0:1:16.50|16.50:0|0:.:0.0:.:0.0:0|30:0|27 +1 257682 STR_106 AAAAAAAAAAACAAAAAAAA AAAAGAAAAAACAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=257682;END=257701;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=21;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:21:0:0:0:6.02|14.98:0|0:8.29:-1.31:17:0.0:0|14:0|14 +1 260191 STR_107 CTCTCCCTCTCTCTCTTTCTCT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=260191;END=260212;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=28;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:28:0:0:2:14.00|14.00:0|0:.:0.0:.:0.0:0|14;2|1;3|1:0|14 +1 260862 STR_108 ACACACACACAAAAATCACACACACA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=260862;END=260887;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=75;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:75:0:0:3:37.50|37.50:0|0:.:0.0:.:0.0:0|60;11|1:0|57 +1 265761 STR_109 TATATATAAATATATAT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=265761;END=265777;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=20;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:20:0:0:2:10.00|10.00:0|0:.:0.0:.:0.0:0|9;8|1:0|8 +1 267560 STR_111 TTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=267560;END=267574;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 524187 STR_112 CACACAGACAGACACACCCACCCACACACA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=524187;END=524216;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=23;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:23:0:0:1:11.50|11.50:0|0:.:0.0:.:0.0:0|15;5|1:0|14 +1 526035 STR_113 TAAAAAATAAATAAATAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=526035;END=526053;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=44;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:44:0:0:1:22.00|22.00:0|0:.:0.0:.:0.0:0|24:0|24 +1 526349 STR_114 AAACAAACAAACAAACAAAAAACA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=526349;END=526372;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=56;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:56:0:1:2:28.00|28.00:0|0:.:0.0:.:0.0:-23|1;-7|1;0|30:0|30 +1 527112 STR_115 TCAAAAAAAAAAAAAAAAAA TCAAAAAAAAAAAAAAAAAAAA,TAAAAAAAAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=2,3;START=527114;END=527131;PERIOD=1;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=21;DSNP=0;DSTUTTER=3;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:2|3:0.98:0.49:21:0:3:0:14.13|6.87:0|0:1.76:-1.24:14:-0.3:-9|1;0|4;1|2;2|4;3|1:1|1;2|3;3|1 +1 531684 STR_116 ACACACATACACACAC ACACACAC . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-8;START=531684;END=531699;PERIOD=2;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=54;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-8:1.0:0.5:54:0:0:2:49.50|4.50:0|0:4.78:-11.36:49:0.0:-13|1;-8|2;0|41:-8|2;0|39 +1 531898 STR_117 ACACACATACACACAC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=531898;END=531913;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=67;DSNP=0;DSTUTTER=8;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:67:0:8:3:33.50|33.50:0|0:.:0.0:.:0.0:-2|5;0|51:-2|5;0|47 +1 532433 STR_118 ACACACTCACACACACA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=532433;END=532449;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=36;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:36:0:0:3:18.00|18.00:0|0:.:0.0:.:0.0:-6|1;0|27:0|23 +1 533066 STR_119 AAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=533066;END=533079;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 534315 STR_120 GGGGGGGGGGG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=534315;END=534325;PERIOD=1;AN=0;REFAC=0;NSKIP=1;NFILT=0;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 534668 STR_121 TTTTCTTTTTTTTCTTTTCTTTTCTTTCTTTCTTTCTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=534668;END=534707;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=57;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:57:0:0:2:28.50|28.50:0|0:.:0.0:.:0.0:-14|1;-4|1;0|19:0|19 +1 535063 STR_122 TTTTGTTTTGTTTTGTTTTGTTTTGTTTT TTTTGTTTTGTTTTGTTTTTTTTGTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=535063;END=535091;PERIOD=5;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=55;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:55:0:0:2:44.95|10.05:0|0:39.16:-7.1:45:-0.18:-19|1;-1|4;0|28;23|1:-1|4;0|28 +1 535329 STR_123 TGTGTGTGTGTGTGTGTGTATGTCTGTGTGAGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=535329;END=535368;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=54;DSNP=0;DSTUTTER=5;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:54:0:5:5:27.00|27.00:0|0:.:0.0:.:0.0:-30|1;-2|4;0|28;4|1;12|1;23|1:-2|4;0|27;4|1 +1 536202 STR_124 TATATATGTATAATATATATTATATAT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=536202;END=536228;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=44;DSNP=0;DSTUTTER=3;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:44:0:3:5:23.45|20.55:0|0:.:0.0:.:0.0:-8|1;-5|1;0|17:0|15 +1 536252 STR_125 TGCATATATGTATAATATATATTATATATGGA TCCATATATGCATAATATATATTATATATATG . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=536255;END=536280;PERIOD=2;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=21;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:0.98:0.49:21:0:0:3:20.00|1.00:0|0:1.8:-4.68:21:0.0:-22|1;-18|1;0|13:0|12 +1 536385 STR_126 TATATATGTATAATATATATTATATAT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=536385;END=536411;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=29;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:29:0:0:0:14.50|14.50:0|0:.:0.0:.:0.0:0|18:0|17 +1 536524 STR_127 TATAATATATATTATATAT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=536524;END=536542;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:31:0:0:0:15.50|15.50:0|0:.:0.0:.:0.0:0|20:0|17 +1 539782 STR_128 AAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=539782;END=539799;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 541158 STR_129 AAAAAAAAAAA AAAAAAAAACA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=541158;END=541168;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=37;DSNP=0;DSTUTTER=2;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:37:0:2:1:31.29|5.71:0|0:8.66:-5.21:34:-0.22:0|28;1|2:0|28;1|2 +1 542673 STR_130 AGGAGGAAGAGGAGGAGGAG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=542673;END=542692;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=50;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:50:0:0:3:25.00|25.00:0|0:.:0.0:.:0.0:0|34:0|33 +1 543247 STR_131 CTATCTATCATCTATCTA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=543247;END=543264;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=56;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:56:0:0:2:28.00|28.00:0|0:.:0.0:.:0.0:0|41:0|40 +1 548784 STR_132 AAAAAAGAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=548784;END=548800;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=36;DSNP=0;DSTUTTER=3;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:36:0:3:0:18.00|18.00:0|0:.:0.0:.:0.0:-1|3;0|26:-1|3;0|23 +1 553371 STR_133 TTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=553371;END=553381;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=36;DSNP=0;DSTUTTER=0;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:36:0:0:5:18.00|18.00:0|0:.:0.0:.:0.0:-4|1;0|26;18|1:0|21 +1 556734 STR_134 AAAAAAAAAAAAAA AAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1;START=556734;END=556747;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=60;DSNP=0;DSTUTTER=9;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|1:1.0:0.5:60:0:9:4:33.21|26.79:0|0:13.72:-0.61:47:-0.25:-6|1;0|23;1|9;2|4;3|2;6|1:0|20;1|6;2|4;3|2 +1 559052 STR_135 GTGTGTGTGTGTGTGTGTGTGTGTGTGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=559052;END=559079;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=43;DSNP=0;DSTUTTER=3;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:43:0:3:2:21.50|21.50:0|0:.:0.0:.:0.0:-19|1;-4|2;0|27:-4|2;0|26 +1 561897 STR_137 TTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=561897;END=561914;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 562017 STR_138 TTTTTTTTTTTTTTTTTTTT TTTCTTTTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1;START=562017;END=562036;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=32;DSNP=0;DSTUTTER=4;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|1:1.0:0.5:32:0:4:4:21.32|10.68:0|0:14.1:-1.38:20:0.0:-5|1;-3|1;-2|1;-1|2;0|5;1|2:-1|1;0|5;1|2 +1 562162 STR_139 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=562162;END=562201;PERIOD=2;AN=0;REFAC=0;NSKIP=1;NFILT=0;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 571518 STR_140 CAAACAAACAAACAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=571518;END=571533;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=90;DSNP=0;DSTUTTER=1;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:90:0:1:4:45.00|45.00:0|0:.:0.0:.:0.0:-5|1;0|76:0|75 +1 571833 STR_141 TTTTCTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=571833;END=571848;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=81;DSNP=0;DSTUTTER=2;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:81:0:2:4:40.50|40.50:0|0:.:0.0:.:0.0:-9|1;0|62;1|2:0|55;1|2 +1 573397 STR_142 ATAAATAAATAATAAATAAATAAAT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=573397;END=573421;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=44;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:44:0:0:1:22.00|22.00:0|0:.:0.0:.:0.0:0|23;4|1:0|24 +1 575209 STR_143 GTTTTTTTTTTTTT GCTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=575210;END=575222;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=56;DSNP=0;DSTUTTER=3;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:56:0:3:4:40.42|15.58:0|0:16.84:-3.95:41:-1.3:-6|1;0|31;1|3:0|27;1|2 +1 576279 STR_144 TTTTCTTTTCTTTTTCTTTTTTTTTTTTTT TTTTCTTTTCTTTTTCTTTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=2;START=576279;END=576308;PERIOD=6;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=41;DSNP=0;DSTUTTER=2;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|2:1.0:0.5:41:0:2:4:27.70|13.30:0|0:27.18:-2.36:22:0.0:-5|1;-2|1;0|6;2|1:-4|1;0|5;2|2 +1 576458 STR_145 TTTTTTTTTTTTTTT TTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=576458;END=576472;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=36;DSNP=0;DSTUTTER=5;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:36:0:5:4:15.95|20.05:0|0:6.15:-0.25:26:0.0:-22|1;-2|5;-1|11;0|9;1|1:-2|3;-1|10;0|6;1|1 +1 578602 STR_146 GTGTGTGTGCGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=578602;END=578618;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=33;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:33:0:0:2:16.50|16.50:0|0:.:0.0:.:0.0:-7|1;0|26:0|23 +1 580568 STR_147 TTTATGTATTTATTTATTTACTTATTTATTTATTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=580568;END=580602;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=27;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:27:0:1:1:13.50|13.50:0|0:.:0.0:.:0.0:0|12:0|10 +1 580624 STR_148 TTTTTTTCTTCTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=580624;END=580647;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=27;DSNP=0;DSTUTTER=2;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:27:0:2:1:13.50|13.50:0|0:.:0.0:.:0.0:0|12;1|1:0|10;1|1 +1 582871 STR_149 AAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=582871;END=582888;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 583216 STR_150 AAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=583216;END=583233;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 584861 STR_151 AAAATAAAATAAAATAAAATAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=584861;END=584884;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=47;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:47:0:0:1:23.50|23.50:0|0:.:0.0:.:0.0:-30|1;0|25:0|25 +1 585764 STR_152 ACACACACACACACACACACACACACACACACACACACAC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=585764;END=585803;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 587341 STR_153 AAAAAAAAAAAAAAAAAGAAGT AAAAAAAAAAAAAAAAAAAA,AAAAAAAAAAAAAAAAGAAGT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-2,-1;START=587341;END=587357;PERIOD=1;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=24;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:-2|-1:0.92:0.46:24:0:2:2:4.26|19.74:0|0:1.04:-2.83:21:-0.28:-2|1;-1|12;0|3:-2|1;-1|13;0|1 +1 587417 STR_154 ACACACACACAAACAC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=587417;END=587432;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=19;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:19:0:0:1:9.50|9.50:0|0:.:0.0:.:0.0:0|13;2|1:0|12 +1 591775 STR_156 ATATATAATATGTACATATTATATATTATAT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=591775;END=591805;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=22;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:22:0:0:2:11.00|11.00:0|0:.:0.0:.:0.0:-15|1;-1|1;0|16:0|15 +1 592470 STR_157 TGTGTGTGTGTGTGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=592470;END=592484;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=65;DSNP=0;DSTUTTER=0;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:65:0:0:4:32.50|32.50:0|0:.:0.0:.:0.0:0|57:0|56 +1 596165 STR_158 TTTGTTTTGTTTTGCTTTGTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=596165;END=596187;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:31:0:0:3:15.50|15.50:0|0:.:0.0:.:0.0:-18|1;0|21:0|21 +1 601985 STR_159 TTTTTTTTTTTCTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=601985;END=602001;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=90;DSNP=0;DSTUTTER=5;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:90:0:5:5:45.00|45.00:0|0:.:0.0:.:0.0:-18|1;-1|2;0|66;1|2:0|55;1|2 +1 605964 STR_161 GGAGGAGGAGGAGGAGGAG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=605964;END=605982;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:31:0:0:0:15.50|15.50:0|0:.:0.0:.:0.0:0|24:0|23 +1 609013 STR_162 AAAAATAAATAAATAAAAATAAAAATAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=609013;END=609043;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=30;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:30:0:0:0:15.00|15.00:0|0:.:0.0:.:0.0:0|14:0|14 +1 611695 STR_163 TTTTTTTTTTTTTTT TTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=611695;END=611709;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=28;DSNP=0;DSTUTTER=2;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:28:0:2:3:16.83|11.17:0|0:4.75:-0.54:22:-0.42:-2|2;-1|5;0|10:-2|2;-1|5;0|8 +1 628625 STR_164 AGAGAGAGAGAAGAGA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=628625;END=628640;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=28;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:28:0:0:0:14.00|14.00:0|0:.:0.0:.:0.0:0|24:0|20 +1 628792 STR_165 AATGAATGAATGAATG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=628792;END=628807;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=48;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:48:0:0:2:24.00|24.00:0|0:.:0.0:.:0.0:-3|1;0|33:0|31 +1 631657 STR_166 AAAAAAAAAAAAAAA AAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-2;START=631657;END=631671;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=10;DSNP=0;DSTUTTER=1;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-2:1.0:0.5:10:0:1:0:5.91|4.09:0|0:3.37:-0.16:6:0.0:-2|2;-1|1;0|2:-2|2;-1|1 +1 637730 STR_167 AAAAAAAAGAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=637730;END=637749;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=45;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:45:0:2:2:22.50|22.50:0|0:.:0.0:.:0.0:0|28;1|2:0|26;1|1 +1 640239 STR_168 CTCTCCCTCTCTCTCTTTCTCT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=640239;END=640260;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:35:0:0:0:17.50|17.50:0|0:.:0.0:.:0.0:0|24:0|22 +1 640910 STR_169 ACACACACACAAAAATCACACACACA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=640910;END=640935;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=74;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:74:0:0:1:37.00|37.00:0|0:.:0.0:.:0.0:0|55:0|53 +1 645809 STR_170 TATATATAAATATATAT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=645809;END=645825;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=19;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:19:0:1:2:9.50|9.50:0|0:.:0.0:.:0.0:0|14:0|13 +1 646877 STR_171 TTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=646877;END=646887;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=50;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:50:0:0:1:25.00|25.00:0|0:.:0.0:.:0.0:0|43:0|41 +1 647609 STR_173 TTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=647609;END=647623;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=16;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:16:0:1:1:8.00|8.00:0|0:.:0.0:.:0.0:0|10;1|1:0|9;1|1 +1 649426 STR_174 TATATATATATATGTGTGTGTGTATATATATAGTATATATATA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=649426;END=649468;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=25;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:25:0:0:2:12.50|12.50:0|0:.:0.0:.:0.0:0|7;4|1:0|7 +1 651212 STR_175 AAAAAAAAAAAGAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=651212;END=651228;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=51;DSNP=0;DSTUTTER=5;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:51:0:5:3:25.50|25.50:0|0:.:0.0:.:0.0:-12|1;-4|1;-1|3;0|34;1|1;2|1:-1|3;0|31;1|1;2|1 +1 654953 STR_176 TTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=654953;END=654968;PERIOD=1;AN=0;REFAC=0;NSKIP=1;NFILT=0;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 656035 STR_177 TTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=656035;END=656050;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=38;DSNP=0;DSTUTTER=5;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:38:0:5:4:19.00|19.00:0|0:.:0.0:.:0.0:-16|1;-2|1;-1|3;0|20:-2|1;-1|3;0|16 +1 656643 STR_178 AAAAAGAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=656643;END=656658;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=3;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:35:0:3:1:17.50|17.50:0|0:.:0.0:.:0.0:-5|1;-1|1;0|26;1|1:-1|1;0|24;1|1 +1 660432 STR_179 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=660432;END=660460;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 661533 STR_180 GAGGCCGAGGCCGAGGCCGGGCC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=661533;END=661555;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=38;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:38:0:0:1:19.00|19.00:0|0:.:0.0:.:0.0:0|20:0|20 +1 678883 STR_181 ATTTGTATTTTATTTTATTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=678883;END=678903;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=48;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:48:0:0:2:24.00|24.00:0|0:.:0.0:.:0.0:-5|1;0|29:0|29 +1 680245 STR_182 CGTATATATATATATATAT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=680247;END=680263;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 680575 STR_183 AAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=680575;END=680589;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=47;DSNP=0;DSTUTTER=6;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:47:0:6:4:23.50|23.50:0|0:.:0.0:.:0.0:-10|1;-9|1;-4|1;-2|1;0|17;2|1:-2|1;0|11;2|1 +1 683124 STR_184 AACAACAACAACAATAACAAAAACAAAAACAACAACAACAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=683124;END=683164;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=120;DSNP=0;DSTUTTER=0;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:120:0:0:4:60.00|60.00:0|0:.:0.0:.:0.0:0|64:0|58 +1 685369 STR_185 AAAAAAAAAAAGAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=685369;END=685388;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 686143 STR_186 TTTATTTTATTTTATTAAATTTATTTTTTTTATTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=686143;END=686178;PERIOD=5;AN=0;REFAC=0;NSKIP=1;NFILT=0;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 687007 STR_187 TTTCTTTCTTTCTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=687007;END=687021;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=38;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:38:0:0:0:19.00|19.00:0|0:.:0.0:.:0.0:0|26:0|25 +1 687170 STR_188 TTTTTTTTTTTTTTTTTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=687170;END=687186;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 689406 STR_189 AAAAAGAAAAGAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=689406;END=689425;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=15;DSNP=0;DSTUTTER=1;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:15:0:1:0:7.50|7.50:0|0:.:0.0:.:0.0:-1|1:-1|1 +1 691543 STR_190 TTAAAAAAAAAAAAA TAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=691545;END=691557;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=30;DSNP=0;DSTUTTER=3;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:30:0:3:2:11.69|18.31:0|0:26.21:-0.68:23:-0.16:-2|1;-1|1;0|18:-2|1;-1|2;0|12 +1 691684 STR_191 TTTTATTTTATTTTATTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=691684;END=691702;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=45;DSNP=0;DSTUTTER=0;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:45:0:0:4:22.50|22.50:0|0:.:0.0:.:0.0:-17|1;0|30;34|1:0|31 +1 691964 STR_192 CTCATTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=691968;END=691978;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 692795 STR_193 AAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=692795;END=692807;PERIOD=1;AN=0;REFAC=0;NSKIP=1;NFILT=0;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 694827 STR_194 ACACACACAAACACACACACACACACACACACACACACACACACACACACAC ACACACACAAACACACACACACACACACACACACACACACACACACACACCC . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=694827;END=694878;PERIOD=2;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=47;DSNP=0;DSTUTTER=2;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:47:0:2:4:23.95|23.05:0|0:17.53:-0.0:45:0.0:-31|1;-10|2;0|13:0|12 +1 696317 STR_195 TTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=696317;END=696331;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 698025 STR_196 AAGGAAGGAAAGAAAAAAGGAAGGAAGGAGGGAAGGAGGGAAAAAGGGAAGGAGGGAAGGAAAGGAAGGAAGGGAAAGAAGGAAAGGAAGGAAGG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=698025;END=698119;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=50;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:50:0:0:2:25.00|25.00:0|0:.:0.0:.:0.0:0|7:0|6 +1 698132 STR_197 GAGGGAAGGAGGAAGGGAGGGAAGGAGGGAGGGAGGGAGAGAGGGAGGGAGGG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=698132;END=698184;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=42;DSNP=0;DSTUTTER=1;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:42:0:1:5:21.00|21.00:0|0:.:0.0:.:0.0:-4|1;0|11;1|1:-4|1;0|10 +1 698192 STR_198 AGAAAAGGGAAGAGAAGGGAAAGGAGGAAGAAAAGGAAAGGAAAGGAA ATAAAAGGGAAGAGAAGGTAAAGTAGGAATAAAAGGAAAGGAAAGGAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=698195;END=698239;PERIOD=5;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=51;DSNP=0;DSTUTTER=0;DFLANKINDEL=6 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:51:0:0:6:43.00|8.00:0|0:4.14:-8.55:39:0.0:0|17;34|1:0|16 +1 699655 STR_199 AAAAAAAAAGAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=699655;END=699669;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=54;DSNP=0;DSTUTTER=1;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:54:0:1:3:27.00|27.00:0|0:.:0.0:.:0.0:-3|1;0|41;1|1:0|38;1|1 +1 699970 STR_200 AAAACAAAACAAAACAAAACAAAAT AAAACAAAACAAAACAAAACAAAAC . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=699970;END=699993;PERIOD=5;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=57;DSNP=0;DSTUTTER=1;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:57:0:1:3:46.97|10.03:0|0:15.66:-6.92:51:-0.38:-28|1;0|42:-5|1;0|41 +1 700514 STR_201 AAAAAAAAAAAAAAAAAAT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=700514;END=700531;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 701124 STR_202 AAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=701124;END=701136;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=32;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:32:0:1:1:16.00|16.00:0|0:.:0.0:.:0.0:0|18:0|15 +1 702959 STR_203 TTTATTTATTTACTTATTTATTT TTTATTTATTTATTTATTTATTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=702959;END=702981;PERIOD=4;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=71;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:71:0:0:1:58.97|12.03:0|0:10.53:-9.76:59:-0.17:0|47:0|47 +1 704598 STR_204 AAAAACAAAAACAAAAACA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=704598;END=704616;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:31:0:0:1:15.50|15.50:0|0:.:0.0:.:0.0:0|21:0|21 +1 705486 STR_205 AAAACAAAACAAAACAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=705486;END=705504;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=48;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:48:0:0:2:24.00|24.00:0|0:.:0.0:.:0.0:-9|1;-2|1;0|26:0|26 +1 705688 STR_206 TTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=705688;END=705701;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 706734 STR_207 GTTTTGTTTTGTTTTGTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=706734;END=706753;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=50;DSNP=0;DSTUTTER=0;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:50:0:0:5:23.02|26.98:0|0:.:0.0:.:0.0:0|34:0|34 +1 710589 STR_208 AAAAAAAAAAAAAAAGAAAAAA AAAAAAAAAAAAAAGAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=710589;END=710610;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=4;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:0.97:0.49:31:0:4:3:22.15|8.85:0|0:1.57:-2.18:24:0.0:-13|1;-1|4;0|13;2|1:-1|4;0|10;2|1 +1 710813 STR_209 CACAGCACACACACAC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=710813;END=710828;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=28;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:28:0:0:1:14.00|14.00:0|0:.:0.0:.:0.0:0|18:0|18 +1 711217 STR_210 TGTCAAAAAAAAAAAAAAAAAAAACAGAAAAAGAAAAAGAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=711221;END=711261;PERIOD=1;AN=0;REFAC=0;NSKIP=1;NFILT=0;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 711985 STR_211 AAAACAAAACAAAACAAAACAAAACAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=711985;END=712013;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=56;DSNP=0;DSTUTTER=0;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:56:0:0:5:28.00|28.00:0|0:.:0.0:.:0.0:-20|1;0|25;3|1:0|24 +1 712918 STR_212 TTTGTTTGTTTGTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=712918;END=712932;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:31:0:0:3:15.50|15.50:0|0:.:0.0:.:0.0:-6|1;0|22;24|1:0|23 +1 715641 STR_213 TTTTTTTTCTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=715641;END=715655;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=34;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:34:0:0:2:17.00|17.00:0|0:.:0.0:.:0.0:-10|1;0|24:0|23 +1 718787 STR_214 TTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=718787;END=718800;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=28;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:28:0:1:1:14.00|14.00:0|0:.:0.0:.:0.0:-12|1;0|20:0|17 +1 719459 STR_215 TACTTTATATATAGTATTTATATATATA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=719464;END=719486;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 721746 STR_216 ATTTTTTATTATTTATTTATTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=721746;END=721767;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=39;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:39:0:0:0:19.50|19.50:0|0:.:0.0:.:0.0:0|24:0|23 +1 722365 STR_217 ATTTATTTATTTATTTATTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=722365;END=722384;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=38;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:38:0:0:1:19.00|19.00:0|0:.:0.0:.:0.0:0|27:0|26 +1 723749 STR_218 AGAGAGAGAGAGGGAGAGAGGGAGAGAGAAAGGAAGAGACGATGAGAGACAGAGAGAAGGAGAGAGA AGAGAGAGAGAGGGAGAGAGGGAGAGAGAAAGGAAGAGACGATGAGAGACAGAGAAGGAGAGAGA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-2;START=723749;END=723815;PERIOD=2;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=49;DSNP=0;DSTUTTER=0;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:-2|-2:1.0:1.0:49:0:0:4:24.50|24.50:0|0:7.47:0.0:.:0.0:-40|1;-25|1;-17|1;-2|15:-2|13 +1 730990 STR_220 TTTTGTTTTGTTTTGTTTTGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=730990;END=731010;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=38;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:38:0:0:0:19.00|19.00:0|0:.:0.0:.:0.0:0|21:0|21 +1 734461 STR_221 GGAAAAAAAAAAAAAA GAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=734463;END=734476;PERIOD=1;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=21;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:0|0:1.0:1.0:21:0:2:2:10.50|10.50:0|0:4.65:0.0:.:0.0:-1|1;0|15:-1|2;0|11 +1 734581 STR_222 AAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=734581;END=734591;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=30;DSNP=0;DSTUTTER=2;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:30:0:2:3:15.00|15.00:0|0:.:0.0:.:0.0:-8|1;-1|1;0|19;1|1:-1|1;0|19 +1 738815 STR_223 AAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=738815;END=738826;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=21;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:21:0:2:2:10.50|10.50:0|0:.:0.0:.:0.0:-3|1;-1|1;0|13;4|1:-3|1;-1|1;0|9 +1 739131 STR_224 AAAAAAAAAAATAGC AAAAAAAAAAAAAGA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=739131;END=739141;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=20;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:0.94:0.47:20:0:0:2:17.80|2.20:0|0:1.21:-3.84:18:0.0:0|20:0|16 +1 747692 STR_225 AAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=747692;END=747704;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 751489 STR_226 AAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=751489;END=751501;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 759601 STR_227 GTGTGTGTTTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=759601;END=759617;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=21;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:21:0:0:0:10.50|10.50:0|0:.:0.0:.:0.0:0|20:0|18 +1 762968 STR_228 GGGCCGGGCCGGGCCGGGGCGGG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=762968;END=762990;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=43;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:43:0:0:2:21.50|21.50:0|0:.:0.0:.:0.0:-12|1;0|29:0|28 +1 763770 STR_229 TTTTTTTTTTT TTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1;START=763770;END=763780;PERIOD=1;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=32;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:1|1:1.0:1.0:32:0:1:2:16.00|16.00:0|0:5.79:0.0:.:0.0:0|2;1|27:0|1;1|26 +1 765085 STR_230 TTTGTTTGTTTGTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=765085;END=765099;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=43;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:43:0:0:3:21.50|21.50:0|0:.:0.0:.:0.0:0|32:0|32 +1 768117 STR_231 GTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTT GTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTT,GTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=5,10;START=768117;END=768161;PERIOD=5;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=45;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:5|10:1.0:0.5:45:0:0:0:21.56|23.44:0|0:7.49:-0.08:24:-1.08:-15|2;-12|2;5|9;10|10:5|9;10|10 +1 770292 STR_232 CATCCACCTATCCATCCACCCATCTATCCAACCCTCCCTCCCTCCATCCACCCATCCACCCACCTACCCACTCACCC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=770292;END=770368;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=55;DSNP=0;DSTUTTER=0;DFLANKINDEL=6 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:55:0:0:6:27.50|27.50:0|0:.:0.0:.:0.0:-36|1;-10|1;-6|1;0|18:0|16 +1 774801 STR_233 ACACACACACCTAGACACACACAC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=774801;END=774824;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=33;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:33:0:0:2:16.50|16.50:0|0:.:0.0:.:0.0:0|25:0|22 +1 774882 STR_235 TGGACACACACACCTAGACACACACAC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=774885;END=774908;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 774955 STR_236 ACACACACACCTAGACACACACAC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=774955;END=774978;PERIOD=2;AN=0;REFAC=0;NSKIP=1;NFILT=0;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 775790 STR_237 AAAAAAAAAAAAAAA AAAAAAAAAAAAA,AAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-2,-1;START=775790;END=775804;PERIOD=1;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=26;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:-2|-1:1.0:0.5:26:0:2:2:8.93|17.07:0|0:3.61:-1.03:23:-0.18:-3|1;-2|6;-1|14:-3|1;-2|6;-1|12 +1 779907 STR_238 TTTTGTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=779907;END=779922;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=2;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:31:0:2:3:15.50|15.50:0|0:.:0.0:.:0.0:-14|1;-1|1;0|22:-1|1;0|19 +1 786028 STR_239 TTATTATTATTATTAT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=786028;END=786043;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=27;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:27:0:0:1:13.50|13.50:0|0:.:0.0:.:0.0:0|18:0|17 +1 790840 STR_240 GTGTGTGTAGTGTGTGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=790840;END=790856;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=47;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:47:0:0:3:23.50|23.50:0|0:.:0.0:.:0.0:0|35:0|33 +1 793329 STR_241 TTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=793329;END=793339;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=23;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:23:0:1:1:11.50|11.50:0|0:.:0.0:.:0.0:0|20;2|1:0|18 +1 795559 STR_242 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=795559;END=795591;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 795982 STR_243 CCCTCCCTCCATCCCTCCC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=795982;END=796000;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=43;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:43:0:0:2:21.50|21.50:0|0:.:0.0:.:0.0:0|31:0|26 +1 803753 STR_245 AGAGAGAGAAAGAGAG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=803753;END=803768;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=38;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:38:0:0:2:19.00|19.00:0|0:.:0.0:.:0.0:0|29:0|26 +1 804594 STR_246 AAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=804594;END=804605;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=33;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:33:0:2:2:16.50|16.50:0|0:.:0.0:.:0.0:-1|3;0|23:-1|1;0|20 +1 804638 STR_247 GCAAACAACAAACAAACAAAAAACAGAGGA GAAAAAAACAAACAAACAAAAAACCGAGGG . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=804639;END=804662;PERIOD=4;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=26;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:26:0:0:1:23.60|2.40:0|0:4.45:-4.71:25:-1.03:0|21:0|20 +1 804843 STR_248 TATCTATCATCTATCTATCTACCTGCCTATCATCTATCTATCTATTTACTATCTATCT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=804843;END=804900;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:35:0:0:2:17.50|17.50:0|0:.:0.0:.:0.0:-29|1;-10|1;0|15:0|15 +1 804979 STR_249 AAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=804979;END=804989;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=28;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:28:0:1:1:14.00|14.00:0|0:.:0.0:.:0.0:0|22;1|1:0|22;1|1 +1 807303 STR_250 TTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=807303;END=807318;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 818315 STR_251 TTTTCTTTTCTTTTTTTCTTTCTCTCTTTTCTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=818315;END=818357;PERIOD=5;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 821623 STR_252 TGTGCTGTGCTGTGCTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=821623;END=821639;PERIOD=5;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 823701 STR_253 GAAGAAAGGAAGGCAGGAAGGCAGGGTGAAAGGAAGGAAGGAAGGAAGAAGGAAGGA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=823701;END=823757;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=46;DSNP=0;DSTUTTER=2;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:46:0:2:3:23.00|23.00:0|0:.:0.0:.:0.0:-4|1;0|17;10|1:-4|1;0|17 +1 823973 STR_254 GGAAGCAGGGAGGGAGAGAAAGAGGAAGGGAGAGGAAGGAGGGAGGGAGGGAAAGGAGACAGGGAGGGAGAGAGGGAGGGAGGGAGGAAA GACAGAAGGGAGGGAGAGAAAGAGGAAGGGAGAGGAAGGAGGGAGGGAGGGAAAGGAGAAAGGGAGGGAGTGAGGGAAGGAGGGAGACAG . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=823979;END=824059;PERIOD=4;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=50;DSNP=0;DSTUTTER=1;DFLANKINDEL=7 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:0.94:0.47:50:0:1:7:47.10|2.90:0|0:1.22:-12.17:47:0.0:0|14:0|13 +1 825825 STR_255 TCAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=825827;END=825837;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 829511 STR_256 TGTGTGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=829511;END=829524;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=45;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:45:0:0:1:22.50|22.50:0|0:.:0.0:.:0.0:0|34:0|30 +1 830242 STR_257 TTTTTTTATTTTTATTTTTTCATTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=830242;END=830271;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=56;DSNP=0;DSTUTTER=0;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:56:0:0:4:28.00|28.00:0|0:.:0.0:.:0.0:-31|1;-24|1;0|25:0|22 +1 834405 STR_258 TTTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=834405;END=834425;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 838154 STR_259 AAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=838154;END=838168;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 842617 STR_260 AAAAAAAAAAAAAA AAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=842617;END=842630;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=43;DSNP=0;DSTUTTER=0;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:43:0:0:5:25.34|17.66:0|0:6.24:-0.88:36:-0.51:-41|1;-17|1;-2|1;-1|11;0|19:-1|11;0|17 +1 842919 STR_261 AAAAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=842919;END=842942;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=28;DSNP=0;DSTUTTER=1;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:28:0:1:3:14.00|14.00:0|0:.:0.0:.:0.0:-17|1;-1|1;0|7:-1|1;0|2 +1 850329 STR_262 AAAAAAAAAAAAAAAAGAAGAAAGAAAAAGAAAAAAA AAAAAAAAAAAAAAAGAAGAAAGAAAAAGAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=850329;END=850365;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=27;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|0:-1|0:1.0:0.5:27:0:1:1:11.08|15.92:0|0:3.74:-0.42:21:-0.19:-2|1;-1|1;0|2:-2|1;0|1 +1 856020 STR_263 TGTGCTGTGTGTGTGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=856020;END=856035;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=47;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:47:0:0:1:23.50|23.50:0|0:.:0.0:.:0.0:0|34:0|34 +1 859291 STR_264 GGCGGCGGCGTCGGCGGCGG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=859291;END=859310;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=37;DSNP=0;DSTUTTER=0;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:37:0:0:4:18.50|18.50:0|0:.:0.0:.:0.0:0|20;20|1:0|18 +1 866512 STR_265 CCCTCCCTCCCTCCCA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=866512;END=866526;PERIOD=4;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 872777 STR_266 CCCCCCCCCCC CCCCCCCCC . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-2;START=872777;END=872787;PERIOD=1;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=43;DSNP=0;DSTUTTER=2;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:-2|-2:1.0:1.0:43:0:2:3:21.50|21.50:0|0:7.51:0.0:.:0.0:-12|1;-8|1;-2|34;0|2:-3|1;-2|25 +1 875669 STR_267 CGCCGCCGCCCCCCCCCCCCGCCCCGCC CGCCGCCGCCCCCCCCCCGCCCCGCC . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-2;START=875669;END=875696;PERIOD=5;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=29;DSNP=0;DSTUTTER=3;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-2:1.0:0.5:29:0:3:4:16.13|12.87:0|0:61.12:-0.17:23:-0.16:-3|1;-2|7;0|7:-5|1;-2|7;0|7 +1 878907 STR_268 TTTTTTTTTTTTTTTTTTTTTTGCCA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=878907;END=878928;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 879055 STR_269 CCCTCCCTCCCTCCC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=879055;END=879069;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=26;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:26:0:0:0:13.00|13.00:0|0:.:0.0:.:0.0:0|22:0|22 +1 879887 STR_270 CCAGCCCAGCCCAGCCCAGC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=879887;END=879906;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=41;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:41:0:0:0:20.50|20.50:0|0:.:0.0:.:0.0:0|33:0|33 +1 886040 STR_271 CACACACACACAG CACACACACA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-3;START=886040;END=886051;PERIOD=2;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=52;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-3:1.0:0.5:52:0:0:1:27.00|25.00:0|0:163.68:-0.05:52:-0.11:-3|19;0|22:-3|19;0|21 +1 891677 STR_272 CACCCTCACCCTCACCCTCA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=891677;END=891696;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=37;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:37:0:0:3:18.50|18.50:0|0:.:0.0:.:0.0:-20|1;-10|1;0|19:0|22 +1 893442 STR_273 TTTTTTTTTTTTTTTTTTTTC TTTTTTTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=893442;END=893461;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=30;DSNP=0;DSTUTTER=3;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:30:0:3:3:17.57|12.43:0|0:9.71:-0.3:20:-0.44:-1|1;0|10;4|1:-1|1;0|6 +1 894390 STR_274 TCGGACTCGGATTCGGACTCGGA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=894390;END=894412;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=50;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:50:0:0:1:25.00|25.00:0|0:.:0.0:.:0.0:-3|1;0|28:0|29 +1 895658 STR_275 GGAGGAGGAGGAGGAGGAGG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=895658;END=895677;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=26;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:26:0:1:2:12.96|13.04:0|0:.:0.0:.:0.0:-5|1;-3|1;0|19:-3|1;0|19 +1 896150 STR_276 CGCCGCCGCCTCCACCGCCGCAGCCGCCG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=896150;END=896178;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=15;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:15:0:0:0:7.50|7.50:0|0:.:0.0:.:0.0:0|8:0|8 +1 897453 STR_277 GCCCCCCACCCCACCCCACCCCA GTCCCCCACCCCACCCCACCCCA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=897456;END=897475;PERIOD=5;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=42;DSNP=0;DSTUTTER=4;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:42:0:4:5:23.01|18.99:0|0:43.98:-0.22:34:-0.16:0|24;1|4:0|23 +1 900684 STR_278 TTTATTTAGTTGTTTATTTATTTAGTTATTTATCTTATTTATTGAGG TTTATTTAGTTGTTTATTTATTTAGTTATTTATCTTATTGAGA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-4;START=900684;END=900726;PERIOD=4;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=53;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-4:1.0:0.5:53:0:0:1:27.52|25.48:0|0:90.38:-0.06:38:-0.48:-20|1;-4|12;0|11:-4|12;0|11 +1 904695 STR_279 GTGTGTCTGTGTGTGCGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=904695;END=904719;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=56;DSNP=0;DSTUTTER=1;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:56:0:1:3:28.00|28.00:0|0:.:0.0:.:0.0:0|38:0|33 +1 904801 STR_280 GTGTGTGTTGGTGTATTTGTGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=904801;END=904829;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=44;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:44:0:0:3:22.00|22.00:0|0:.:0.0:.:0.0:0|28;12|1:0|25 +1 906221 STR_281 GTGTGTGTATGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=906221;END=906237;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=44;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:44:0:0:3:22.25|21.75:0|0:.:0.0:.:0.0:-3|1;0|32:0|31 +1 911558 STR_282 GCTGGGGCTGGGGCTGTGGCTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=911558;END=911579;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=36;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:36:0:0:1:18.00|18.00:0|0:.:0.0:.:0.0:-23|1;0|28:0|29 +1 918840 STR_283 TTTGCTTGTTTGTTTGTTTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=918840;END=918859;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:35:0:0:0:17.50|17.50:0|0:.:0.0:.:0.0:0|29:0|28 +1 920256 STR_284 CTATCTATCTATCTATC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=920256;END=920272;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=38;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:38:0:0:2:19.00|19.00:0|0:.:0.0:.:0.0:-13|1;0|25:0|24 +1 922667 STR_285 TTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=5;START=922667;END=922682;PERIOD=1;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=17;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:5|5:1.0:1.0:17:0:1:1:8.50|8.50:0|0:2.41:0.0:.:0.0:-13|4;-11|1;-4|2;0|1;5|1;6|1:5|1 +1 923964 STR_286 TCAAAAAAAAAAAAAAAGAAAGAAAAGAAAAGAAAAGA TAAAAAAAAAAAAAGAAGAAAGAAAAGAAAAGAAAAGA,TCAAAAAAAAAAAAAGAAGAAAGAAAAGAAAAGAAAAGA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0,1;START=923967;END=924001;PERIOD=5;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=0;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:0|1:1.0:0.5:35:0:0:5:8.14|26.86:0|0:5.96:-4.18:23:-0.33:-4|1;0|2;1|6;17|1:0|2;1|5 +1 925364 STR_287 TGTTTTGTTTTGCTTTGTTTTTGTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=925364;END=925390;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:35:0:0:0:17.50|17.50:0|0:.:0.0:.:0.0:0|25:0|25 +1 925679 STR_288 TTTTTTTTTTTTT TTTTTCTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=925679;END=925691;PERIOD=1;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=50;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:0|0:1.0:1.0:50:0:0:0:25.00|25.00:0|0:12.94:0.0:.:0.0:0|37:0|34 +1 926890 STR_289 TTTCATTTTCTTTTCTTTTCTTTTTTTTTCTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=926890;END=926923;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=37;DSNP=0;DSTUTTER=1;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:37:0:1:3:18.50|18.50:0|0:.:0.0:.:0.0:-6|1;-4|1;0|14:0|14 +1 927531 STR_290 GTTTTTTTGTTTGTTTGTTTGTTTTTTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=927531;END=927558;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=39;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:39:0:1:1:19.50|19.50:0|0:.:0.0:.:0.0:-29|1;-4|1;0|21:-4|1;0|21 +1 929702 STR_291 AAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=929702;END=929714;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 930889 STR_292 TTTTTTTTTTTTT TTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-5;START=930889;END=930901;PERIOD=1;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=36;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:-5|-5:1.0:1.0:36:0:0:1:18.00|18.00:0|0:8.41:0.0:.:0.0:-5|34:-5|32 +1 934124 STR_293 GCGGAGGGGAGGGCGCGGAGCGGAGGGCGCGGAGCGGAG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=934124;END=934162;PERIOD=5;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 937563 STR_294 TTTTTATTTATTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=937563;END=937582;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=37;DSNP=0;DSTUTTER=1;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:37:0:1:3:13.96|23.04:0|0:.:0.0:.:0.0:-7|1;-1|1;0|16:-1|1;0|12 +1 937795 STR_295 CTTTTTTTTTTTTTTTTTTTT CATTTTTTTTTTTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=5;START=937796;END=937815;PERIOD=1;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=40;DSNP=0;DSTUTTER=5;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:5|5:1.0:1.0:40:0:5:5:20.00|20.00:0|0:8.11:0.0:.:0.0:-25|1;-23|1;3|1;4|3;5|9;6|1:4|2;5|8;7|1 +1 938021 STR_296 TTTTTTTTTTTCTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=938021;END=938038;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=3;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:31:0:3:0:15.50|15.50:0|0:.:0.0:.:0.0:0|17;1|3:0|16;1|3 +1 942969 STR_297 AAAAAGAAAAAGAAAAGAAAAAAGAAAAAG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=942969;END=942998;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=47;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:47:0:0:0:23.50|23.50:0|0:.:0.0:.:0.0:0|22:0|22 +1 943127 STR_298 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=943127;END=943160;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 943884 STR_299 TTGTTTGTTTTGTTTGTTTGTTTCTTTCTTTCTTT TTGTTTGTTTTGTTTGTTTGTTTGTTTCTTTCTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=943884;END=943918;PERIOD=4;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=37;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:0|0:1.0:1.0:37:0:0:2:18.50|18.50:0|0:7.47:0.0:.:0.0:-19|1;0|13:0|12 +1 944374 STR_300 TTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=944374;END=944384;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=28;DSNP=0;DSTUTTER=4;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:28:0:4:4:14.00|14.00:0|0:.:0.0:.:0.0:-1|2;0|20;1|2:-1|2;0|19;1|1 +1 945059 STR_301 AAAAAAAAAAAAAAGAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=945059;END=945077;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=29;DSNP=0;DSTUTTER=4;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:29:0:4:3:14.50|14.50:0|0:.:0.0:.:0.0:-12|1;-3|2;0|11;1|2:-3|1;0|9;1|2 +1 945862 STR_302 TTATTTATTTATTTATTTGAATCTTATTTAAATATTTTATTTATTTGTTTATT TTATTTATTTATTTGAATCTTATTTAAATATTTTATTTATTTGTTTATT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-4;START=945862;END=945914;PERIOD=4;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:-4|-4:1.0:1.0:31:0:1:1:15.50|15.50:0|0:5.3:0.0:.:0.0:-39|1;-4|11:-4|11 +1 946128 STR_303 TTTTTTTTTTTTTTTTTT TTTTTTGTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=946128;END=946145;PERIOD=1;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=29;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:-1|-1:1.0:1.0:29:0:0:1:14.50|14.50:0|0:6.02:0.0:.:0.0:-10|1;-4|1;-1|15:-1|15 +1 947927 STR_304 TTTTTTTTTTATTTTTATTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=947927;END=947949;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=1;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:35:0:1:3:17.50|17.50:0|0:.:0.0:.:0.0:0|21;1|1:0|15;1|1 +1 951048 STR_305 GGGCAGGGCAGGGCAGGGC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=951048;END=951066;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=54;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:54:0:0:2:27.00|27.00:0|0:.:0.0:.:0.0:0|37:0|37 +1 951437 STR_306 GTGCTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=951441;END=951456;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 952058 STR_307 TTTTGTATTTGTTTTGTTTTGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=952058;END=952079;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=39;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:39:0:0:1:19.50|19.50:0|0:.:0.0:.:0.0:0|31:0|30 +1 952495 STR_308 TTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=952495;END=952506;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=36;DSNP=0;DSTUTTER=1;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:36:0:1:5:18.00|18.00:0|0:.:0.0:.:0.0:-1|1;0|32:-1|1;0|22 +1 954850 STR_309 GGCGGGGCCTGGGGGGGCGGGGCCGGGAGGGGCGGGGC GGCGGGGCCTGGGGGGCGGGGCCGGGAGGGGCGGGGC . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=954850;END=954887;PERIOD=5;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=23;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:-1|-1:1.0:1.0:23:0:0:1:11.50|11.50:0|0:5.12:0.0:.:0.0:-15|1;-1|12:-1|12 +1 955432 STR_311 CTGGCCCCGCCCCCCCCCGCCCGCCCGCCCGC CGGGCCCCGCCCCCCCCGCCCGCCCGCCCGC,CTGGCCCCGCCCCCCCCGCCCGCCCGCCCGC . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1,-1;START=955437;END=955463;PERIOD=4;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=23;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:-1|-1:1.0:0.5:23:0:0:2:4.59|18.41:0|0:2.47:-2.59:20:-0.27:-1|15:-1|15 +1 955485 STR_312 CGTCCCGTCCTGTCCAGTCCCGTCCC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=955485;END=955510;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=27;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:27:0:0:1:13.50|13.50:0|0:.:0.0:.:0.0:0|18;23|1:0|18 +1 955942 STR_313 CGCCGCCGCCGTCCTCCGCCCGCCGCCGCC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=955942;END=955971;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=39;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:39:0:0:1:19.50|19.50:0|0:.:0.0:.:0.0:-13|1;0|16:0|16 +1 958089 STR_314 CCTCCTGCCTCCTCCCCTCCTCC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=958089;END=958111;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=48;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:48:0:0:1:24.00|24.00:0|0:.:0.0:.:0.0:0|32:0|30 +1 962615 STR_315 TGTGTTTGTGTGTGTGTGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=962615;END=962633;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=51;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:51:0:0:2:25.50|25.50:0|0:.:0.0:.:0.0:0|42:0|40 +1 963701 STR_316 CCCCCCCCCCCCCCCCGCCCT CACCCCCCCCCCCCGCCCC,CCCCCCCCCCCCCCGCCCC . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-2,-2;START=963701;END=963716;PERIOD=1;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=44;DSNP=0;DSTUTTER=6;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:-2|-2:1.0:0.5:44:0:6:3:34.92|9.08:0|0:2.78:-4.37:40:-1.48:-4|1;-3|2;-2|26;-1|1;0|3;1|2;3|1:-4|2;-3|2;-2|28;-1|1 +1 964971 STR_317 GTGTGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=964971;END=964983;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=53;DSNP=0;DSTUTTER=2;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:53:0:2:1:26.50|26.50:0|0:.:0.0:.:0.0:-20|1;-2|2;0|42:-2|2;0|41 +1 965008 STR_318 CATGTGTGTGTGTGTGTG CGTGTGTGTGTGTG,CGTGTGTGTGTGTGTGTGTG . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-4,2;START=965010;END=965025;PERIOD=2;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=40;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 2|1:2|-4:1.0:0.5:40:0:0:0:21.33|18.67:0|0:8.33:-0.07:30:-0.58:-9|1;-4|2;-3|1;0|4;2|19:2|18 +1 965052 STR_319 TGTGTGTGTGTGTGTG TGTGTGTGTG . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-6;START=965052;END=965067;PERIOD=2;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=26;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:-6|-6:1.0:1.0:26:0:0:0:13.00|13.00:0|0:5.99:0.0:.:0.0:-6|20:-6|18 +1 965205 STR_320 GTGTGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=965205;END=965217;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 965277 STR_321 GTGTGTGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=965277;END=965291;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 965320 STR_322 TGTGTGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=965320;END=965333;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 965362 STR_323 TGTGTGTGTGTGTGTG TGTGTGTGTGTGTGTGTG . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=2;START=965362;END=965377;PERIOD=2;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=18;DSNP=0;DSTUTTER=2;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|2:1.0:0.5:18:0:2:1:6.24|11.76:0|0:3.86:-0.84:12:0.0:-34|1;-32|1;-19|1;-4|1;-1|1;0|1;2|7:0|1;2|5 +1 965442 STR_324 TGTGTGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=965442;END=965455;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 965480 STR_325 CATGTGTGTGTGTGTGTG CGTGTGTGTGTGTGTG . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-2;START=965482;END=965497;PERIOD=2;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=41;DSNP=0;DSTUTTER=4;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-2:0.98:0.49:41:0:4:1:3.01|37.99:0|0:1.64:-8.55:39:0.0:-23|1;-16|1;-9|1;-7|1;-6|1;-4|2;-2|28;3|1:-4|2;-2|21 +1 965522 STR_326 CATGTGTGTGTGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=965524;END=965541;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 965641 STR_327 GTGTGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=965641;END=965653;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 965680 STR_328 CATGTGTGTGTGTGCAGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=965682;END=965693;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 965756 STR_329 CATGTGTGTGTGTGTGTGCAGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=965758;END=965773;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 965799 STR_330 GTGTGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=965799;END=965811;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 965840 STR_331 TGTGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=965840;END=965851;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 965985 STR_332 GTGTGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=965985;END=965997;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 966028 STR_333 TGTGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=966028;END=966039;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 966063 STR_334 GTGTGTGTGTGTGCAGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=966063;END=966075;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 966104 STR_335 TGTGTGTGTGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=966104;END=966121;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 966146 STR_336 CATGTGTGTGTGTGTGTGTGTG CATGTGTGTGTGTGTGTGTG,CGTGTGTGTGTGTGTGTGTGTG . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-2,0;START=966148;END=966167;PERIOD=2;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=3;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:-2|0:1.0:0.5:35:0:3:4:20.42|14.58:0|0:13.23:-0.54:22:-0.18:-8|1;-2|21;0|5;3|1:-2|11;0|5 +1 966229 STR_337 GTGTGTGTGTGTGCAGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=966229;END=966241;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 966306 STR_339 CGTGTGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=966307;END=966319;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 966348 STR_340 TGTGTGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=966348;END=966361;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 966431 STR_341 TGTGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=966431;END=966442;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 966468 STR_342 TGTGTGTGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=966468;END=966483;PERIOD=2;AN=0;REFAC=0;NSKIP=1;NFILT=0;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 966506 STR_343 TGTGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=966506;END=966517;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 966664 STR_344 TGTGTGTGTATGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=966664;END=966681;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=50;DSNP=0;DSTUTTER=0;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:50:0:0:5:25.00|25.00:0|0:.:0.0:.:0.0:-50|1;-10|2;0|35:0|33 +1 970550 STR_346 GGGGGGGGGGGGGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=970550;END=970562;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 976265 STR_347 GCGGGGCGGGGCCGGTGCCTGGGGCGGGGAGGGGCGGGGC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=976265;END=976304;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:31:0:0:3:15.50|15.50:0|0:.:0.0:.:0.0:-45|1;-35|1;0|15:0|14 +1 984148 STR_349 AAAAAAAAAAAAAAAAAAAAAAGCAG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=984148;END=984169;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 985444 STR_350 GGGGGGGGGGGGGGG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=985444;END=985458;PERIOD=1;AN=0;REFAC=0;NSKIP=1;NFILT=0;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 987895 STR_351 GTGTGTGTGTGTGTG GTGTGTGTGTGTGTGTG . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=2;START=987895;END=987909;PERIOD=2;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|2:1.0:0.5:35:0:0:0:17.57|17.43:0|0:10.68:0.0:28:-0.35:-2|1;0|13;2|13:0|10;2|13 +1 988367 STR_352 GTGTGTCTGTGTGTGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=988367;END=988382;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=32;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:32:0:0:1:16.00|16.00:0|0:.:0.0:.:0.0:0|27:0|27 +1 991341 STR_353 TCCCCACCCCCATCCCATCCCCACCCCCAGCCCCA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=991341;END=991375;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=51;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:51:0:0:2:25.50|25.50:0|0:.:0.0:.:0.0:-3|1;0|29:0|28 +1 991739 STR_354 GTGTGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=991739;END=991751;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=32;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:32:0:2:2:16.00|16.00:0|0:.:0.0:.:0.0:-2|1;0|25;2|1;5|1:-2|1;0|22;2|1 +1 991987 STR_355 GGGTGCGTGTGCGTGTGGGTGCGTGTGC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=991989;END=992014;PERIOD=6;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 992119 STR_357 GTGTGTGTGTGTGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=992119;END=992139;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=43;DSNP=0;DSTUTTER=2;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:43:0:2:0:21.50|21.50:0|0:.:0.0:.:0.0:-2|2;0|23:-2|2;0|22 +1 993134 STR_358 AAAAAAAAAAAGAAAAAAGAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=993134;END=993156;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:31:0:2:2:15.50|15.50:0|0:.:0.0:.:0.0:-1|2;0|15:-1|2;0|12 +1 999026 STR_360 TGTGTGTGCGTGTGCATGTGTGTGTGTGTGTGTGTGCGTGTG TGTGTGTGCGTGTGCATGTGTGTGTGTGTGTGTGCGTGTG . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-2;START=999026;END=999067;PERIOD=2;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=40;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-2:1.0:0.5:40:0:0:0:17.61|22.39:0|0:11.93:-0.33:31:0.0:-2|11;0|11:-2|11;0|11 +1 1004248 STR_361 CGCCCCCGCCCCCGCCCCC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1004248;END=1004266;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=37;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:37:0:0:1:18.50|18.50:0|0:.:0.0:.:0.0:0|31:0|31 +1 1006649 STR_362 TGTTTTTTTTTGTTTTGTTTTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1006649;END=1006670;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=33;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:33:0:0:2:16.50|16.50:0|0:.:0.0:.:0.0:0|21:0|20 +1 1009795 STR_363 GGAGGGCAGGGAGGGAGGG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1009795;END=1009813;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=53;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:53:0:0:1:27.03|25.97:0|0:.:0.0:.:0.0:-18|1;0|37:0|38 +1 1010337 STR_364 CACACACACACACA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1010337;END=1010350;PERIOD=2;AN=0;REFAC=0;NSKIP=1;NFILT=0;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1015437 STR_365 CGCCCCACCCCGCCCCGCCCCG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1015437;END=1015458;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=42;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:42:0:0:1:21.00|21.00:0|0:.:0.0:.:0.0:-6|1;0|31:0|31 +1 1018824 STR_366 GAGAGAGAGGCAGAGAGAGA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1018824;END=1018843;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=44;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:44:0:0:2:22.00|22.00:0|0:.:0.0:.:0.0:0|32:0|29 +1 1028418 STR_367 AAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1028418;END=1028428;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1029472 STR_368 TTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1029472;END=1029482;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=60;DSNP=0;DSTUTTER=2;DFLANKINDEL=6 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:60:0:2:6:30.00|30.00:0|0:.:0.0:.:0.0:-1|1;0|49;1|2:-1|1;0|42;1|1 +1 1029792 STR_369 TTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1029792;END=1029802;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=36;DSNP=0;DSTUTTER=2;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:36:0:2:5:18.00|18.00:0|0:.:0.0:.:0.0:-1|1;0|32;1|1:0|30;1|1 +1 1032965 STR_370 TTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1032965;END=1032983;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1033457 STR_371 TTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1033457;END=1033468;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=38;DSNP=0;DSTUTTER=3;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:38:0:3:1:19.00|19.00:0|0:.:0.0:.:0.0:-1|2;0|27;1|1:-1|2;0|22;1|1 +1 1034622 STR_372 AGAGAGAGAGAGAG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1034622;END=1034635;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=48;DSNP=0;DSTUTTER=0;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:48:0:0:4:24.00|24.00:0|0:.:0.0:.:0.0:0|43:0|40 +1 1035085 STR_373 GAGAGAGAGAGAG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1035085;END=1035097;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:31:0:0:1:15.50|15.50:0|0:.:0.0:.:0.0:0|24:0|23 +1 1037755 STR_375 CACCCTTTTTTTTTTTT CCCCCTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1037760;END=1037771;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=22;DSNP=0;DSTUTTER=3;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:22:0:3:3:16.50|5.50:0|0:3.09:-1.9:17:-0.69:-10|1;-2|1;-1|1;0|14:-1|1;0|10;1|1;3|1 +1 1037995 STR_376 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1037995;END=1038029;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1038178 STR_377 AAATAAATAAATAAAATAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1038178;END=1038197;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=42;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:42:0:0:2:21.00|21.00:0|0:.:0.0:.:0.0:0|24:0|24 +1 1040199 STR_378 AAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1040199;END=1040209;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=33;DSNP=0;DSTUTTER=1;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:33:0:1:3:16.50|16.50:0|0:.:0.0:.:0.0:0|24:0|17 +1 1041265 STR_379 AAATAAATAAATAAATAGATAGATAAATAAATAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1041265;END=1041299;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:35:0:1:2:17.50|17.50:0|0:.:0.0:.:0.0:-35|1;-13|1;0|15:-12|1;0|15 +1 1044792 STR_380 TTTCCTTTCCTTTTTCCTTTCCTCTTTTCTCCTTTCTTTCCTTTCCT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1044792;END=1044838;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=49;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:49:0:0:1:24.50|24.50:0|0:.:0.0:.:0.0:0|24:0|24 +1 1044850 STR_381 TTTCTTTCTTTCTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1044850;END=1044864;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=42;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:42:0:0:1:21.00|21.00:0|0:.:0.0:.:0.0:0|26:0|26 +1 1046746 STR_382 AAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1046746;END=1046766;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1046913 STR_383 CAACAACAACAACAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1046913;END=1046927;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=36;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:36:0:0:0:18.00|18.00:0|0:.:0.0:.:0.0:0|25:0|25 +1 1048576 STR_384 AAAAAAAAAAAAAAAA AAAAAAAAAAAAAAA,AAAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1,1;START=1048576;END=1048591;PERIOD=1;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=34;DSNP=0;DSTUTTER=4;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:-1|1:1.0:0.5:34:0:4:1:23.31|10.69:0|0:6.14:-1.72:27:-0.17:-3|1;-2|2;-1|13;0|2;1|5:-3|1;-2|1;-1|11;0|1;1|4 +1 1049294 STR_385 TTTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1049294;END=1049314;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=22;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:22:0:1:1:11.00|11.00:0|0:.:0.0:.:0.0:-22|1;-2|1;0|2:-2|1;0|2 +1 1051841 STR_386 AGGCGGAGGCGGAGGCGGAG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1051841;END=1051860;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=42;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:42:0:0:2:21.00|21.00:0|0:.:0.0:.:0.0:-3|1;0|30:0|30 +1 1055252 STR_387 AAAAATAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1055252;END=1055266;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=44;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:44:0:1:1:22.00|22.00:0|0:.:0.0:.:0.0:0|37;1|1:0|33;1|1 +1 1055399 STR_388 ATCTCCAAAAAAAAAAAACCCAAAAAACGAAAAAAAAAAAAAAA ACCTCAAAAAAAAAAAAACCCAAAAAACGAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1055405;END=1055442;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=21;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:21:0:0:3:13.91|7.09:0|0:3.32:-1.18:11:0.0:-35|2;0|7:0|6 +1 1061692 STR_389 TTTTTTTTTTTTTTTTGA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1061692;END=1061707;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1065567 STR_390 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1065567;END=1065596;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1069464 STR_391 AAAAAAAAAAAAAAAAAAG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1069464;END=1069481;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1073154 STR_392 CCCTCCCCGCCTCCCTCCCCCTCTCCCTCCC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1073154;END=1073184;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=48;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:48:0:0:1:24.00|24.00:0|0:.:0.0:.:0.0:0|35:0|35 +1 1073950 STR_393 AAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1073950;END=1073969;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1077604 STR_395 TTTTTTTTTATTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1077604;END=1077619;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=54;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:54:0:0:3:27.00|27.00:0|0:.:0.0:.:0.0:0|35;2|1:0|33 +1 1085624 STR_396 CACACACAGACACACA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1085624;END=1085639;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=48;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:48:0:0:0:24.00|24.00:0|0:.:0.0:.:0.0:0|36:0|34 +1 1090170 STR_397 AAAAAAAAAAAAAAA AAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1090170;END=1090184;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=54;DSNP=0;DSTUTTER=4;DFLANKINDEL=8 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:54:0:4:8:21.70|32.30:0|0:9.75:-0.98:46:-0.45:-5|1;-2|4;-1|25;0|16:-2|4;-1|22;0|15 +1 1090264 STR_398 TTTTTCTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1090264;END=1090278;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=38;DSNP=0;DSTUTTER=2;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:38:0:2:1:19.00|19.00:0|0:.:0.0:.:0.0:0|27;1|2:0|26;1|1 +1 1092839 STR_400 CCCCGCCCCGCCCGCAGCCCCGCCCCAGCCC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1092839;END=1092869;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:31:0:0:3:15.50|15.50:0|0:.:0.0:.:0.0:0|19:0|18 +1 1101898 STR_401 CACCCCCACCCACACCCCCACCCCCACCCCC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1101898;END=1101928;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:35:0:0:3:17.50|17.50:0|0:.:0.0:.:0.0:0|23;1|1:0|21 +1 1105635 STR_402 CTCCTCCTCCTCCTCCTC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1105635;END=1105652;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=48;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:48:0:0:0:24.00|24.00:0|0:.:0.0:.:0.0:0|32:0|32 +1 1108387 STR_404 AAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1108387;END=1108398;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1110504 STR_405 AAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1110504;END=1110514;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=36;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:36:0:1:2:18.00|18.00:0|0:.:0.0:.:0.0:0|24;1|1:0|18;1|1 +1 1112367 STR_406 TGTGTGCGTCTGTGTGTCTGTGTGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1112367;END=1112391;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=46;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:46:0:0:3:23.00|23.00:0|0:.:0.0:.:0.0:-25|1;0|33:0|30 +1 1112425 STR_407 TGTGTGTGTGGGTGTCTGTGTGTGTGTGTGGGTGTCTGTGTGTGTGTCTGTGTGTACGTGTGTGTGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1112425;END=1112491;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=53;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:53:0:2:2:26.50|26.50:0|0:.:0.0:.:0.0:-5|1;0|15:0|14 +1 1112633 STR_408 TGTGTGTGTCTGTGTGTAGCTGTGTGTCTGTGCGTGTGTGTGTGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1112633;END=1112677;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1112699 STR_409 TTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1112699;END=1112709;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=40;DSNP=0;DSTUTTER=2;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:40:0:2:5:20.00|20.00:0|0:.:0.0:.:0.0:-2|1;-1|1;0|25:-2|1;-1|1;0|21 +1 1113942 STR_410 AAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1113942;END=1113956;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=20;DSNP=0;DSTUTTER=3;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:20:0:3:2:10.00|10.00:0|0:.:0.0:.:0.0:-3|2;-1|1;0|7;1|1:-3|1;-1|1;0|7;1|1 +1 1116390 STR_412 GCCCCTGCCCCTGCCCTTGCCCCTGCCCCTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1116390;END=1116420;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=38;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:38:0:0:2:19.00|19.00:0|0:.:0.0:.:0.0:-18|1;0|23:0|22 +1 1116652 STR_413 CATCCATCCAATCCATCCA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1116652;END=1116670;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=47;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:47:0:0:0:23.50|23.50:0|0:.:0.0:.:0.0:0|39:0|39 +1 1121393 STR_414 TCTCTCTCTCTC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1121393;END=1121404;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=34;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:34:0:0:3:17.00|17.00:0|0:.:0.0:.:0.0:0|31:0|30 +1 1121463 STR_415 TTTTCTTTTCTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1121463;END=1121486;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1122211 STR_416 TTTTTTTTGTTTGTTTTTTGTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1122211;END=1122243;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:35:0:0:2:17.50|17.50:0|0:.:0.0:.:0.0:0|17:0|15 +1 1123010 STR_417 AAAAAACAAAAAAATAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1123010;END=1123029;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=43;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:43:0:0:2:21.50|21.50:0|0:.:0.0:.:0.0:0|29:0|27 +1 1123285 STR_418 AAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1123285;END=1123299;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=32;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:32:0:1:2:16.00|16.00:0|0:.:0.0:.:0.0:0|19;1|1;52|1:0|16 +1 1123786 STR_419 TTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1123786;END=1123803;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=40;DSNP=0;DSTUTTER=6;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:40:0:6:3:20.00|20.00:0|0:.:0.0:.:0.0:-1|3;0|18;1|4:-1|2;0|15;1|2 +1 1125107 STR_420 TTATTATTATTATTA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1125107;END=1125121;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=33;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:33:0:0:2:16.50|16.50:0|0:.:0.0:.:0.0:0|30:0|29 +1 1125492 STR_421 AAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1125492;END=1125507;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1125628 STR_422 TTTTTTTTTTTTTCTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1125628;END=1125646;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1125807 STR_423 ACTAATTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1125812;END=1125825;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1126194 STR_424 TATTTTTATTTTTATTTTTTATTTTATTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1126194;END=1126222;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=37;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:37:0:0:3:18.50|18.50:0|0:.:0.0:.:0.0:-15|1;0|12:0|11 +1 1128709 STR_425 AATAATAATAATAATAAT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1128709;END=1128726;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=23;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:23:0:0:2:11.50|11.50:0|0:.:0.0:.:0.0:0|20:0|18 +1 1128850 STR_426 TTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1128850;END=1128860;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=27;DSNP=0;DSTUTTER=2;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:27:0:2:1:13.50|13.50:0|0:.:0.0:.:0.0:0|21;1|2:0|19;1|2 +1 1130362 STR_427 CTCTCTCTCTCTCT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1130362;END=1130375;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=43;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:43:0:0:1:21.50|21.50:0|0:.:0.0:.:0.0:-28|1;0|32:0|31 +1 1130881 STR_428 TTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1130881;END=1130898;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1139879 STR_429 GTGGGGGGAGGGAGGGAGGGAGG GGGGGGGGAGGGAGGGAGGGAGG . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1139884;END=1139901;PERIOD=4;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=68;DSNP=0;DSTUTTER=2;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:68:0:2:1:52.07|15.93:0|0:5.73:-6.12:57:-2.94:-20|1;-4|1;0|49:-4|1;0|48 +1 1144920 STR_430 TTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1144920;END=1144930;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=28;DSNP=0;DSTUTTER=2;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:28:0:2:1:14.00|14.00:0|0:.:0.0:.:0.0:-1|2;0|21:-1|2;0|18 +1 1145482 STR_431 AAAAAAAAAAAAAGAAAGAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1145482;END=1145505;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=39;DSNP=0;DSTUTTER=4;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:39:0:4:4:19.50|19.50:0|0:.:0.0:.:0.0:-21|1;-3|1;-1|3;0|13;1|1:-3|1;-1|2;0|6;1|1 +1 1150226 STR_432 AAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1150226;END=1150240;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1150735 STR_433 GAGGGAGGGAGTGGAGGGAG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1150735;END=1150754;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=47;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:47:0:0:3:23.50|23.50:0|0:.:0.0:.:0.0:-2|1;0|33:0|33 +1 1158412 STR_434 CACACACACAGCACAC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1158412;END=1158427;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=38;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:38:0:0:1:19.00|19.00:0|0:.:0.0:.:0.0:0|32;1|1:0|29 +1 1164208 STR_435 AGGGGCAGGGGCAGGGGCAG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1164208;END=1164227;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=47;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:47:0:0:1:23.50|23.50:0|0:.:0.0:.:0.0:0|31:0|33 +1 1165843 STR_436 TTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1165843;END=1165856;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=27;DSNP=0;DSTUTTER=4;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:27:0:4:1:13.50|13.50:0|0:.:0.0:.:0.0:-2|1;-1|1;0|13;1|2:-2|1;-1|1;0|10;1|2 +1 1180392 STR_438 CCTCCTCTCCCACTCCTCCCCCTCCTCCCCCCACTCCTCATCCCCCTCCTCCCCCACTCCCCCCTCCTCCCCCTACTCCTC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1180392;END=1180472;PERIOD=3;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1185371 STR_439 GAGAGAGAGAGA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1185371;END=1185382;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=45;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:45:0:0:0:22.50|22.50:0|0:.:0.0:.:0.0:0|39:0|38 +1 1186737 STR_440 TTTTTTTTTTTTTTTT TTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1186737;END=1186752;PERIOD=1;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=42;DSNP=0;DSTUTTER=6;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:-1|-1:1.0:1.0:42:0:6:3:21.00|21.00:0|0:5.53:0.0:.:0.0:-14|1;-11|1;-2|6;-1|17:-2|4;-1|18 +1 1187398 STR_441 AAAAAAAAAAAAAAAGTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1187398;END=1187412;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1188282 STR_442 CTCTCTCTCTCTC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1188282;END=1188294;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=46;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:46:0:0:0:23.00|23.00:0|0:.:0.0:.:0.0:0|42:0|40 +1 1192106 STR_443 AAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1192106;END=1192116;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=17;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:17:0:1:1:8.50|8.50:0|0:.:0.0:.:0.0:-1|1;0|14:-1|1;0|11 +1 1192774 STR_445 CCCCCCCCCCCCCCC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1192774;END=1192788;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1193409 STR_446 TTTTTTTTGTTTTGTTTTGTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1193409;END=1193435;PERIOD=5;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1195951 STR_447 CACACACACACA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1195951;END=1195962;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=51;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:51:0:0:2:25.50|25.50:0|0:.:0.0:.:0.0:0|44:0|40 +1 1197032 STR_448 TTTTTTTTTTTTTTTTTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1197032;END=1197048;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1199212 STR_449 AAAAAAAAAAA AAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1;START=1199212;END=1199222;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=36;DSNP=0;DSTUTTER=1;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|1:1.0:0.5:36:0:1:3:16.40|19.60:0|0:8.38:-0.25:26:-0.0:-1|1;0|11;1|15:-1|1;0|10;1|12 +1 1200945 STR_450 GTGTGTGTGTGTGTGTGTGTGTGTGTGTTTTCTCTCCATTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1200945;END=1201029;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=47;DSNP=0;DSTUTTER=6;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:47:0:6:0:23.50|23.50:0|0:.:0.0:.:0.0:-2|2;0|6;4|1:-2|2;0|6;4|1 +1 1202261 STR_451 ATTTTATTTTATTTTATTTTATTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1202261;END=1202285;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=33;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:33:0:0:2:16.50|16.50:0|0:.:0.0:.:0.0:0|16:0|16 +1 1204225 STR_452 TTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1204225;END=1204237;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=38;DSNP=0;DSTUTTER=2;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:38:0:2:4:19.00|19.00:0|0:.:0.0:.:0.0:-2|1;0|26;1|1:-2|1;0|21 +1 1204841 STR_453 TTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1204841;END=1204856;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1207355 STR_454 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1207355;END=1207384;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1207530 STR_455 AAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1207530;END=1207541;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=28;DSNP=0;DSTUTTER=2;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:28:0:2:1:14.00|14.00:0|0:.:0.0:.:0.0:-8|1;-1|1;0|13:0|12 +1 1209175 STR_456 CCGCCGCAGCGCCGCCGCCGCCGCC CCGCCGCAGCGCCGCCGCCGCCGCCGCC . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=3;START=1209175;END=1209199;PERIOD=3;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=39;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|3:1.0:0.5:39:0:0:0:18.38|20.62:0|0:11.97:-0.07:32:-0.3:0|14;3|17:0|14;3|15 +1 1211865 STR_457 TTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1211865;END=1211875;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=46;DSNP=0;DSTUTTER=4;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:46:0:4:2:23.00|23.00:0|0:.:0.0:.:0.0:-1|2;0|33;1|2:-1|1;0|30;1|2 +1 1212507 STR_458 TTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1212507;END=1212519;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1213211 STR_459 AAAAAAAAAAAAAT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1213211;END=1213223;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1213872 STR_460 TTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1213872;END=1213889;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1214781 STR_461 TTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1214781;END=1214800;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1215849 STR_462 AAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1215849;END=1215860;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=32;DSNP=0;DSTUTTER=4;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:32:0:4:4:16.00|16.00:0|0:.:0.0:.:0.0:-7|1;-1|4;0|22:-1|4;0|16 +1 1218137 STR_463 TTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1218137;END=1218150;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=2;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:35:0:2:3:17.50|17.50:0|0:.:0.0:.:0.0:-3|1;-1|1;0|18;1|1;17|1:-3|1;-1|1;0|16 +1 1218466 STR_464 GTGTGTGTGGTGTGGGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1218466;END=1218485;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=34;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:34:0:0:2:17.00|17.00:0|0:.:0.0:.:0.0:-2|1;0|25:0|22 +1 1219083 STR_465 AAAGAAAGAAAGAAAGA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1219083;END=1219099;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=49;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:49:0:0:1:24.50|24.50:0|0:.:0.0:.:0.0:0|32;15|1:0|31 +1 1219476 STR_466 GTGGGGGGGGGTGAGGGGGGTGGGGGGGTTGGGTGAGGGGGGTGGGGTCGGGGGGGG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1219476;END=1219532;PERIOD=5;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1221336 STR_467 CCACCATCAGCACCACCACCACCACC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1221336;END=1221361;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=61;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:61:0:0:2:30.50|30.50:0|0:.:0.0:.:0.0:-38|1;-26|1;0|46:0|46 +1 1229341 STR_468 CGGGGCGGGGCGGGGCGGGGCG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1229341;END=1229362;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=0;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:35:0:0:5:17.50|17.50:0|0:.:0.0:.:0.0:0|24:0|20 +1 1236639 STR_469 TTTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1236639;END=1236659;PERIOD=1;AN=0;REFAC=0;NSKIP=1;NFILT=0;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1236807 STR_470 TTTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1236807;END=1236827;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1238176 STR_471 CCCCCCCCCCCC CCCCCCCCCCCCC . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1;START=1238176;END=1238187;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=19;DSNP=0;DSTUTTER=1;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|1:1.0:0.5:19:0:1:0:10.85|8.15:0|0:2.47:-0.26:11:0.0:-1|1;0|6;1|4:-1|1;0|6;1|4 +1 1243927 STR_473 GGGGGGGAGGGGGGGGGGG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1243927;END=1243945;PERIOD=1;AN=0;REFAC=0;NSKIP=1;NFILT=0;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1247579 STR_474 GGGGGGGGGGCGGGG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1247579;END=1247593;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1247944 STR_475 CCCTGCCCTGCCCTGCCCAGCCC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1247944;END=1247966;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=56;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:56:0:0:1:28.00|28.00:0|0:.:0.0:.:0.0:-20|1;0|39:0|39 +1 1251152 STR_476 GGGAGGGAGGGAGGGAGGCGGGCAGCGAGGGAGGCAGGGGCAGGGAGTGAGGGGGGCGGGGGCAGGGAGGGAGG GGGAGGGAGGGAGGGAGGCGGGCAGCGAGGGAGGGAGTGGCAGGGAGTGAGGGGGGCTGGGGGAGGGAGGGGGG . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1251152;END=1251225;PERIOD=4;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:31:0:1:2:27.00|4.00:0|0:4.06:-5.25:27:-0.84:0|9:0|9 +1 1252308 STR_477 AAAAATAAATAAATAAA ATAAATAAATAAATAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1252310;END=1252324;PERIOD=4;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=32;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:32:0:0:1:13.64|18.36:0|0:39.57:-0.34:29:-0.15:-16|1;0|22:0|21 +1 1252776 STR_478 AAAAAAAAAAGAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1252776;END=1252797;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=2;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:35:0:2:5:17.50|17.50:0|0:.:0.0:.:0.0:-9|1;0|14;1|2:0|10;1|2 +1 1253245 STR_479 TTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1253245;END=1253256;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=32;DSNP=0;DSTUTTER=2;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:32:0:2:3:16.00|16.00:0|0:.:0.0:.:0.0:-1|2;0|23:-1|2;0|21 +1 1254028 STR_480 AAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1254028;END=1254042;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=27;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:27:0:0:0:13.50|13.50:0|0:.:0.0:.:0.0:0|17:0|17 +1 1257916 STR_481 AGGGGAGGGGAGGGGTAGGGTGGGGGAGGGGGAGGG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1257916;END=1257951;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=18;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:18:0:0:1:9.00|9.00:0|0:.:0.0:.:0.0:-1|1;0|7:0|7 +1 1258960 STR_482 TTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1258960;END=1258971;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=2;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:31:0:2:4:15.50|15.50:0|0:.:0.0:.:0.0:-1|2;0|19:-1|2;0|16 +1 1260143 STR_483 GGGCGAGGGCGGGGCGAGGGCGGGGCGGTGGGCGGGGACGGGGC GGGCGAGGGCGGGGCGAGGGCGGGGAGGTGGGCGGGGACGGGGC,GGGCGAGGGCGGGGCGAGGGCGGGGCGAGGGCGGGGAGGTGGGCGGGGACGGGGC . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0,11;START=1260143;END=1260186;PERIOD=5;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=48;DSNP=0;DSTUTTER=0;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:0|11:1.0:0.5:48:0:0:4:23.44|24.56:0|0:34.55:-0.0:25:0.0:-31|1;-16|1;-9|1;-2|2;0|12;11|6:0|10;11|6 +1 1263906 STR_484 CAGCCCAGCCCAGCCCA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1263906;END=1263922;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=42;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:42:0:0:0:21.00|21.00:0|0:.:0.0:.:0.0:0|33:0|33 +1 1268987 STR_485 GCTGTGCTGCTGCTGCTCCTGCTGCTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1268987;END=1269013;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=54;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:54:0:0:2:27.00|27.00:0|0:.:0.0:.:0.0:0|35;11|1:0|33 +1 1271109 STR_486 AATAAATAAATAAAT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1271109;END=1271123;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=34;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:34:0:0:3:17.00|17.00:0|0:.:0.0:.:0.0:-1|1;0|22:0|22 +1 1276558 STR_487 CACACGCACATCTGCACACGCACACCTGCACACACGCACACGCACAC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1276558;END=1276604;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=42;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:42:0:0:0:21.00|21.00:0|0:.:0.0:.:0.0:0|18:0|18 +1 1276921 STR_488 CACACACATGCACACACACGCACACAC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1276921;END=1276947;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1278638 STR_489 CCCCCCCCCCCC CCCCCCCCCC . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-2;START=1278638;END=1278649;PERIOD=1;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=38;DSNP=0;DSTUTTER=2;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:-2|-2:1.0:1.0:38:0:2:3:19.00|19.00:0|0:7.79:0.0:.:0.0:-12|1;-3|1;-2|30;-1|1:-3|1;-2|28;-1|1 +1 1282567 STR_490 CAGCCCAGCCCAGCCCAGCCC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1282567;END=1282587;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=33;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:33:0:0:2:16.50|16.50:0|0:.:0.0:.:0.0:0|23:0|23 +1 1284511 STR_491 CCCGCCCGCCCGCCTGCGCCCCGCCCGGCCCGCACCGC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1284511;END=1284548;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=5;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:5:0:0:0:2.50|2.50:0|0:.:0.0:.:0.0:0|5:0|3 +1 1296243 STR_493 CACACACACACAAAGACACACA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1296243;END=1296264;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=41;DSNP=0;DSTUTTER=0;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:41:0:0:5:20.50|20.50:0|0:.:0.0:.:0.0:-3|1;0|28:0|24 +1 1296578 STR_494 ACACACACAGACACACA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1296578;END=1296594;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=43;DSNP=0;DSTUTTER=0;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:43:0:0:4:21.50|21.50:0|0:.:0.0:.:0.0:0|36;17|1:0|35 +1 1297849 STR_495 AATTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1297851;END=1297862;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1298161 STR_496 AAAAAAAAAAAAAAAAAAAAGGGTT AAAAAAATTAAAAAAAAAAGGGTG,AAAAAAATTAAAAAAAAAAGGGTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1,-1;START=1298161;END=1298180;PERIOD=1;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=29;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:-1|-1:1.0:0.5:29:0:1:2:9.07|19.93:0|0:3.3:-1.58:21:-0.2:-6|1;-1|17;0|2;3|1:-1|17;0|1 +1 1298462 STR_497 AAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1298462;END=1298474;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=25;DSNP=0;DSTUTTER=3;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:25:0:3:2:12.50|12.50:0|0:.:0.0:.:0.0:-1|3;0|13:-1|3;0|12 +1 1298812 STR_498 TTTTTTCTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1298812;END=1298831;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1298981 STR_499 ATTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1298982;END=1298998;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1300417 STR_500 AAAAAAAAAAAA AAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=2;START=1300417;END=1300428;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=34;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|2:1.0:0.5:34:0:1:2:20.05|13.95:0|0:15.31:-0.64:25:0.0:-1|1;0|14;1|1;2|8:0|10;1|1;2|7 +1 1301014 STR_501 AAAAATAAATAAATAAATAAAAATAAAAATAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1301014;END=1301048;PERIOD=6;AN=0;REFAC=0;NSKIP=1;NFILT=0;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1301200 STR_502 AAAAAAAATAAATAAAAATAAAAA AAAAAAATAAATAAAAATAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1301200;END=1301223;PERIOD=1;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=51;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:-1|-1:1.0:1.0:51:0:0:1:25.50|25.50:0|0:9.71:0.0:.:0.0:-1|29:-1|27 +1 1303559 STR_503 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1303559;END=1303591;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=21;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:21:0:2:2:5.77|15.23:0|0:.:0.0:.:0.0:-7|1;-6|1:-3|1 +1 1304416 STR_504 AAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1304416;END=1304432;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1305181 STR_505 AACTTTTTTTTTTTTTGAGAC ACCTTTTTTTTTTTTTTGAGAT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1;START=1305184;END=1305196;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=44;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|1:1.0:0.5:44:0:2:2:30.90|13.10:0|0:29.11:-2.02:44:0.0:-12|1;-9|1;0|13;1|8;27|1:0|11;1|8 +1 1305934 STR_506 AAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAA,AAAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-3,-1;START=1305934;END=1305951;PERIOD=1;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=39;DSNP=0;DSTUTTER=4;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 2|1:-1|-3:1.0:0.5:39:0:4:5:23.69|15.31:0|0:7.46:-0.59:38:0.0:-10|1;-6|1;-4|1;-3|8;-1|7;0|1:-3|7;-1|6;0|1 +1 1311059 STR_507 AAAAAAAAAAAAA AAAAAAAAAAA,AAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-2,-1;START=1311059;END=1311071;PERIOD=1;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=43;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 2|1:-1|-2:1.0:0.5:43:0:1:2:22.30|20.70:0|0:12.99:-0.06:36:-0.13:-3|1;-2|16;-1|18:-3|1;-2|14;-1|16 +1 1311363 STR_508 AAATAAATAAATAAATAAAATAAA AAATAAATAAATAAAAAAAATAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1311363;END=1311386;PERIOD=4;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=32;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:0|0:1.0:1.0:32:0:0:1:16.00|16.00:0|0:6.01:0.0:.:0.0:-17|1;0|15:0|15 +1 1312861 STR_509 AAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1312861;END=1312876;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1313562 STR_510 TTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1313562;END=1313574;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=33;DSNP=0;DSTUTTER=3;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:33:0:3:4:19.97|13.03:0|0:.:0.0:.:0.0:-1|1;0|22:-1|1;0|19 +1 1313865 STR_511 TTTTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1313865;END=1313886;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1314470 STR_512 TTTTGTTGTTGTTGTTGTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1314472;END=1314488;PERIOD=3;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1315275 STR_513 AAAAAAAAAAAAAGAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1315275;END=1315295;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1318882 STR_514 AAAAAAAAGAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1318882;END=1318901;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=47;DSNP=0;DSTUTTER=2;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:47:0:2:4:23.50|23.50:0|0:.:0.0:.:0.0:-1|2;0|31:-1|1;0|24 +1 1319630 STR_515 TTTTTTTTTTTTTTTTTTTTT TTTTTTGTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1319630;END=1319650;PERIOD=1;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=39;DSNP=0;DSTUTTER=2;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:0|0:1.0:1.0:39:0:2:3:19.50|19.50:0|0:8.7:0.0:.:0.0:-2|1;0|15;1|2:-2|1;0|11;1|1 +1 1319936 STR_516 TTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1319936;END=1319951;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1323902 STR_517 AAAACAAAACAAAACAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1323902;END=1323920;PERIOD=5;AN=0;REFAC=0;NSKIP=1;NFILT=0;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1323946 STR_518 TCTCTCTCTCTCTCTCTCTATATATATATATACATAGACACACACTCACACACA TCTCTCTCTCTCTCTCTATATATATATATACATAGACACACACTCACACACA,TGTCTCTCTCTCTCTCTATATATATATATACATAGACACACACTCACACACA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-2,-2;START=1323946;END=1323999;PERIOD=2;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=36;DSNP=0;DSTUTTER=3;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:-2|-2:1.0:0.5:36:0:3:2:17.37|18.63:0|0:14.71:0.0:21:-0.18:-20|1;-4|2;-2|10:-4|2;-2|8 +1 1324153 STR_519 AAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1324153;END=1324174;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=15;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:15:0:2:2:7.50|7.50:0|0:.:0.0:.:0.0:-11|1;-6|1;0|1;1|1:. +1 1325494 STR_520 AAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1325494;END=1325513;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=44;DSNP=0;DSTUTTER=4;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:44:0:4:5:27.50|16.50:0|0:3.72:-1.28:27:-2.08:-16|1;-7|1;-3|1;-2|1;-1|6;0|15:-2|1;-1|5;0|9 +1 1326472 STR_521 AAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1326472;END=1326482;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=41;DSNP=0;DSTUTTER=2;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:41:0:2:5:20.50|20.50:0|0:.:0.0:.:0.0:-9|1;0|26;1|1;2|1:0|21;2|1 +1 1326739 STR_522 TTCCTCTTCCTCTTCCTC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1326739;END=1326756;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=38;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:38:0:0:1:19.00|19.00:0|0:.:0.0:.:0.0:-13|1;0|29:0|30 +1 1329506 STR_523 AAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1329506;END=1329520;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1330133 STR_524 AAAAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1330133;END=1330156;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=15;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:15:0:0:1:7.50|7.50:0|0:.:0.0:.:0.0:0|3:0|1 +1 1330382 STR_525 CCACTGCCACTGCCACCATGCCACTGC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1330382;END=1330408;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=34;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:34:0:0:0:17.00|17.00:0|0:.:0.0:.:0.0:0|22:0|22 +1 1330443 STR_526 AAAAAAAAAGAAAACAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1330443;END=1330466;PERIOD=1;AN=0;REFAC=0;NSKIP=1;NFILT=0;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1331571 STR_527 AAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1331571;END=1331589;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=19;DSNP=0;DSTUTTER=2;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:19:0:2:0:9.50|9.50:0|0:.:0.0:.:0.0:0|8;1|1;2|1:0|3;1|1;2|1 +1 1331952 STR_528 TTTTTTTTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1331952;END=1331977;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=27;DSNP=0;DSTUTTER=2;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:27:0:2:4:13.50|13.50:0|0:.:0.0:.:0.0:0|7:0|2 +1 1332127 STR_529 TTTTTTTTTTATTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1332127;END=1332146;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=24;DSNP=0;DSTUTTER=2;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:24:0:2:0:12.00|12.00:0|0:.:0.0:.:0.0:-1|1;0|13;1|1:-1|1;0|11;1|1 +1 1334664 STR_530 GCCGCCGCCGCCGCCGCCGCC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1334664;END=1334684;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=41;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:41:0:0:0:20.50|20.50:0|0:.:0.0:.:0.0:0|27:0|26 +1 1338502 STR_531 GTATCCAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1338508;END=1338518;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1338621 STR_532 CTTTCTTTCTTTCTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1338621;END=1338636;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=39;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:39:0:0:2:19.50|19.50:0|0:.:0.0:.:0.0:0|33:0|32 +1 1339466 STR_533 GCCTCTGCCTCTGCCTCT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1339466;END=1339483;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=48;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:48:0:0:3:24.00|24.00:0|0:.:0.0:.:0.0:0|42:0|41 +1 1339538 STR_534 TTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1339538;END=1339551;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1339885 STR_535 TTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1339885;END=1339898;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=24;DSNP=0;DSTUTTER=3;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:24:0:3:2:12.00|12.00:0|0:.:0.0:.:0.0:-14|1;-6|1;-1|1;0|9;1|1:-1|1;0|8;1|1 +1 1344145 STR_536 TTGTTTTGTTTTGTTTTTTTCTGTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1344145;END=1344171;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=43;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:43:0:0:1:21.50|21.50:0|0:.:0.0:.:0.0:-4|1;0|22:0|22 +1 1344833 STR_537 TTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1344833;END=1344843;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=45;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:45:0:2:2:22.50|22.50:0|0:.:0.0:.:0.0:-1|1;0|36;1|1:-1|1;0|31;1|1 +1 1351002 STR_538 TTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1351002;END=1351014;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=1;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:35:0:1:3:17.50|17.50:0|0:.:0.0:.:0.0:-11|1;-1|1;0|29:-1|1;0|25 +1 1352432 STR_539 AAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-2;START=1352432;END=1352451;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=30;DSNP=0;DSTUTTER=4;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-2:1.0:0.5:30:0:4:1:20.00|10.00:0|0:4.18:-1.67:16:-0.29:-2|4;-1|2;0|6;2|1:-2|4;-1|2;0|5;2|1 +1 1352658 STR_540 TTTTTTTTTCTTTTTT . . . 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INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1434967;END=1434991;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1435274 STR_606 TTTTTTTTTTTTTCTTTTT TTTTTTTTTTTTCTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1435274;END=1435292;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=34;DSNP=0;DSTUTTER=1;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:34:0:1:4:15.81|18.19:0|0:7.68:-0.18:21:0.0:-17|1;-15|1;-3|1;-1|8;0|7:-1|7;0|6 +1 1435934 STR_607 AAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1435934;END=1435948;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=21;DSNP=0;DSTUTTER=3;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:21:0:3:3:10.50|10.50:0|0:.:0.0:.:0.0:-2|2;0|15:-2|2;0|13 +1 1435985 STR_608 ATATATATATATATGTATAAATGTATATATAAATGTGTATATATATATA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1435985;END=1436033;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=17;DSNP=0;DSTUTTER=1;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:17:0:1:0:8.50|8.50:0|0:.:0.0:.:0.0:0|5:0|4 +1 1436641 STR_609 TTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1436641;END=1436652;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=34;DSNP=0;DSTUTTER=3;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:34:0:3:1:17.00|17.00:0|0:.:0.0:.:0.0:-1|1;0|20;1|1:-1|1;0|16;1|1 +1 1437234 STR_610 GTTTTTTTTTGTTTTTGTTTTGTTTTGTTTTGTTTGTTTTTTTTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1437234;END=1437278;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=45;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:45:0:0:3:22.50|22.50:0|0:.:0.0:.:0.0:0|25;5|1:0|25 +1 1437601 STR_611 TTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1437601;END=1437611;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=24;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:24:0:0:1:12.00|12.00:0|0:.:0.0:.:0.0:0|12:0|11 +1 1437888 STR_612 TTTTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1437888;END=1437909;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1438285 STR_613 GTCTAATATATATATATATAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1438290;END=1438304;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1438604 STR_614 AAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1438604;END=1438619;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=24;DSNP=0;DSTUTTER=2;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:24:0:2:0:12.00|12.00:0|0:.:0.0:.:0.0:-3|1;0|14:-2|1;-1|1;0|13 +1 1439335 STR_615 TTGCATTGCATTGCATTGCATTGCATT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1439335;END=1439361;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=46;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:46:0:0:2:23.00|23.00:0|0:.:0.0:.:0.0:0|32:0|32 +1 1440031 STR_616 AAAAACAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1440031;END=1440047;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=37;DSNP=0;DSTUTTER=0;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:37:0:0:4:18.50|18.50:0|0:.:0.0:.:0.0:0|28:0|27 +1 1440309 STR_617 TGTGTGTGTGTGTGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1440309;END=1440330;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=51;DSNP=0;DSTUTTER=1;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:51:0:1:3:25.50|25.50:0|0:.:0.0:.:0.0:-2|1;0|36;11|1:-2|1;0|34 +1 1440634 STR_618 AGAGAGAGGGAGGGAGGGAGAGAGAGAGA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1440634;END=1440662;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=42;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:42:0:0:0:21.00|21.00:0|0:.:0.0:.:0.0:0|23:0|23 +1 1441782 STR_619 TTTTCTTTTTTTTTTTTTC TTTTCTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1441782;END=1441799;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=23;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:23:0:2:2:17.03|5.97:0|0:3.21:-1.72:19:0.0:0|12;1|1:0|9;1|1 +1 1442156 STR_620 TTTTCTTTTTTCTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1442156;END=1442185;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=24;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:24:0:2:2:12.00|12.00:0|0:.:0.0:.:0.0:-1|1;0|4:-1|1;0|1 +1 1445295 STR_621 AAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1445295;END=1445313;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1445463 STR_622 AAAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1445463;END=1445485;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1445862 STR_623 TTTTCTTTTTCTTTTTTTTTTCTTTTCTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1445862;END=1445898;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1446187 STR_624 TTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1446187;END=1446202;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1447618 STR_625 CGGCGGCGGTAGCGGCGGCGGCGG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1447618;END=1447641;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:31:0:0:1:15.50|15.50:0|0:.:0.0:.:0.0:-6|1;0|24:0|23 +1 1450257 STR_626 TTTATTTATTTATTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1450257;END=1450271;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=38;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:38:0:0:0:19.00|19.00:0|0:.:0.0:.:0.0:0|30:0|28 +1 1451800 STR_627 TTTATTTATTTATTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1451800;END=1451814;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=42;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:42:0:0:1:21.00|21.00:0|0:.:0.0:.:0.0:-12|1;0|26:0|26 +1 1453620 STR_628 CACACACACACACAGATACGCACACACACACCACACACA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1453620;END=1453658;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=41;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:41:0:0:2:20.50|20.50:0|0:.:0.0:.:0.0:0|24;23|1:0|20 +1 1453673 STR_629 CACACACACACA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1453673;END=1453684;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=24;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:24:0:0:2:12.00|12.00:0|0:.:0.0:.:0.0:0|13:0|13 +1 1453728 STR_630 CGGGCACACACACAGCCCCACACACACAGGCGCACACCCACACACACATGGG CCGGCACACACACACCCCCACACACACACTCACACACCCACACACACATGGA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1453732;END=1453775;PERIOD=2;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=24;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:24:0:0:2:22.50|1.50:0|0:5.77:-5.24:23:0.0:0|12:0|11 +1 1453799 STR_631 ACACACACACACCCACACACA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1453799;END=1453819;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=16;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:16:0:1:1:8.00|8.00:0|0:.:0.0:.:0.0:0|12;2|2:0|9;2|1 +1 1453951 STR_632 ACACACACACACACCCG ACACACACACACCACCC . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1453951;END=1453964;PERIOD=2;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=13;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:0.95:0.48:13:0:1:1:11.51|1.49:0|0:1.32:-2.2:12:0.0:0|12;2|1:0|11;2|1 +1 1454047 STR_633 ACACACACACACACACACACACAC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1454047;END=1454070;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1454611 STR_634 TTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1454611;END=1454624;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1456679 STR_635 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1456679;END=1456709;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1457081 STR_636 TTTGTTTGTTTGTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1457081;END=1457095;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=55;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:55:0:0:3:27.50|27.50:0|0:.:0.0:.:0.0:-6|1;0|36:0|35 +1 1457419 STR_637 TTTGTTTGTTTGTTTTTTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1457419;END=1457437;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=58;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:58:0:0:1:29.00|29.00:0|0:.:0.0:.:0.0:0|41:0|40 +1 1460794 STR_638 TTTTTTTTTTTTTTTTTTTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1460794;END=1460812;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1461392 STR_639 TTTCTTTTCTTTTTCTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1461392;END=1461420;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=28;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:28:0:0:2:14.00|14.00:0|0:.:0.0:.:0.0:0|10;1|1:0|11 +1 1463339 STR_640 TTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1463339;END=1463356;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1466209 STR_641 AAAAAAAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1466209;END=1466235;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1466832 STR_642 AAAACGAAAACGAAAACTAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1466832;END=1466853;PERIOD=6;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1467158 STR_643 AAAAATAAAAAAATAAAAAATAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1467158;END=1467182;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=27;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:27:0:0:2:13.50|13.50:0|0:.:0.0:.:0.0:0|18:0|16 +1 1468636 STR_644 ACCCTGACCCTGACCCTGACCC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1468636;END=1468657;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=38;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:38:0:0:1:19.00|19.00:0|0:.:0.0:.:0.0:0|23:0|24 +1 1475889 STR_645 GGGGGGGGGGG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1475889;END=1475899;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1478431 STR_646 CAGAGGCAGAGGCAGAGGCAGAGGC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1478431;END=1478455;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=52;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:52:0:0:2:26.00|26.00:0|0:.:0.0:.:0.0:0|37;22|1:0|36 +1 1481154 STR_647 AAAAAGAAAAAGAAAAAAAAACAGAA AAAAAGAAAAAGAAAAAAAAAAAGAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1481154;END=1481179;PERIOD=6;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=44;DSNP=0;DSTUTTER=2;DFLANKINDEL=6 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:44:0:2:6:17.93|26.07:0|0:32.67:-0.83:31:0.0:-35|1;-31|1;0|18:0|14 +1 1482412 STR_648 AAAAGAAAAGAAAAAAAAGA AAAAGAAAAGAAAAAAAGA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1482412;END=1482431;PERIOD=5;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=28;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:28:0:0:1:23.50|4.50:0|0:7.07:-4.68:21:-0.37:-1|1;0|16:-1|1;0|16 +1 1483935 STR_649 AAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1483935;END=1483956;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=29;DSNP=0;DSTUTTER=2;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:29:0:2:3:14.50|14.50:0|0:.:0.0:.:0.0:-26|1;-11|1;-1|1;0|4;1|1:0|3 +1 1484899 STR_650 AAAAAAAAAAAAGAAAGAAAAAGAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1484899;END=1484930;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=4;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:35:0:4:1:17.50|17.50:0|0:.:0.0:.:0.0:-31|1;-1|1;0|10:-1|1;0|9 +1 1485354 STR_651 AAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1485354;END=1485369;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=14;DSNP=0;DSTUTTER=2;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:14:0:2:0:6.98|7.02:0|0:.:0.0:.:0.0:-1|2;0|8:-1|2;0|8 +1 1488399 STR_652 AAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1488399;END=1488419;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1489000 STR_653 AAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1489000;END=1489021;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1489172 STR_654 AAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1489172;END=1489188;PERIOD=1;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=25;DSNP=0;DSTUTTER=3;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:-1|-1:0.94:0.94:25:0:3:2:12.50|12.50:0|0:1.19:0.0:.:0.0:-3|1;-2|1;-1|7;0|1:-2|1;-1|6 +1 1491923 STR_655 AAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1491923;END=1491935;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=33;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:33:0:2:2:16.50|16.50:0|0:.:0.0:.:0.0:-1|1;0|22;1|2:0|21;1|2 +1 1492800 STR_656 TAAATAAATAAATAAATAAATAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1492800;END=1492823;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=36;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:36:0:0:2:18.00|18.00:0|0:.:0.0:.:0.0:-23|1;-9|1;0|20:0|20 +1 1492876 STR_657 ATATATATATATAT ATATATATATAT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-2;START=1492876;END=1492889;PERIOD=2;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=23;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-2:1.0:0.5:23:0:0:1:15.76|7.24:0|0:2.61:-1.11:21:-0.44:-2|6;0|14:-2|5;0|13 +1 1493585 STR_658 AAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=5;START=1493585;END=1493600;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=26;DSNP=0;DSTUTTER=3;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|5:1.0:0.5:26:0:3:0:15.53|10.47:0|0:34.74:-0.52:15:-0.3:-2|1;-1|1;0|9;5|2;6|1:0|8;6|1 +1 1493755 STR_659 AATAATAATAATAAT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1493755;END=1493769;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:31:0:0:0:18.04|12.96:0|0:.:0.0:.:0.0:0|23:0|23 +1 1498918 STR_660 AAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1;START=1498918;END=1498938;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=15;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|1:0.94:0.47:15:0:1:2:8.46|6.54:0|0:1.21:-0.16:6:-0.4:-24|1;-1|1;0|4;1|1:-1|1;0|2;1|1 +1 1499766 STR_661 GCACGCACGCACACACGCACGCAC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1499766;END=1499789;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=34;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:34:0:0:0:17.00|17.00:0|0:.:0.0:.:0.0:0|17:0|17 +1 1501480 STR_662 AAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1501480;END=1501495;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=38;DSNP=0;DSTUTTER=3;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:38:0:3:3:16.52|21.48:0|0:.:0.0:.:0.0:-1|4;0|18:-1|3;0|11 +1 1502235 STR_663 AAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1502235;END=1502249;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1503291 STR_664 TCAAAAAAAAAAAAAAAAA TAAAAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1503293;END=1503309;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=25;DSNP=0;DSTUTTER=2;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:25:0:2:3:16.71|8.29:0|0:4.96:-1.11:21:-1.73:-19|1;-4|1;0|12;5|1:0|10 +1 1503807 STR_665 ACTTTAAAAAAAAAATAAAAAAATAAAAAAA AGTTTAAAAAAAAAATAAAAAAATAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1503812;END=1503837;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=45;DSNP=0;DSTUTTER=1;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:45:0:1:0:21.97|23.03:0|0:55.77:-0.0:39:0.0:-1|1;0|29:-1|1;0|26 +1 1504252 STR_666 AAATAAATAAATAAATAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1504252;END=1504269;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=40;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:40:0:0:2:20.00|20.00:0|0:.:0.0:.:0.0:-1|1;0|28:0|27 +1 1505664 STR_667 AAAAAAAAAACAAAAAAAAAA AAAAAAAAAACAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1505664;END=1505684;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=25;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:25:0:2:2:8.95|16.05:0|0:5.18:-0.94:20:-0.8:-1|9;0|8:-1|9;0|5 +1 1506623 STR_668 TCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1506625;END=1506662;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1506815 STR_669 AAAAAAAAAAAAAAA AAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1;START=1506815;END=1506829;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=26;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|1:1.0:0.5:26:0:1:2:14.13|11.87:0|0:3.66:-0.2:17:-0.21:-16|1;0|10;1|5;2|1:0|10;1|4;2|1 +1 1507175 STR_670 TTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1507175;END=1507185;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1507831 STR_671 TTTATTTTATTTATGTATTTATTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1507831;END=1507854;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=25;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:25:0:0:0:12.50|12.50:0|0:.:0.0:.:0.0:0|17:0|17 +1 1508258 STR_672 GGGGGGGGGGGGG GGGGGGGGGGGG . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1508258;END=1508270;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=1;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:35:0:1:0:17.27|17.73:0|0:8.51:-0.07:30:-0.32:-1|14;0|13:-2|1;-1|15;0|7 +1 1508646 STR_673 AAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1508646;END=1508660;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1508810 STR_674 AAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-18;START=1508810;END=1508836;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=33;DSNP=0;DSTUTTER=3;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-18:1.0:0.5:33:0:3:1:7.51|25.49:0|0:50.38:-2.84:30:0.0:-18|21;-11|1;-1|2;0|1:-18|20;-1|1 +1 1509402 STR_675 AAAAAAAAAAAAAG AAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-3;START=1509402;END=1509414;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=41;DSNP=0;DSTUTTER=3;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-3:1.0:0.5:41:0:3:4:18.37|22.63:0|0:44.82:-0.22:34:-0.56:-3|14;-2|3;-1|1;0|11:-3|11;-2|2;-1|1;0|9 +1 1511374 STR_676 AAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1511374;END=1511388;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=46;DSNP=0;DSTUTTER=2;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:46:0:2:5:23.00|23.00:0|0:.:0.0:.:0.0:-2|1;-1|1;0|25:-2|1;-1|1;0|24 +1 1512215 STR_677 AAAAAAATAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1512215;END=1512231;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=39;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:39:0:1:2:19.50|19.50:0|0:.:0.0:.:0.0:-14|1;0|28:0|25 +1 1514791 STR_678 TTTTTTTTTTTTTTTT TTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1514791;END=1514806;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:31:0:0:2:13.93|17.07:0|0:4.59:-0.32:18:0.0:-1|10;0|7:-1|8;0|4 +1 1515017 STR_679 ACACACACACACA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1515017;END=1515029;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=24;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:24:0:0:1:12.00|12.00:0|0:.:0.0:.:0.0:0|21:0|21 +1 1515401 STR_680 TTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1515401;END=1515414;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=43;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:43:0:2:2:21.50|21.50:0|0:.:0.0:.:0.0:-1|2;0|22:-1|2;0|21 +1 1519323 STR_681 TTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1519323;END=1519338;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1519616 STR_682 TTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1519616;END=1519633;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1519924 STR_683 TTTTTGTTTTTGTTTTTGTTTTTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1519924;END=1519947;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=47;DSNP=0;DSTUTTER=0;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:47:0:0:4:23.50|23.50:0|0:.:0.0:.:0.0:-25|1;-14|1;0|29:0|30 +1 1520671 STR_684 TTTGTTTGTTTATTTGTTTGTTTGTTTGTTT TTTGTTTATTTGTTTGTTTGTTTGTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-4;START=1520671;END=1520701;PERIOD=4;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=42;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:-4|-4:1.0:1.0:42:0:0:2:21.00|21.00:0|0:9.29:0.0:.:0.0:-8|1;-4|24:-4|24 +1 1521159 STR_685 AAACAAACAAGCAAACAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1521159;END=1521177;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=12;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:12:0:0:0:6.00|6.00:0|0:.:0.0:.:0.0:0|11:0|11 +1 1521330 STR_686 AATAATAATAATAATAATAATAATAATAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1521330;END=1521358;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=6;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:6:0:0:0:3.00|3.00:0|0:.:0.0:.:0.0:.:. +1 1522282 STR_687 GTTTTTTTTGGTTTTTTTGTTTGTTTTGTTTTGTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1522282;END=1522318;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=48;DSNP=0;DSTUTTER=2;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:48:0:2:4:24.00|24.00:0|0:.:0.0:.:0.0:-22|1;-17|1;-9|1;-5|1;0|21:-5|1;0|21 +1 1522603 STR_688 TTTTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1;START=1522603;END=1522620;PERIOD=1;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=20;DSNP=0;DSTUTTER=3;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:1|1:0.98:0.98:20:0:3:2:10.00|10.00:0|0:1.8:0.0:.:0.0:-2|1;-1|1;0|1;1|8;2|1:-1|1;1|7 +1 1522778 STR_689 TTTTTTTTTTTGAGAC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1522778;END=1522788;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1523520 STR_690 TCAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1523522;END=1523539;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1523601 STR_691 TTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1523601;END=1523616;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1523832 STR_692 AAAAAAAAAGAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1523832;END=1523852;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=36;DSNP=0;DSTUTTER=1;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:36:0:1:3:18.00|18.00:0|0:.:0.0:.:0.0:-41|1;0|13:0|10 +1 1524092 STR_693 CTTCGCTTCCCTTCTTCCCTTCCCTTCCC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1524092;END=1524120;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=48;DSNP=0;DSTUTTER=2;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:48:0:2:3:24.00|24.00:0|0:.:0.0:.:0.0:-18|1;-10|1;0|26:0|26 +1 1524541 STR_694 TTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTT TTTATTTATTTATTTATTTATTTATTTATTTATTTATTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-4;START=1524541;END=1524583;PERIOD=4;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=16;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:-4|-4:0.96:0.96:16:0:0:2:8.00|8.00:0|0:1.4:0.0:.:0.0:-4|6;0|1:-4|6 +1 1524798 STR_695 TAAAAAAAAAAAAAAAGAGA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1524799;END=1524813;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1524870 STR_696 GACCTCTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1524876;END=1524888;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1525828 STR_697 AAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1525828;END=1525838;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=40;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:40:0:1:2:20.00|20.00:0|0:.:0.0:.:0.0:-7|1;0|29;1|1:0|26;1|1 +1 1526194 STR_698 AAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1526194;END=1526206;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1526643 STR_699 TTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1526643;END=1526655;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1527899 STR_700 AAATAAATAAATAAATAAATAAATA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1527899;END=1527923;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=34;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:34:0:0:2:17.00|17.00:0|0:.:0.0:.:0.0:-6|1;0|22;5|1:0|22 +1 1528227 STR_701 AAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAA,AAAAAAAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1,2;START=1528227;END=1528245;PERIOD=1;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=17;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:1|2:0.98:0.49:17:0:0:1:8.74|8.26:0|0:1.9:-0.0:7:0.0:-4|1;-3|1;0|4;1|1;2|1:1|1;2|2 +1 1528543 STR_702 AAAAAAAAATAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1528543;END=1528557;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:31:0:2:2:15.50|15.50:0|0:.:0.0:.:0.0:-1|1;0|26;1|1:-1|1;0|23;1|1 +1 1528650 STR_703 ATCTCAAAAAAAAAAAAAACAAAAAGAAAAAAAA AACTCAAAAAAAAAAAAACAAAAAGGAAAAAAA,ATCTCAAAAAAAAAAAAACAAAAAGAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1,-1;START=1528655;END=1528683;PERIOD=1;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=28;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:-1|-1:1.0:0.5:28:0:0:0:4.05|23.95:0|0:2.68:-4.06:26:0.0:-1|11:-1|10 +1 1528970 STR_704 AAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1528970;END=1528980;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=38;DSNP=0;DSTUTTER=4;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:38:0:4:4:19.00|19.00:0|0:.:0.0:.:0.0:-23|1;-2|1;-1|3;0|25:-2|1;-1|3;0|21 +1 1529090 STR_705 AAAAGAAAAGGAAAGAAAAAAAGAAAAGAAAAG AAAAGAAAAGGAAAGAAAAAAACAAAAGAAAAG . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1529090;END=1529122;PERIOD=5;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=46;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:46:0:0:2:23.01|22.99:0|0:56.41:0.0:34:-0.14:-18|1;-8|1;0|22:0|22 +1 1532224 STR_706 GAGAGAGACAGAGAGAG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1532224;END=1532240;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=43;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:43:0:0:1:21.50|21.50:0|0:.:0.0:.:0.0:-24|1;0|37:0|35 +1 1532832 STR_707 CTCCTCCTCCCCCTCCCCCTCCGCCCCCCCCCCCCC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1532832;END=1532867;PERIOD=6;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1537946 STR_709 AAGGAAGGAAGGAGGGAAGG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1537946;END=1537965;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=52;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:52:0:0:1:26.00|26.00:0|0:.:0.0:.:0.0:-18|1;0|41:0|40 +1 1539674 STR_710 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTAG TTTTTTTTTTTTTTTTTTGTAT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-11;START=1539674;END=1539702;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=19;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-11:1.0:0.5:19:0:0:2:12.66|6.34:0|0:9.55:-1.41:9:-0.35:-11|1;-10|2;0|1:-11|1;0|1 +1 1541248 STR_711 TGGGCTGGGCTGGGCTGGTCTGGTGTGGACTGGGCTGG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1541248;END=1541285;PERIOD=5;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1541470 STR_712 GCGTGGGCTGGGCTGGTCAGGCGTGGGGTGGGCTGGTCAGGCGTGGGCTGGGCTGGTCAGGTGTGGGCTGGGCTGG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1541473;END=1541545;PERIOD=5;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1541888 STR_713 TGGGCTGGGCTGGGCTGGTCAGGCGTGGGCTGGGCTGG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1541888;END=1541925;PERIOD=5;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1542722 STR_714 TTTTTTTTTTTTTTTTTTTTGAG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1542722;END=1542741;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1543410 STR_715 ATATATATATATAATATATGTACTATATATTATATATGTATATATATAATATGTATTATATATAATGTATGTATAATATATATAATTATATATATAT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1543410;END=1543506;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=10;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:10:0:0:1:5.00|5.00:0|0:.:0.0:.:0.0:.:. +1 1544112 STR_716 AATAATAATAATAATA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1544112;END=1544127;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=26;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:26:0:0:2:13.00|13.00:0|0:.:0.0:.:0.0:-28|1;0|21:0|19 +1 1544577 STR_717 AAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1544577;END=1544596;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1544890 STR_718 AAAAAAAAAAAAAAAAAGGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1544890;END=1544906;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1545200 STR_719 AAAAAAAAAAAAAGAAAAGAAAAAAGAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1545200;END=1545231;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=4;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:35:0:4:3:17.50|17.50:0|0:.:0.0:.:0.0:-1|1;0|12;1|2:-1|1;0|8;1|1 +1 1546948 STR_720 TTCTTTTTTTTTTTTTTTTTTTTTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1546951;END=1546971;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1547904 STR_721 TTTTGTTTTTTCTTTTTCTTTTCTTTTTTTTTTTTTGTTTTTTTTGTTTTTGAG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1547904;END=1547954;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1548239 STR_722 TTTTTTTTCTTTTTTTTTTTTTTT TTTTTTTTCTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1548239;END=1548262;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=1;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:35:0:1:3:19.85|15.15:0|0:3.6:-0.44:19:-0.21:-18|1;-3|1;-1|4;0|9;1|1:-1|4;0|7;1|1 +1 1548541 STR_723 TTTTTTTTTTTTTTTTTTTGA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1548541;END=1548559;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1548711 STR_724 TTTTTTTTTTTT TTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1;START=1548711;END=1548722;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=34;DSNP=0;DSTUTTER=3;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|1:1.0:0.5:34:0:3:4:14.55|19.45:0|0:7.05:-0.37:25:0.0:-7|1;-2|1;-1|3;0|7;1|14:-2|1;-1|2;0|7;1|12 +1 1549112 STR_725 CAAATACAAAACAAAACAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1549112;END=1549132;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=51;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:51:0:0:2:23.52|27.48:0|0:.:0.0:.:0.0:-21|1;-1|1;0|27:0|27 +1 1553481 STR_726 GCTGGGCTGTGGCTGTGGCTGT GCTGGGCTGTGGCTGTGACTGT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1553481;END=1553502;PERIOD=6;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=50;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:50:0:0:2:28.04|21.96:0|0:62.66:-0.35:44:0.0:0|37:0|37 +1 1561897 STR_727 GGGGTCGGGGTCGGGGCCGGGG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1561897;END=1561918;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=56;DSNP=0;DSTUTTER=1;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:56:0:1:4:28.00|28.00:0|0:.:0.0:.:0.0:-30|1;-1|1;0|32;2|1:0|33 +1 1577063 STR_728 CTCCTCCTCCTCCTCTTCCTCTTCCTCCTCCTCCTCCTC CTCCTCCTCCTCCTCTTCCTCTTCCTCCTC . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-9;START=1577063;END=1577101;PERIOD=3;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=56;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-9:1.0:0.5:56:0:1:2:43.99|12.01:0|0:14.15:-6.03:44:-0.42:-26|1;-9|5;0|29:-9|5;0|26 +1 1577124 STR_729 TCCTCCTCCTCCTCTTCCTCCTCCTCCTC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1577124;END=1577152;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=51;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:51:0:0:2:25.50|25.50:0|0:.:0.0:.:0.0:0|32:0|31 +1 1580356 STR_730 AAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1580356;END=1580369;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1585467 STR_731 CAACAACAACAACAACAAAACAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1585467;END=1585489;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:31:0:0:2:15.50|15.50:0|0:.:0.0:.:0.0:0|24:0|23 +1 1588196 STR_732 AAAAACAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1588196;END=1588210;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=32;DSNP=0;DSTUTTER=0;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:32:0:0:4:16.00|16.00:0|0:.:0.0:.:0.0:-9|1;0|27:0|25 +1 1590380 STR_733 CGCCGCCGCCGCTGCCGCCGCCGCCGCCGCCG CGCCGCCGCCGCTGCCGCCGCCGCCGCCGCCGCCG . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=3;START=1590380;END=1590411;PERIOD=3;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=42;DSNP=0;DSTUTTER=1;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|3:0.98:0.49:42:0:1:0:12.43|29.57:0|0:1.71:-2.68:32:-0.71:-2|1;0|7;3|17;6|1:0|7;3|17;6|1 +1 1591691 STR_734 TTTTTTTATTTTTATTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1591691;END=1591711;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=40;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:40:0:0:2:20.00|20.00:0|0:.:0.0:.:0.0:0|30:0|25 +1 1591880 STR_735 TTTTTTTTTTATTTTC TTTTTTTTTTATTTTG . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1591880;END=1591894;PERIOD=1;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=20;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:0|0:1.0:1.0:20:0:0:1:10.00|10.00:0|0:3.91:0.0:.:0.0:-2|1;0|14:0|14 +1 1592073 STR_736 TTTTTATTTTTATTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1592073;END=1592093;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=32;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:32:0:0:1:16.00|16.00:0|0:.:0.0:.:0.0:0|15:0|15 +1 1598691 STR_737 AAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1598691;END=1598702;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1598856 STR_738 AAATAAATAAATAAAATAAAATACATAAACAAATAAAT AAATAAATAAATAAAATAAAATAAAATACATAAACAAATAAAT,AAATAAATAAAATAAAATAAAATAAAATACATAAACAAATAAAT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=5,6;START=1598856;END=1598893;PERIOD=4;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=49;DSNP=0;DSTUTTER=0;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:5|6:1.0:0.5:49:0:0:4:27.50|21.50:0|0:101.01:-0.49:26:0.0:-57|1;-17|1;-15|1;-7|1;-2|1;1|1;5|6;6|4:5|6;6|4 +1 1599296 STR_739 TTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1599296;END=1599308;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1600090 STR_740 TTTGTTTGTTTGTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1600090;END=1600104;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=54;DSNP=0;DSTUTTER=1;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:54:0:1:4:27.00|27.00:0|0:.:0.0:.:0.0:-16|1;-2|2;0|41:-4|1;0|41 +1 1600426 STR_741 TCTCCAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1600431;END=1600447;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1600797 STR_742 AAAAATAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1600797;END=1600813;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=53;DSNP=0;DSTUTTER=3;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:53:0:3:3:26.50|26.50:0|0:.:0.0:.:0.0:-5|1;-1|3;0|31:-1|3;0|27 +1 1600882 STR_743 AAACAAAACAAACAAACAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1600882;END=1600900;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=41;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:41:0:0:1:20.50|20.50:0|0:.:0.0:.:0.0:0|34:0|34 +1 1601863 STR_744 TTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1601863;END=1601878;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1605401 STR_745 AAAAAAGAAAAAAAAAAAAAAGAAAAAAAAAA AAAAAAGAAAAAAAAAAAAAGAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1605401;END=1605432;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=20;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:20:0:0:2:10.08|9.92:0|0:5.69:0.0:12:0.0:-1|3;0|4:-1|3;0|2 +1 1606064 STR_746 AAAAAAAACAAAAAAAAAAAAACAAAAAAAAA AAAAAAAACAAAAAAAAAAAAAACAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1;START=1606064;END=1606095;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=21;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|1:1.0:0.5:21:0:1:1:11.43|9.57:0|0:5.11:-0.11:12:-0.62:-1|1;0|2;1|5:-1|1;0|1;1|5 +1 1608918 STR_747 TTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1608918;END=1608934;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=14;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:14:0:1:2:7.00|7.00:0|0:.:0.0:.:0.0:0|6:0|3 +1 1609094 STR_748 TTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1609094;END=1609106;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1611270 STR_749 AAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-6;START=1611270;END=1611289;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=25;DSNP=0;DSTUTTER=1;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-6:1.0:0.5:25:0:1:3:16.44|8.56:0|0:14.59:-1.93:11:0.0:-6|1;-3|1;-2|1;0|7:-6|1;-3|1;0|3 +1 1611567 STR_750 AAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1611567;END=1611578;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=24;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:24:0:0:1:12.00|12.00:0|0:.:0.0:.:0.0:0|16:0|16 +1 1612245 STR_751 TTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1612245;END=1612260;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1612804 STR_752 TTTTGTTTTTTTTTGTATTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1612804;END=1612827;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=39;DSNP=0;DSTUTTER=1;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:39:0:1:4:19.50|19.50:0|0:.:0.0:.:0.0:-17|1;0|19;6|1:0|15 +1 1613428 STR_753 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1613428;END=1613479;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1616229 STR_754 AAAAAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1616229;END=1616253;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1616548 STR_755 AAAAAAAAAAAAAAAA AAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1616548;END=1616563;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=28;DSNP=0;DSTUTTER=2;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:28:0:2:4:17.34|10.66:0|0:6.1:-0.64:25:-0.18:-18|1;-1|8;0|12;1|2:-1|7;0|8;1|2 +1 1616850 STR_756 TCAGAAAAAAAAAAAAAAAAAAGAAAAGGAAAAAGAAA TAAGAAAAAAAAAAAAAAAAAAAGAAAAGGAAAAAGAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1;START=1616855;END=1616887;PERIOD=6;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=39;DSNP=0;DSTUTTER=0;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|1:1.0:0.5:39:0:0:4:23.50|15.50:0|0:54.96:-0.77:26:-0.37:-40|1;-13|1;0|5;1|4:0|4;1|3 +1 1617746 STR_757 TTTTCTTTTTTTTTCTTTTTTTTTTTTTTTTTT TTTTCTTTTTTTTTCTTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-3;START=1617746;END=1617778;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=30;DSNP=0;DSTUTTER=3;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-3:1.0:0.5:30:0:3:4:14.72|15.28:0|0:8.07:0.0:10:0.0:-3|3;11|1:-3|1 +1 1617913 STR_758 AAAAATAAAAATAAAAATGAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1617913;END=1617936;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=46;DSNP=0;DSTUTTER=1;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:46:0:1:5:23.00|23.00:0|0:.:0.0:.:0.0:-23|1;-8|1;-2|1;0|21:0|22 +1 1618499 STR_759 ACAAATAAATAAATAAATAAA ATAAATAAATAAATAAATAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1618501;END=1618519;PERIOD=4;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=17;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:17:0:0:0:9.53|7.47:0|0:13.36:-0.1:14:0.0:0|7:0|6 +1 1619174 STR_760 AAAAAAAAAAAAAAAA AAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-2;START=1619174;END=1619189;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=45;DSNP=0;DSTUTTER=3;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-2:1.0:0.5:45:0:3:4:23.88|21.12:0|0:25.18:-0.07:28:-0.94:-11|1;-2|11;-1|2;0|8;1|1:-2|9;-1|2;0|6 +1 1621426 STR_761 AAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1621426;END=1621441;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1621879 STR_762 AAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1621879;END=1621891;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1622179 STR_763 GTAAAGAAAAAAAAAAAACAAAA GAAAAGAAAAAAAAAAAACAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1622185;END=1622201;PERIOD=1;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=10;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:0|0:0.98:0.98:10:0:0:0:5.00|5.00:0|0:1.8:0.0:.:0.0:0|3:0|3 +1 1623506 STR_764 AAAAAAAAAAAGAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1623506;END=1623521;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=33;DSNP=0;DSTUTTER=3;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:33:0:3:2:16.50|16.50:0|0:.:0.0:.:0.0:-12|1;-1|1;0|20;1|2:-1|1;0|16;1|1 +1 1623571 STR_765 TGTTTTGTTTTGTGTTTTTTTGTTGTTGTTGTT TGTTTTGTTTTGTGTTTTTCTGTTGTTGTTGTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1623571;END=1623603;PERIOD=3;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=44;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:44:0:1:1:28.51|15.49:0|0:39.27:-1.33:37:-0.31:0|28:0|27 +1 1624340 STR_766 TTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=3;START=1624340;END=1624355;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=20;DSNP=0;DSTUTTER=3;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|3:1.0:0.5:20:0:3:2:9.07|10.93:0|0:16.13:-0.11:12:0.0:-22|1;-21|1;-10|1;0|7;1|1;2|1;3|1;4|1:0|5;1|1;3|1 +1 1625733 STR_767 ATAAATAAATAAATAAATAAATA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1625733;END=1625755;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=34;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:34:0:0:0:17.00|17.00:0|0:.:0.0:.:0.0:0|20:0|20 +1 1626129 STR_768 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1626129;END=1626163;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=20;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:20:0:0:3:10.00|10.00:0|0:.:0.0:.:0.0:33|1:. +1 1626445 STR_769 AAAAAAAAAAAAAAAAAAAAAAGGAAG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1626445;END=1626466;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1628267 STR_770 TGTGTGTGTATCTGTGTGAGTCTGTGTGTGTGGTGTGTTTGTGTCTGAGTGTGTGGTGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1628267;END=1628325;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1628362 STR_771 TGTGTGATGTGTCTGTGTGTGTGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1628362;END=1628385;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1628439 STR_772 TGTGTGGTGTGTCTGTTTGTGTGTGTGTG TGTGTGGTGTGTCTTTTTGTGTGTGTGTG . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1628439;END=1628467;PERIOD=2;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=69;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:69:0:0:2:52.50|16.50:0|0:35.67:-5.32:62:0.0:0|49;20|1:0|47 +1 1640273 STR_773 CTCCTCCTCCTCCTCTTCCTCTTCCTCCTCCTCCTCCTC CTCCTCCTCCTCCTCTTCCTCTTCCTCCTC . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-9;START=1640273;END=1640311;PERIOD=3;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=43;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-9:1.0:0.5:43:0:0:1:29.00|14.00:0|0:37.66:-1.7:37:0.0:-9|8;0|19:-9|8;0|18 +1 1640334 STR_774 TCCTCCTCCTCCTCTTCCTCCTCCTCCTC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1640334;END=1640362;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=53;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:53:0:0:3:26.50|26.50:0|0:.:0.0:.:0.0:-15|1;0|29:0|28 +1 1643571 STR_775 AAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1643571;END=1643585;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1648249 STR_777 ATCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1648254;END=1648291;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1648356 STR_778 ATCTTTTTTTTTTTTTTTTTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1648359;END=1648375;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1650078 STR_779 TTTTTTTTTTTTTT TTTTTTTTTTTTTTT,TTTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1,2;START=1650078;END=1650091;PERIOD=1;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=26;DSNP=0;DSTUTTER=3;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 2|1:2|1:1.0:0.5:26:0:3:3:10.86|15.14:0|0:7.09:-0.42:21:-0.74:-1|1;0|4;1|9;2|6:-1|1;0|1;1|7;2|7 +1 1651055 STR_780 TTTTTTTTTTTTTTTTTTTAGAC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1651055;END=1651073;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1651508 STR_781 TTATTTATTTAATTTAATTTTATTTATTTATTTATTTTATTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1651508;END=1651549;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=51;DSNP=0;DSTUTTER=0;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:51:0:0:5:25.50|25.50:0|0:.:0.0:.:0.0:-39|1;-36|1;-24|1;-9|1;0|16:0|15 +1 1652637 STR_782 AAAAAAAAAAA AAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1652637;END=1652647;PERIOD=1;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=37;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:-1|-1:1.0:1.0:37:0:1:1:18.50|18.50:0|0:6.82:0.0:.:0.0:-32|1;-1|27;0|1:-1|28;0|1 +1 1653546 STR_783 AAAAACAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1653546;END=1653560;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:31:0:1:2:15.50|15.50:0|0:.:0.0:.:0.0:-3|1;0|20;1|1:0|19 +1 1654675 STR_784 AAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1654675;END=1654693;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1654928 STR_785 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAGAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-15;START=1654928;END=1654962;PERIOD=1;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=24;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:-15|-15:1.0:1.0:24:0:1:1:12.00|12.00:0|0:5.12:0.0:.:0.0:-15|10:-15|9 +1 1656980 STR_786 TTTTTTTATTTTTATTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1656980;END=1657000;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:35:0:0:1:14.50|20.50:0|0:.:0.0:.:0.0:-9|1;0|17:0|14 +1 1657169 STR_787 TTTTTTTTTTATTTTC TTTTTTTTTTATTTTG . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1657169;END=1657183;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=41;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:41:0:0:1:16.52|24.48:0|0:35.77:-0.59:38:-0.49:0|33:0|29 +1 1657362 STR_788 TTTTTATTTTTATTTTTTTTT TTTTTATTTTTATTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1657362;END=1657382;PERIOD=6;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:35:0:0:3:29.51|5.49:0|0:6.64:-6.09:26:-0.37:-1|1;0|15;3|1:-1|1;0|17 +1 1662820 STR_789 AAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=2;START=1662820;END=1662836;PERIOD=1;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=21;DSNP=0;DSTUTTER=2;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:2|2:0.95:0.95:21:0:2:3:10.50|10.50:0|0:1.32:0.0:.:0.0:0|5;1|2;2|3:1|2;2|3 +1 1663344 STR_790 AAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1663344;END=1663362;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1663497 STR_791 AAAAGTAAAATAAAATAAAATAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1663497;END=1663519;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=26;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:26:0:0:0:13.00|13.00:0|0:.:0.0:.:0.0:0|15:0|15 +1 1663681 STR_792 AAAAAAAAAAAAAAAGTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1663681;END=1663708;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1664332 STR_793 TTTTTTTTTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1664332;END=1664354;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=27;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:27:0:2:2:13.44|13.56:0|0:3.63:-0.0:13:-0.23:-23|1;-2|2;-1|2;0|3:-2|2;-1|2;0|3 +1 1665647 STR_794 TTTTTTTGTTTTATTTATTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1665647;END=1665671;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=48;DSNP=0;DSTUTTER=1;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:48:0:1:5:29.00|19.00:0|0:.:0.0:.:0.0:-7|1;-3|2;0|25:0|24 +1 1667937 STR_795 AAAAAAAGAAAAAAAGAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1667937;END=1667957;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=24;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:24:0:0:2:12.00|12.00:0|0:.:0.0:.:0.0:-9|1;0|18:0|17 +1 1668241 STR_796 AAAAAAAAAAAAAAAAAAGAAAGAAAGAAAGAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1668241;END=1668285;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1668920 STR_797 AAAAAAAACAAAAGAAAAAAAACAAAAAAAAA AAAAAAAACAAAAGAAAAAAAACCAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1668920;END=1668951;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=58;DSNP=0;DSTUTTER=0;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:58:0:0:4:31.51|26.49:0|0:75.65:-0.24:51:-0.25:-1|1;0|39:0|32 +1 1672526 STR_798 TTTTCTTTTTTTTTTTT TTTTCTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1672526;END=1672542;PERIOD=1;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=23;DSNP=0;DSTUTTER=2;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:-1|-1:1.0:1.0:23:0:2:1:11.50|11.50:0|0:4.86:0.0:.:0.0:-3|1;-1|15:-3|1;-1|12 +1 1672678 STR_799 AAAAATAAAAATAAAAATGAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1672678;END=1672701;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=42;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:42:0:0:3:14.02|27.98:0|0:.:0.0:.:0.0:0|31:0|31 +1 1673559 STR_800 AAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1673559;END=1673576;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=22;DSNP=0;DSTUTTER=2;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:22:0:2:3:11.92|10.08:0|0:2.59:-0.0:11:-0.26:-2|3;-1|5;0|3:-1|4;0|3;1|1 +1 1673872 STR_801 AAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAA,AAAAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1,1;START=1673872;END=1673888;PERIOD=1;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=26;DSNP=0;DSTUTTER=2;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:-1|1:1.0:0.5:26:0:2:3:12.29|13.71:0|0:10.55:-0.08:20:0.0:-1|7;0|2;1|8:-1|5;1|8 +1 1675154 STR_802 AAAAAAAAAAAAA AAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1;START=1675154;END=1675166;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=29;DSNP=0;DSTUTTER=4;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|1:0.99:0.5:29:0:4:3:17.81|11.19:0|0:2.2:-0.78:19:-0.2:-1|3;0|9;1|5;2|1:-1|3;0|7;1|2;2|1 +1 1675448 STR_803 CAAAAAGAAAAGAAAAAAAAAAAACAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1675449;END=1675476;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1676781 STR_804 AAAAAAAAAAAGAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1676781;END=1676796;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=29;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:29:0:2:2:14.50|14.50:0|0:.:0.0:.:0.0:0|17:0|14 +1 1676846 STR_805 TGTTTTGTTTTGTGTTTTTTTGTTGTTGTTGTT TGTTTTGTTTTGTGTTTTTCTGTTGTTGTTGTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1676846;END=1676878;PERIOD=3;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=36;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:36:0:0:2:25.95|10.05:0|0:9.69:-2.43:28:-0.45:-6|1;0|19;1|1:0|18 +1 1677615 STR_806 TTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1677615;END=1677634;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1678681 STR_807 AAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1678681;END=1678695;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1680971 STR_808 TGTGTGTATCTGTGTGAGTCTGTGTGTGTGGTGTGTTTGTGTCTGAGTGTGTGGTGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1680971;END=1681027;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1681062 STR_809 TGTGTGGTGTGTCTGTTTGTGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1681062;END=1681090;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1684348 STR_810 CCTCCTCCTCCTCCTCCTCCTCCTCCTC CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=3;START=1684348;END=1684375;PERIOD=3;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=55;DSNP=0;DSTUTTER=2;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|3:1.0:0.5:55:0:2:3:28.18|26.82:0|0:12.74:-0.06:38:-0.12:-8|1;-3|1;0|18;3|12;6|2;20|1:0|18;3|11;6|2 +1 1684562 STR_811 CCCTTCCTCCCTCCCTCCCT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1684562;END=1684581;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=38;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:38:0:0:0:19.00|19.00:0|0:.:0.0:.:0.0:0|23:0|23 +1 1688819 STR_812 AAAATAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1688819;END=1688834;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=26;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:26:0:2:2:13.00|13.00:0|0:.:0.0:.:0.0:-9|1;-1|2;0|17:-1|1;0|16 +1 1694199 STR_813 AATGAATGAATGAATGAATGAATGAATGAATGAAT AATGAATGAATGAATGAATGAATGAATGAAT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-4;START=1694199;END=1694233;PERIOD=4;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=59;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-4:1.0:0.5:59:0:0:2:31.73|27.27:0|0:18.35:-0.18:48:0.0:-4|15;0|17:-4|15;0|17 +1 1696898 STR_815 AAATAAATAATGTAAATAAAGTAAATAAATA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1696898;END=1696928;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=27;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:27:0:0:1:13.48|13.52:0|0:.:0.0:.:0.0:0|18:0|18 +1 1697850 STR_816 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1697850;END=1697889;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1698117 STR_817 CTTTTTCTTTTTCTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1698117;END=1698139;PERIOD=6;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1698361 STR_818 TTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1698361;END=1698371;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=43;DSNP=0;DSTUTTER=2;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:43:0:2:4:21.50|21.50:0|0:.:0.0:.:0.0:0|36;1|2:0|34;1|2 +1 1699611 STR_819 AAAAAAAAAAAAAAAAGAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1699611;END=1699633;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1699814 STR_820 AAAACAAAAACAAAAACAAAACCAAAACAAAAACA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1699814;END=1699848;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=33;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:33:0:0:2:16.50|16.50:0|0:.:0.0:.:0.0:-1|1;0|15:0|15 +1 1700990 STR_821 AAAAAAAAAACAAAAAACAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1700990;END=1701013;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=25;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:25:0:0:0:12.50|12.50:0|0:.:0.0:.:0.0:0|15:0|15 +1 1701172 STR_822 AAAAGAAAAAAAAAAAAAGAAAAAA AAAAGAAAAAAAAAAAAGAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1701172;END=1701196;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=37;DSNP=0;DSTUTTER=2;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:37:0:2:5:24.80|12.20:0|0:2.47:-1.54:26:-0.73:-26|1;-7|1;-2|2;-1|6;0|16:-2|1;-1|5;0|14 +1 1701409 STR_823 AAAACAAAAACAAAAACAAAAACAAAAACAAAAACAAAAACAAAAA AAAACAAAAACAAAAACAAAAACAAAAACAAAAA,AAAACAAAAACAAAAACAAAAACAAAAACAAAAACAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-12,-6;START=1701409;END=1701454;PERIOD=6;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=28;DSNP=0;DSTUTTER=1;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:-12|-6:0.99:0.5:28:0:1:0:11.71|16.29:0|0:2.15:-0.52:15:0.0:-18|1;-12|3;-6|7:-18|1;-12|3;-6|8 +1 1701616 STR_824 AAAAAGAAAAAAGAAAAAAAGAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1701616;END=1701645;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=36;DSNP=0;DSTUTTER=0;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:36:0:0:4:18.00|18.00:0|0:.:0.0:.:0.0:-25|1;-5|1;0|11;3|1:0|9 +1 1702173 STR_825 AATAATAATAATAATAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1702173;END=1702189;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=29;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:29:0:0:2:14.50|14.50:0|0:.:0.0:.:0.0:-23|1;0|19:0|17 +1 1703242 STR_827 TTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1703242;END=1703254;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=50;DSNP=0;DSTUTTER=3;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:50:0:3:1:25.00|25.00:0|0:.:0.0:.:0.0:-1|2;0|39:-1|3;0|31 +1 1703413 STR_828 TTTTTTTTTTTTTTT TTTTTTTTTTTT,TTTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-3,1;START=1703413;END=1703427;PERIOD=1;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=33;DSNP=0;DSTUTTER=4;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:-3|1:1.0:0.5:33:0:4:1:10.50|22.50:0|0:4.84:-2.12:18:0.0:-10|1;-3|2;-2|2;-1|1;0|4;1|8:-3|2;-2|1;-1|1;0|2;1|8 +1 1703600 STR_829 TTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1703600;END=1703613;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=41;DSNP=0;DSTUTTER=4;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:41:0:4:2:20.50|20.50:0|0:.:0.0:.:0.0:-2|1;-1|1;0|29;1|1;2|1:-2|1;-1|1;0|26;1|1;2|1 +1 1704481 STR_830 AAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1704481;END=1704497;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1705116 STR_831 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAGAGAGAGAGAGA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1705116;END=1705182;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1705591 STR_832 TGTGTGTGTGTGTATATATATACACACACACACACACATATATATATAT TGTGTGTGTGTGTGTATATATACACACACACACACACATATATATATAT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1705591;END=1705639;PERIOD=2;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=24;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:24:0:0:0:8.04|15.96:0|0:17.15:-0.94:20:-0.2:0|11:0|9 +1 1706552 STR_833 AAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1706552;END=1706563;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=28;DSNP=0;DSTUTTER=2;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:28:0:2:3:14.00|14.00:0|0:.:0.0:.:0.0:-1|3;0|19:-1|1;0|15 +1 1706700 STR_834 CACACACACACA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1706700;END=1706711;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:31:0:0:1:15.50|15.50:0|0:.:0.0:.:0.0:0|26:0|25 +1 1707211 STR_835 CACACACACACA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1707211;END=1707222;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=34;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:34:0:0:0:17.00|17.00:0|0:.:0.0:.:0.0:0|26:0|24 +1 1707901 STR_836 AAACAAACAAACAAA AAACAAACAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-4;START=1707901;END=1707915;PERIOD=4;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=38;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-4:1.0:0.5:38:0:0:1:20.72|17.28:0|0:11.03:-0.22:34:-0.78:-4|15;0|16:-4|15;0|15 +1 1708212 STR_837 AAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-2;START=1708212;END=1708233;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=27;DSNP=0;DSTUTTER=2;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-2:0.99:0.5:27:0:2:4:9.02|17.98:0|0:2.15:-1.65:13:0.0:-4|2;-3|2;-2|6;0|3;28|1:-4|1;-3|1;-2|6;0|1 +1 1709786 STR_838 CCGCCGCCGCGCCGCCGCCAGCCG . . . 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INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1717243;END=1717254;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1719468 STR_845 AAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1719468;END=1719485;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=3;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:0.93:0.47:35:0:3:4:22.46|12.54:0|0:1.15:-1.46:23:0.0:-16|1;-2|1;-1|4;0|15;1|2:-1|4;0|10;1|1 +1 1721135 STR_846 AAAAAAAAAAAAAAAA . . . 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INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1724136;END=1724160;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1724504 STR_849 AAAAAAAAAAAAA AAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1;START=1724504;END=1724516;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=24;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|1:1.0:0.5:24:0:0:1:10.58|13.42:0|0:3.76:-0.22:15:-0.5:-4|1;0|6;1|8;21|1:0|5;1|9 +1 1728885 STR_850 TTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1728885;END=1728895;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=32;DSNP=0;DSTUTTER=2;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:32:0:2:0:16.00|16.00:0|0:.:0.0:.:0.0:-1|2;0|19:-1|2;0|16 +1 1730365 STR_851 TTTTTTTTTTTTTT TTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1;START=1730365;END=1730378;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=40;DSNP=0;DSTUTTER=4;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|1:1.0:0.5:40:0:4:5:20.81|19.19:0|0:8.56:-0.07:28:-0.0:-8|1;-5|1;-2|1;-1|3;0|13;1|8:-2|1;-1|3;0|10;1|6 +1 1730683 STR_852 TGTGTGTGTGTGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1730683;END=1730695;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=46;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:46:0:0:2:23.00|23.00:0|0:.:0.0:.:0.0:0|36:0|32 +1 1732193 STR_853 AAAAAAAAAAAAAAAAAAGAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1732193;END=1732216;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1734203 STR_854 AAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=2;START=1734203;END=1734218;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=22;DSNP=0;DSTUTTER=3;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|2:1.0:0.5:22:0:3:2:9.54|12.46:0|0:6.92:-0.26:11:-0.26:-15|1;-2|1;-1|1;0|6;1|1;2|3:-1|1;0|2;1|1;2|3 +1 1735417 STR_855 TCTTTAAAAAAAAAAAAAAAAAAAAAGAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1735422;END=1735450;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1735746 STR_856 TAATTAATTAATTAATTAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1735746;END=1735764;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=24;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:24:0:0:0:12.00|12.00:0|0:.:0.0:.:0.0:0|13:0|13 +1 1738413 STR_857 AAGAAAGAAAGAAAGAAAGGAAAG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1738413;END=1738436;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=46;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:46:0:0:2:23.00|23.00:0|0:.:0.0:.:0.0:-7|1;0|32:0|32 +1 1738903 STR_858 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1738903;END=1738932;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=16;DSNP=0;DSTUTTER=2;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:16:0:2:1:8.00|8.00:0|0:.:0.0:.:0.0:-31|1;-9|1;-1|1:-1|1 +1 1739138 STR_859 TTTTTTCTTTTTTTCTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1739138;END=1739164;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=22;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:22:0:0:2:11.00|11.00:0|0:.:0.0:.:0.0:0|10:0|6 +1 1740064 STR_860 GTTTTTTGTTTGTTTGTTTTTGTTTGTTTGTTTGTTTG GTTTTTTGTTTGTTTGTTTTTGTTTGTTTGTTTG . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-4;START=1740064;END=1740101;PERIOD=4;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=42;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-4:1.0:0.5:42:0:1:2:17.64|24.36:0|0:11.14:-0.58:29:-0.16:-15|1;-4|11;0|6:-4|11;0|6 +1 1740629 STR_861 TTTTTTTTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1740629;END=1740650;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=32;DSNP=0;DSTUTTER=4;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:0.97:0.48:32:0:4:0:10.07|21.93:0|0:1.45:-1.97:23:-0.94:-4|1;-2|2;-1|9;0|5:-4|1;-2|2;-1|8;0|3 +1 1741515 STR_862 ATATATATATATAT AAATATATATATAT,ATATATATATGTAT . . 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INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1742057;END=1742071;PERIOD=4;AN=0;REFAC=0;NSKIP=1;NFILT=0;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1743505 STR_865 AAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1743505;END=1743515;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=24;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:24:0:2:2:12.00|12.00:0|0:.:0.0:.:0.0:0|17;1|1:0|14;1|1 +1 1743780 STR_866 AAAAAAAAAAAA . . . 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INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1748084;END=1748105;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=32;DSNP=0;DSTUTTER=2;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:32:0:2:1:15.98|16.02:0|0:5.01:0.0:16:-0.0:-2|2;-1|6;0|3:-2|2;-1|6;0|3 +1 1749739 STR_873 TCTATTAAAAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1749745;END=1749768;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1750312 STR_874 AAAATAATAATAAAATAAAATAAA . . . 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INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1750962;END=1750972;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1751145 STR_877 TTTTTTTTTTTTTTTT TTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1751145;END=1751160;PERIOD=1;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=42;DSNP=0;DSTUTTER=6;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:-1|-1:1.0:1.0:42:0:6:5:21.00|21.00:0|0:3.24:0.0:.:0.0:-16|1;-2|3;-1|20;0|1:-2|3;-1|18 +1 1751796 STR_878 AAAAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1751796;END=1751819;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=19;DSNP=0;DSTUTTER=2;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:19:0:2:1:7.52|11.48:0|0:.:0.0:.:0.0:-21|1;0|1;1|1:-1|1;1|1 +1 1753740 STR_879 TTTTTTTTTTTTTTTTTTTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1753740;END=1753758;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1753912 STR_880 TTTTTTTTGTATTTTTTTTCTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1753912;END=1753935;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=27;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:27:0:0:3:13.50|13.50:0|0:.:0.0:.:0.0:-28|1;0|12:0|11 +1 1754682 STR_881 AAAAAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1754682;END=1754706;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=17;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:17:0:1:2:8.50|8.50:0|0:.:0.0:.:0.0:-47|1;-13|1;0|3:0|2 +1 1756018 STR_882 TTTTTTTTTTATTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1756018;END=1756033;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=34;DSNP=0;DSTUTTER=3;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:34:0:3:2:17.00|17.00:0|0:.:0.0:.:0.0:-1|1;0|19;1|2;5|1:-1|1;0|17;1|2 +1 1757304 STR_883 AAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1757304;END=1757317;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=14;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:14:0:1:2:7.00|7.00:0|0:.:0.0:.:0.0:-1|1;0|7:0|5 +1 1760314 STR_884 ACACACACACATACACACATACACACACACACACACACA ACACACACACATACACACATACACACACACACACACACACA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=2;START=1760314;END=1760352;PERIOD=2;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=43;DSNP=0;DSTUTTER=0;DFLANKINDEL=6 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|2:1.0:0.5:43:0:0:6:21.96|21.04:0|0:14.69:0.0:35:-0.31:-11|1;-3|1;0|14;2|10;25|1:0|12;2|10 +1 1760492 STR_885 TTTTCTTTTCTTTTCTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1760492;END=1760510;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=27;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:27:0:0:1:13.50|13.50:0|0:.:0.0:.:0.0:-13|1;0|18:0|18 +1 1761178 STR_886 TTTTTTCTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1761178;END=1761194;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=2;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:35:0:2:1:17.50|17.50:0|0:.:0.0:.:0.0:-1|2;0|19:-1|2;0|18 +1 1761705 STR_887 TTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1761705;END=1761717;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=28;DSNP=0;DSTUTTER=4;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:28:0:4:2:14.00|14.00:0|0:.:0.0:.:0.0:-15|1;-2|1;-1|3;0|15;1|1:-1|3;0|12;1|1 +1 1763503 STR_888 AAAAAAAAAAAAAAAAGAAAAGAAAAAAGAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1763503;END=1763536;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1766107 STR_889 TTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1766107;END=1766125;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1767550 STR_891 AAAAAACAAAAAAAAC AAAAAACAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1767550;END=1767564;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=22;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:22:0:0:1:13.78|8.22:0|0:27.18:-0.42:21:-0.17:0|19:0|17 +1 1767827 STR_892 TTTTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1767827;END=1767848;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1768296 STR_893 TTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1768296;END=1768315;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1768695 STR_894 TTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1768695;END=1768711;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1768993 STR_895 TTTTTGTTTTTGTTTTTGTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1768993;END=1769015;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=40;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:40:0:0:2:20.00|20.00:0|0:.:0.0:.:0.0:-16|1;0|22:0|21 +1 1769835 STR_896 TTTTGTTTTGTTTTGTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1769835;END=1769853;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=38;DSNP=0;DSTUTTER=0;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:38:0:0:4:19.00|19.00:0|0:.:0.0:.:0.0:0|29:0|28 +1 1769875 STR_897 TTTTTTTTCTTTTCTTTTTTTTTTTTT TTTTTTTTCTTTTCTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1;START=1769875;END=1769901;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=42;DSNP=0;DSTUTTER=2;DFLANKINDEL=6 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|1:1.0:0.5:42:0:2:6:21.81|20.19:0|0:12.0:-0.08:24:-0.17:-12|1;-4|1;0|6;1|6:-2|1;0|4;1|5 +1 1771132 STR_898 AAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1771132;END=1771142;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=40;DSNP=0;DSTUTTER=4;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:40:0:4:1:20.00|20.00:0|0:.:0.0:.:0.0:-1|2;0|31;1|2:-1|2;0|29;1|2 +1 1771483 STR_899 AAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1771483;END=1771493;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=39;DSNP=0;DSTUTTER=3;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:39:0:3:2:19.50|19.50:0|0:.:0.0:.:0.0:-40|1;0|32;1|2:0|31;1|2 +1 1771668 STR_900 AAAAGAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1771668;END=1771686;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1771970 STR_901 ACACACACGCACACACACACACAGACACAACAC ACACACACGCACACACACACACGCACACACACACACAGACACAACAC . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=14;START=1771970;END=1772002;PERIOD=2;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=52;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|14:1.0:0.5:52:0:0:1:44.47|7.53:0|0:20.31:-9.11:41:0.0:0|34;14|2:0|33;14|2 +1 1773874 STR_902 AAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1773874;END=1773889;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=45;DSNP=0;DSTUTTER=6;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:45:0:6:5:22.50|22.50:0|0:.:0.0:.:0.0:-2|1;-1|1;0|19;1|3:-2|1;-1|1;0|13;1|2 +1 1774423 STR_903 GTGTGTGTGTGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1774423;END=1774434;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=39;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:39:0:0:3:19.50|19.50:0|0:.:0.0:.:0.0:-1|1;0|34:0|32 +1 1774833 STR_904 ATATATATATAT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1774833;END=1774844;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=21;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:21:0:0:1:7.52|13.48:0|0:.:0.0:.:0.0:-5|1;0|13:0|13 +1 1775634 STR_905 AAAAAAAAATTAAAATAAAATAAAAATAAATTTAAAAAATAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1775634;END=1775678;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=32;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:32:0:0:3:16.00|16.00:0|0:.:0.0:.:0.0:0|9:0|9 +1 1775831 STR_906 AAAAAAAAAAAAAAGAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1775831;END=1775850;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1776589 STR_907 CAACCAACCAACCAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1776589;END=1776603;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=22;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:22:0:0:0:11.00|11.00:0|0:.:0.0:.:0.0:0|18:0|18 +1 1777018 STR_908 AATAATAATAAAATAAAATAAAAATAATAATAATAAT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1777018;END=1777054;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:31:0:0:2:15.50|15.50:0|0:.:0.0:.:0.0:-42|1;-34|1;0|13:0|13 +1 1777264 STR_909 ACACACACACACACACACACACACACACACACACACACACACACACAC ACACACACACACACACAC,ACACACACACACACACACACACACACACACACACACACACACACAC . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-30,-2;START=1777264;END=1777311;PERIOD=2;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=34;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:-30|-2:1.0:0.5:34:0:0:2:16.48|17.52:0|0:7.85:-0.0:25:-0.16:-40|1;-30|12;-2|6:-30|10;-2|6 +1 1777652 STR_910 AAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1777652;END=1777662;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=25;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:25:0:0:1:12.50|12.50:0|0:.:0.0:.:0.0:0|20:0|19 +1 1778008 STR_911 AATCAATCAATCAATCAATCA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1778008;END=1778028;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=43;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:43:0:0:1:21.50|21.50:0|0:.:0.0:.:0.0:0|32:0|32 +1 1779795 STR_912 GCAAAAAAAAAAAAAAAAAGAAAAAGAAAAAATAAAACGAAAAAGAAA GCAAAAAAAAAAAAAAAAGAAAAAGAAAAAATAAAACGAAAAAGAAA,GTAAAAAAAAAAAAAAAAAGAAAAAGAAAAAATAAAACGAAAAAGAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1,0;START=1779797;END=1779842;PERIOD=6;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=25;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:-1|0:1.0:0.5:25:0:2:2:13.66|11.34:0|0:16.27:-0.0:17:-0.53:-1|4;0|1:-1|4;0|1 +1 1781572 STR_913 TTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1781572;END=1781585;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1782854 STR_914 AAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1782854;END=1782870;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=4;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:35:0:4:2:16.95|18.05:0|0:9.73:-0.0:29:0.0:-8|1;-2|2;-1|11;0|13:-2|2;-1|11;0|11 +1 1783518 STR_915 AAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1783518;END=1783528;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=39;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:39:0:1:1:19.50|19.50:0|0:.:0.0:.:0.0:-2|1;0|35:-2|1;0|34 +1 1784126 STR_916 AAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1784126;END=1784139;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1786598 STR_917 AAAAAAAAAAAAAACAGCT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1786598;END=1786611;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1786755 STR_918 TGTGTCAAAAAAAAAAAAAAAGAAAAGAAAAGAAGAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1786761;END=1786795;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1787139 STR_919 TCTCAAAAAAAAAACAAAAAAAAA TACCAAAACAAAACCCAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1787143;END=1787162;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=1;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:35:0:1:3:33.50|1.50:0|0:2.49:-8.39:34:-0.49:-4|1;0|20;4|1:0|18 +1 1787867 STR_920 TTTCTTTCTTTCTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1787867;END=1787881;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:35:0:0:1:17.50|17.50:0|0:.:0.0:.:0.0:0|24:0|24 +1 1790460 STR_921 TTTTCTTTTTTTTTTTTTT TTTTCTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1790460;END=1790478;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=24;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:24:0:0:2:15.76|8.24:0|0:2.61:-1.02:18:0.0:-1|4;0|13;1|1:-1|4;0|13 +1 1792080 STR_922 AAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1792080;END=1792094;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1792544 STR_923 TCTCACAAAAAAAAAAAAAAAAAA . . . 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INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1793911;END=1793923;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=44;DSNP=0;DSTUTTER=3;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:44:0:3:3:22.00|22.00:0|0:.:0.0:.:0.0:-6|2;-1|3;0|23:-1|3;0|19 +1 1795754 STR_926 AAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1795754;END=1795775;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1796701 STR_927 AAAAAACAAAAAAAAAACAAAAAAAAACCAAAAAAAAAAAA . . . 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INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1804496;END=1804508;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1806045 STR_936 AAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-2;START=1806045;END=1806071;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=20;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-2:0.92:0.46:20:0:2:2:11.46|8.54:0|0:1.08:-0.43:5:0.0:-10|2;-2|1;0|1:-2|1 +1 1806231 STR_937 AAAAAAAAAAGACAAAAAAAAA . . . 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INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=10;START=1807932;END=1807954;PERIOD=2;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=36;DSNP=0;DSTUTTER=5;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|10:1.0:0.5:36:0:5:0:11.40|24.60:0|0:81.95:-1.62:29:0.0:-18|1;-16|1;-4|1;-2|1;0|8;8|2;10|11;14|1:-4|1;-2|1;0|5;8|2;10|11;14|1 +1 1811148 STR_940 AAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1811148;END=1811163;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=27;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:27:0:0:2:13.50|13.50:0|0:.:0.0:.:0.0:-17|1;0|16:0|9 +1 1811366 STR_941 TTGTTGTTGTTGTTGTT . . . 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INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0,1;START=1812860;END=1812876;PERIOD=1;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=30;DSNP=0;DSTUTTER=4;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:0|1:1.0:0.5:30:0:4:2:10.44|19.56:0|0:14.38:-1.12:26:-0.38:-2|1;0|3;1|13;2|1;15|1:-2|1;0|3;1|11 +1 1813866 STR_944 AAAAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1813866;END=1813889;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1814360 STR_945 AAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1814360;END=1814372;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=39;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:39:0:1:1:19.50|19.50:0|0:.:0.0:.:0.0:0|30;1|1:0|27;1|1 +1 1814718 STR_946 AAAAAAAAAAAAAAAAGAAAAAGAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1814718;END=1814749;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=29;DSNP=0;DSTUTTER=4;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:29:0:4:3:14.50|14.50:0|0:.:0.0:.:0.0:-11|1;-3|1;-2|1;0|7:-3|1;0|4 +1 1815407 STR_947 TTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1815407;END=1815423;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=2;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:31:0:2:0:15.50|15.50:0|0:.:0.0:.:0.0:-2|1;-1|1;0|17:-2|1;-1|1;0|12 +1 1815572 STR_948 TTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1815572;END=1815587;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=32;DSNP=0;DSTUTTER=3;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:32:0:3:4:16.94|15.06:0|0:.:0.0:.:0.0:-15|1;-2|1;-1|1;0|15;1|1:-2|1;-1|1;0|11 +1 1816125 STR_949 TTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1816125;END=1816137;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=30;DSNP=0;DSTUTTER=3;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:30:0:3:0:15.00|15.00:0|0:.:0.0:.:0.0:-1|2;0|15;1|1:-1|2;0|14 +1 1816853 STR_950 AAAAAAAAAAGAAAGAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1816853;END=1816873;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1816991 STR_951 TTTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1816991;END=1817011;PERIOD=1;AN=0;REFAC=0;NSKIP=1;NFILT=0;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1817308 STR_952 AAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1817308;END=1817321;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=15;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:15:0:0:0:7.50|7.50:0|0:.:0.0:.:0.0:0|11:0|10 +1 1818143 STR_953 TTTTTTTTATTTTTATTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1818143;END=1818163;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=53;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:53:0:0:3:26.50|26.50:0|0:.:0.0:.:0.0:-22|1;0|37:0|28 +1 1819807 STR_954 AAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1819807;END=1819821;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1821099 STR_955 AAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1821099;END=1821116;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1821306 STR_956 CCCCACTCCCCACCCCCACCCCG CCCCACTCCCCCCCCCCACCCCC . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1821306;END=1821327;PERIOD=6;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=30;DSNP=0;DSTUTTER=1;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:30:0:1:4:22.90|7.10:0|0:10.72:-2.81:24:-0.59:-16|1;0|20;5|1:0|18 +1 1822454 STR_957 CCGCCGCCGCCGCCGCCGCCTCCGTCCGCC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1822454;END=1822483;PERIOD=3;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1822573 STR_958 CGCGCGTCGCGCGCGC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1822573;END=1822588;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=11;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:11:0:0:0:5.50|5.50:0|0:.:0.0:.:0.0:0|9:0|8 +1 1824493 STR_960 TTTCTTTCTTTCTTTCTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1824493;END=1824511;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=19;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:19:0:0:0:9.50|9.50:0|0:.:0.0:.:0.0:0|15:0|15 +1 1827836 STR_961 TTTTTTTTTTTTTT TTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1827836;END=1827849;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=36;DSNP=0;DSTUTTER=3;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:36:0:3:5:18.05|17.95:0|0:7.53:0.0:20:-0.19:-11|1;-3|2;-1|8;0|8;1|1;3|1;9|1:-3|1;-1|8;0|7;1|1 +1 1828330 STR_962 TTTTTGTTTTTTGTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1828330;END=1828349;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=29;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:29:0:0:1:14.50|14.50:0|0:.:0.0:.:0.0:-16|1;-9|1;0|17:0|16 +1 1828630 STR_963 TTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1828630;END=1828647;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1829122 STR_964 AAAAAAAAAAAACAACAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1829122;END=1829143;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1831769 STR_965 TTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1831769;END=1831779;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=36;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:36:0:0:2:18.00|18.00:0|0:.:0.0:.:0.0:0|27:0|27 +1 1831931 STR_966 TTTTGTATTTTTATTTTTATTTATTTATTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1831931;END=1831962;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=37;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:37:0:0:3:18.50|18.50:0|0:.:0.0:.:0.0:0|21:0|21 +1 1833758 STR_968 AAAAAAAAAAAAAAA AAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1;START=1833758;END=1833772;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=30;DSNP=0;DSTUTTER=3;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|1:1.0:0.5:30:0:3:4:13.21|16.79:0|0:5.13:-0.28:22:0.0:-1|2;0|8;1|8;2|1:-1|2;0|5;1|7;2|1 +1 1834061 STR_969 TCAAAAAAAAAAAAAA TAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1834063;END=1834076;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=14;DSNP=0;DSTUTTER=1;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:0.99:0.49:14:0:1:0:9.19|4.81:0|0:1.86:-0.41:12:0.0:-3|1;0|9:-3|1;0|8 +1 1834114 STR_970 TTTTTATTTTTATTTATTTATTTTTAAATTTTTATTTTTTTGAG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1834114;END=1834152;PERIOD=6;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1834953 STR_971 TTTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1834953;END=1834973;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1835260 STR_972 TTTTTTTTTTTTTTTTC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1835260;END=1835275;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1835864 STR_973 AAATAAATAAATAAATAAATAAATAATATAAAATAAATAAATAA AAATAAATAAATAAATAAATAAATAAATAAATAATATAAAATAAATAAATAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=8;START=1835864;END=1835907;PERIOD=4;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=25;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:8|8:0.99:0.99:25:0:0:2:12.50|12.50:0|0:2.09:0.0:.:0.0:8|5:8|5 +1 1836973 STR_974 TTTTTTTTTTTTTTTT TTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1836973;END=1836988;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=25;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:25:0:2:2:14.91|10.09:0|0:8.82:-0.48:17:0.0:-13|1;-4|1;-1|4;0|11;1|1:-4|1;-1|4;0|8;1|1 +1 1837137 STR_975 TTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1837137;END=1837153;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1839155 STR_976 TTTTTTTTGTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1839155;END=1839169;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=40;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:40:0:0:0:20.00|20.00:0|0:.:0.0:.:0.0:0|30:0|29 +1 1840669 STR_977 GGGGGGGGGGGGGG GGGGAGGGAGGGGG,GGGGGGGTGGGGGG . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0,0;START=1840669;END=1840682;PERIOD=1;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=36;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:0|0:1.0:0.5:36:0:1:1:21.49|14.51:0|0:29.14:-0.51:35:-1.07:0|29:0|28 +1 1841131 STR_978 AAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1841131;END=1841145;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=28;DSNP=0;DSTUTTER=3;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:28:0:3:4:14.00|14.00:0|0:.:0.0:.:0.0:-2|1;0|13;1|1:0|8 +1 1841483 STR_979 TTTGTTTGTTTGTTTTTGTTTGTTTTATTGTTGTTTGTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1841483;END=1841522;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=38;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:38:0:0:1:19.00|19.00:0|0:.:0.0:.:0.0:0|16:0|14 +1 1841665 STR_980 TTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1841665;END=1841675;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=26;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:26:0:0:3:13.00|13.00:0|0:.:0.0:.:0.0:-11|1;0|18:0|15 +1 1843588 STR_981 TACTTTTTCTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1843591;END=1843607;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1843761 STR_982 TTTTTATTTTTATTTTTA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1843761;END=1843778;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=29;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:29:0:0:1:14.50|14.50:0|0:.:0.0:.:0.0:-5|1;0|15:0|15 +1 1844360 STR_983 AAAAAAAAAAAAAAAAAAAAAGTCGAATTCTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1844360;END=1844403;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1844553 STR_984 TTTTTTTATTTTTTTATTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1844553;END=1844576;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=33;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:33:0:0:1:16.50|16.50:0|0:.:0.0:.:0.0:0|22:0|18 +1 1844929 STR_985 TTTTCTTTTCTTTTCTTTTTTTTTTTT TTTTCTTTTCTTTTCTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1844929;END=1844955;PERIOD=5;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=51;DSNP=0;DSTUTTER=1;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:51:0:1:4:30.69|20.31:0|0:67.29:-1.1:33:0.0:-31|1;-2|2;-1|4;0|13:-10|1;-1|4;0|12 +1 1856918 STR_986 GGGTGGGTGGTGGGTGGG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1856918;END=1856935;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=46;DSNP=0;DSTUTTER=0;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:46:0:0:4:23.00|23.00:0|0:.:0.0:.:0.0:0|34:0|30 +1 1860803 STR_987 GGGAGGGGGAGAGGGTGGGGGGAGGGTAGGGGAGGGAGGGAGTGAGGGTAGGGAGGGAGCGAGGGGAGAGGGTAGGGGAGGGAGAGGAG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1860803;END=1860891;PERIOD=4;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1862870 STR_988 ATAAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1862872;END=1862893;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1863183 STR_989 AAAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1863183;END=1863205;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1863506 STR_990 AAAAAAAAAAAAACAAAAAACAAAAAACAAAAAA AAAAAAAAAAAAAAAAAAAACAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-7;START=1863506;END=1863539;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=27;DSNP=0;DSTUTTER=2;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-7:1.0:0.5:27:0:2:3:11.02|15.98:0|0:68.73:-0.39:23:-0.4:-9|3;-7|5;-5|1;0|5:-9|1;-7|3;0|4 +1 1863836 STR_991 AAAAAAAAAAAAAAAGAAAAGAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1863836;END=1863861;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1864020 STR_992 TTTTTTTCTTTCTTTTTTTCTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1864020;END=1864050;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1864331 STR_993 TTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1864331;END=1864342;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1864625 STR_994 TTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1864625;END=1864641;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1866036 STR_995 GTGTGTATGTGTGTGTGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1866036;END=1866053;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=36;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:36:0:0:0:15.81|20.19:0|0:.:0.0:.:0.0:0|29:0|25 +1 1867302 STR_996 GCACTACACACACACACACACACAC GAAAAACAAACACACACACACACAC . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1867307;END=1867326;PERIOD=2;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=32;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:0.95:0.48:32:0:0:3:28.47|3.53:0|0:1.3:-6.38:27:-0.35:0|24:0|22 +1 1867657 STR_997 AAAAAAAAAAAAAAGAAAAAAAGAAAAGAAAA AAAAAAAAAAAAAGAAAAAAAGAAAAGAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1867657;END=1867688;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=22;DSNP=0;DSTUTTER=3;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:0.99:0.49:22:0:3:2:12.51|9.49:0|0:1.96:-0.26:11:0.0:-12|1;-2|1;-1|3;0|4;1|1:-2|1;-1|2;0|4;1|1 +1 1867994 STR_998 AAAAAAAGAAAAAAAAGAAAAAAGAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1867994;END=1868021;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=32;DSNP=0;DSTUTTER=2;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:32:0:2:0:16.00|16.00:0|0:.:0.0:.:0.0:0|20;1|1:0|16 +1 1868346 STR_999 AAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1868346;END=1868361;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1869904 STR_1000 CACACACACACA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1869904;END=1869915;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1869998 STR_1001 CACACACACACACA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1869998;END=1870011;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=43;DSNP=0;DSTUTTER=2;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:43:0:2:0:21.50|21.50:0|0:.:0.0:.:0.0:-4|1;-2|1;0|35:-4|1;-2|1;0|33 +1 1870051 STR_1002 ACACACCCACGACACACACAAACACACAC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1870051;END=1870079;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=49;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:49:0:0:2:24.50|24.50:0|0:.:0.0:.:0.0:-5|1;0|26:0|26 +1 1870654 STR_1003 TGTGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1870654;END=1870665;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=45;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:45:0:0:2:22.50|22.50:0|0:.:0.0:.:0.0:-24|1;0|37:0|37 +1 1872555 STR_1004 AAAGAAAGAAAGAAAGAAAGAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1872555;END=1872577;PERIOD=4;AN=0;REFAC=0;NSKIP=1;NFILT=0;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1877267 STR_1005 AAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAGAACAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=7;START=1877267;END=1877284;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=44;DSNP=0;DSTUTTER=6;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|7:1.0:0.5:44:0:6:4:13.38|30.62:0|0:28.82:-2.48:31:0.0:-4|2;0|13;5|1;7|6;8|3:-1|1;0|4;5|1;7|5;8|3 +1 1877451 STR_1006 GCGTGTGTGCGTGTGTACGTGTGTGTG GTGTGTGTGCGTGTGTACGTGTGTGTG . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1877453;END=1877477;PERIOD=2;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=39;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:39:0:0:3:19.50|19.50:0|0:64.32:0.0:38:-0.13:-28|1;0|32:0|31 +1 1879316 STR_1007 TTTTTTTTTTCTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1879316;END=1879330;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=33;DSNP=0;DSTUTTER=1;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:33:0:1:3:16.50|16.50:0|0:.:0.0:.:0.0:-6|1;-1|1;0|20:-1|1;0|18 +1 1879844 STR_1008 ATATATAAATATATATATATATAT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1879844;END=1879867;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1880034 STR_1009 TTTTTTTTTTTTTT TTTTTTTTTTTTTTTT,TTTTTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=2,4;START=1880034;END=1880047;PERIOD=1;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=25;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:2|4:1.0:0.5:25:0:1:1:16.77|8.23:0|0:2.5:-1.24:14:0.0:0|5;2|8;3|1;4|1;5|1:2|9;3|1;4|2 +1 1880929 STR_1011 TTTTTTTTTTATTTTTTATTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1880929;END=1880953;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=37;DSNP=0;DSTUTTER=1;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:37:0:1:3:18.50|18.50:0|0:.:0.0:.:0.0:-16|1;-4|1;0|19:0|17 +1 1881776 STR_1012 TTTTTTTTTTTTTTTTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1881776;END=1881791;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1883792 STR_1013 AAAAAAAAAAAAGAAAAGAAACAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1883792;END=1883819;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1883972 STR_1014 AAGAAAGAAAGAAAAAAGGAAGGAAGGAAGGGAGGGAAAGAGAGAAAGAAGCAAAGAAAAAGAAAGAAAGAAAGAAAGAAAGA AAGAAAGAAAGAAAAAAGGAAGGAAGGAAGGGAGGGAAAGAGAGAAAGAAGCAAAGAAAAAGAAAGAAAGAAAGAAAGAAAGAAAGA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=4;START=1883972;END=1884054;PERIOD=4;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=58;DSNP=0;DSTUTTER=1;DFLANKINDEL=6 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:4|4:1.0:1.0:58:0:1:6:29.00|29.00:0|0:6.97:0.0:.:0.0:0|2;4|9:4|9 +1 1884103 STR_1015 TTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1884103;END=1884114;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=44;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:44:0:0:2:22.00|22.00:0|0:.:0.0:.:0.0:0|29;7|1:0|27 +1 1884736 STR_1016 TTTTTTTTTTTTTTTT TTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1884736;END=1884751;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=3;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:0.97:0.48:31:0:3:3:19.23|11.77:0|0:1.49:-1.02:18:0.0:-2|1;-1|4;0|12;1|1:-2|1;-1|3;0|8;1|1 +1 1890700 STR_1017 TTTTGTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1890700;END=1890714;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=30;DSNP=0;DSTUTTER=2;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:30:0:2:4:15.00|15.00:0|0:.:0.0:.:0.0:-24|1;-4|1;-1|2;0|17:-1|2;0|14 +1 1893911 STR_1018 ATCTCAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1893916;END=1893933;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1894896 STR_1019 AAAAAAAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1894896;END=1894922;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1898277 STR_1020 TTTTTTTTTTTTTTTTT TTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-2;START=1898277;END=1898293;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=34;DSNP=0;DSTUTTER=4;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-2:1.0:0.5:34:0:4:3:26.95|7.05:0|0:2.57:-3.74:28:-0.23:-3|2;-2|2;-1|2;0|16:-3|2;-2|1;-1|1;0|17 +1 1902428 STR_1023 CACACACACACGCACAC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1902428;END=1902444;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=34;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:34:0:0:0:17.00|17.00:0|0:.:0.0:.:0.0:0|21:. +1 1904280 STR_1024 TAAATAAATAAATAATAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1904280;END=1904298;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=48;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:48:0:0:1:24.00|24.00:0|0:.:0.0:.:0.0:0|32:0|29 +1 1908290 STR_1025 TTTTCTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1908290;END=1908304;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1915125 STR_1026 TTTATTTATTTATTTATTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1915125;END=1915143;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=25;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:25:0:0:0:12.50|12.50:0|0:.:0.0:.:0.0:0|17:0|14 +1 1915429 STR_1027 TTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1915429;END=1915442;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1915740 STR_1028 TTTTTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1;START=1915740;END=1915758;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=38;DSNP=0;DSTUTTER=3;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|1:1.0:0.5:38:0:3:5:22.76|15.24:0|0:2.87:-0.94:20:-0.19:-14|1;-3|1;-1|2;0|13;1|5:-1|2;0|12;1|3 +1 1920264 STR_1029 CCCCCACCCCCACCCCCACCCCCACCCCCCCACACCCACCTCCACCCCC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1920264;END=1920312;PERIOD=6;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1920435 STR_1030 AAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1920435;END=1920448;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=44;DSNP=0;DSTUTTER=4;DFLANKINDEL=6 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:44:0:4:6:22.00|22.00:0|0:.:0.0:.:0.0:-27|1;-9|1;-2|2;-1|2;0|32;1|1:-2|2;-1|1;0|28;1|1 +1 1920599 STR_1031 GAGAGAGAGAGAGAGAG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1920599;END=1920615;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=34;DSNP=0;DSTUTTER=2;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:34:0:2:0:17.00|17.00:0|0:.:0.0:.:0.0:-2|2;0|21:-2|2;0|21 +1 1921894 STR_1032 GGGGTGGGGAGTGGGGTGGGGGTGGG GGGGTGGGGCGTGGGGTGGGGGGGGG . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1921894;END=1921919;PERIOD=6;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=28;DSNP=0;DSTUTTER=4;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:28:0:4:3:21.70|6.30:0|0:12.58:-2.81:24:-0.22:0|11;1|1;7|1:0|12 +1 1923479 STR_1033 AAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1923479;END=1923491;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=27;DSNP=0;DSTUTTER=4;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:27:0:4:2:13.50|13.50:0|0:.:0.0:.:0.0:-2|1;-1|3;0|17:-1|3;0|15 +1 1923917 STR_1034 TTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1923917;END=1923929;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=43;DSNP=0;DSTUTTER=6;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:43:0:6:2:21.50|21.50:0|0:.:0.0:.:0.0:-20|1;-1|2;0|29;1|4:-1|2;0|27;1|4 +1 1924638 STR_1035 AAAAAAAAAAAAAAAAAAAAG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1924638;END=1924657;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1925614 STR_1036 AAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1925614;END=1925632;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1926931 STR_1037 AAAAAAAAGAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1926931;END=1926950;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1927418 STR_1038 TTTTTGTTTTTGTTTTTGTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1927418;END=1927440;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=44;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:44:0:0:2:22.00|22.00:0|0:.:0.0:.:0.0:0|26:0|26 +1 1928360 STR_1039 AAAAAAAAAAAAAAAGAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1928360;END=1928386;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1928862 STR_1040 AAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1928862;END=1928875;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=25;DSNP=0;DSTUTTER=3;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:25:0:3:2:12.50|12.50:0|0:.:0.0:.:0.0:0|17;1|1:-2|1;-1|1;0|13;1|1 +1 1930328 STR_1041 AATAAAATAAAATTAAAATTAAAAAATAAAATAAATAAATAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1930328;END=1930370;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=42;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:42:0:0:0:19.48|22.52:0|0:.:0.0:.:0.0:0|12:0|12 +1 1930474 STR_1042 TGTGTGTGTGTGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1930474;END=1930486;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=44;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:44:0:0:2:22.00|22.00:0|0:.:0.0:.:0.0:-1|1;0|33;13|1:0|30 +1 1931603 STR_1043 AAAAAAAAGAAAAAAGAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1931603;END=1931622;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=47;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:47:0:0:2:23.50|23.50:0|0:.:0.0:.:0.0:0|33;8|1:0|30 +1 1932744 STR_1044 TGTTTTTGTTTTGTTTTGTTTTTCATTTTGTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1932744;END=1932783;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=27;DSNP=0;DSTUTTER=0;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:27:0:0:4:13.50|13.50:0|0:.:0.0:.:0.0:-31|1;0|4;1|1:0|5 +1 1934195 STR_1045 TATATATAGTCTATATATTTATATTATATAT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1934195;END=1934225;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=11;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:11:0:0:0:5.50|5.50:0|0:.:0.0:.:0.0:0|7:0|7 +1 1935941 STR_1046 AAAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1935941;END=1935963;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1936395 STR_1047 ACAAACAAACAAACAAAAAACAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1936395;END=1936418;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=52;DSNP=0;DSTUTTER=0;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:52:0:0:4:26.00|26.00:0|0:.:0.0:.:0.0:-10|1;0|29:0|28 +1 1937343 STR_1048 CTCTCTCTCTCTCTCTCTCTCTCGTTCTCTCTCTCTCTCTCTCTATATATATATATATA CTCTCTCTCTCTCTCTCTCTCTCTATATATATATATATA,CTCTCTCTCTCTCTCTCTCTCTCTCTCGTTCTCTCTCTCTCTCTCTCTATATATATATATATATA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-20,6;START=1937343;END=1937401;PERIOD=2;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=41;DSNP=0;DSTUTTER=3;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:-20|6:1.0:0.5:41:0:3:2:18.57|22.43:0|0:80.65:-0.22:32:-0.54:-27|1;-20|8;-18|1;-12|1;6|4:-20|7;-18|1;6|4 +1 1937734 STR_1049 AAAAAAGAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1937734;END=1937750;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=58;DSNP=0;DSTUTTER=1;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:58:0:1:3:29.00|29.00:0|0:.:0.0:.:0.0:-6|1;-1|1;0|38;1|1;3|1:-1|1;0|34 +1 1938036 STR_1050 AAAAAAAAAAAAAAA AAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1;START=1938036;END=1938050;PERIOD=1;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=29;DSNP=0;DSTUTTER=4;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:1|1:1.0:1.0:29:0:4:1:14.50|14.50:0|0:3.86:0.0:.:0.0:-15|1;-5|2;-1|1;0|3;1|17;2|1:-1|1;0|1;1|16;2|1 +1 1938108 STR_1051 ATATATATATAT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1938108;END=1938119;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=26;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:26:0:0:1:13.00|13.00:0|0:.:0.0:.:0.0:0|19:0|17 +1 1938343 STR_1052 TTTTTATTTTTATTTTTA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1938343;END=1938360;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=29;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:29:0:0:1:14.50|14.50:0|0:.:0.0:.:0.0:0|20;4|1:0|20 +1 1938776 STR_1053 TATTTTATTTTATTATTATTATT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1938776;END=1938798;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=42;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:42:0:2:2:21.00|21.00:0|0:.:0.0:.:0.0:-8|1;-3|1;0|23:-6|1;-3|1;0|22 +1 1938922 STR_1054 ATTTTTATTTTTATTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1938922;END=1938939;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=39;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:39:0:0:3:19.50|19.50:0|0:.:0.0:.:0.0:0|28:0|26 +1 1939069 STR_1055 AAAAAAAAAAAAAAAAGAAAAAGAAAAAA AAAAAAAAAAAAAAAGAAAAAGAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1939069;END=1939097;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=20;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:20:0:0:1:10.12|9.88:0|0:6.85:0.0:14:-0.23:-1|5;0|6:-1|5;0|6 +1 1940268 STR_1056 AAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1940268;END=1940279;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=30;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:30:0:1:1:15.00|15.00:0|0:.:0.0:.:0.0:-6|1;0|23;1|1:0|20;1|1 +1 1940557 STR_1057 AAAAACAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1940557;END=1940571;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=48;DSNP=0;DSTUTTER=1;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:48:0:1:3:24.00|24.00:0|0:.:0.0:.:0.0:0|36:0|31 +1 1942711 STR_1058 TTTTTTTTTTT TTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1;START=1942711;END=1942721;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=21;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|1:1.0:0.5:21:0:1:1:11.47|9.53:0|0:3.34:-0.11:12:0.0:0|7;1|4;2|1:0|6;1|3;2|1 +1 1943719 STR_1059 AAAATAAAATAAAATAAAATAAAATAAAATAAAA AAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=10;START=1943719;END=1943752;PERIOD=5;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=30;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|10:1.0:0.5:30:0:0:3:14.64|15.36:0|0:7.88:-0.0:11:-0.62:-32|1;-25|1;0|3;10|4:0|3;10|4 +1 1944044 STR_1060 AAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1944044;END=1944057;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=30;DSNP=0;DSTUTTER=4;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:30:0:4:1:15.00|15.00:0|0:.:0.0:.:0.0:-1|2;0|17;1|1:-1|2;0|13;1|1 +1 1944524 STR_1061 AAAGAAAGAAAGAAAAGAAAG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1944524;END=1944544;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=26;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:26:0:0:1:13.00|13.00:0|0:.:0.0:.:0.0:0|16;24|1:0|16 +1 1948273 STR_1062 AAAGAAAGAAAGAAAGAAAAAGAAAGAAAGAAAGAAAGA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1948273;END=1948311;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=56;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:56:0:0:1:28.00|28.00:0|0:.:0.0:.:0.0:0|24:0|23 +1 1949774 STR_1063 ATAACATAACATAACATAACATAACATAACATAACATAACATAACATAACATAACATAAATAA ATAACATAACATAACATAACATAACATAACATAACATAACATAACATAACATAACATAACATAAATAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=5;START=1949774;END=1949836;PERIOD=5;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=69;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|5:1.0:0.5:69:0:0:0:32.07|36.93:0|0:8.18:-0.34:29:-0.15:0|9;5|12:0|9;5|12 +1 1958273 STR_1064 AAAAAAAAAAAACAAACAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1958273;END=1958297;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1965836 STR_1065 TTTTTTTTTGTTTTTTGTTTTTTGTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1965836;END=1965868;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=38;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:38:0:0:2:19.00|19.00:0|0:.:0.0:.:0.0:0|17:0|13 +1 1966160 STR_1066 TTTGTTTATTTGTTTGTTTGTTTTTTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1966160;END=1966186;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=37;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:37:0:0:2:18.50|18.50:0|0:.:0.0:.:0.0:0|26;2|1:0|25 +1 1968373 STR_1067 AAATAAATAAATCAATAAATAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1968373;END=1968395;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=46;DSNP=0;DSTUTTER=1;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:46:0:1:3:23.00|23.00:0|0:.:0.0:.:0.0:-3|1;0|26:0|24 +1 1972122 STR_1068 AACAAAACAAAACAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1972122;END=1972138;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=52;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:52:0:0:0:26.00|26.00:0|0:.:0.0:.:0.0:0|35:0|35 +1 1973475 STR_1069 TGTGTGTGCTGTGTGTGTGCATGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1973475;END=1973503;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=41;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:41:0:0:0:20.50|20.50:0|0:.:0.0:.:0.0:0|29:0|28 +1 1973551 STR_1070 TGTGTGTGGGTGTGTGCGTGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1973551;END=1973571;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=47;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:47:0:0:1:23.50|23.50:0|0:.:0.0:.:0.0:0|33;8|1:0|33 +1 1973633 STR_1071 GTGTGTGTGTGTGTTTGTGTGTGTGTGTATGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1973633;END=1973665;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=46;DSNP=0;DSTUTTER=1;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:46:0:1:0:23.00|23.00:0|0:.:0.0:.:0.0:-2|1;0|22:-2|1;0|20 +1 1974205 STR_1072 AAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-6;START=1974205;END=1974227;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=20;DSNP=0;DSTUTTER=1;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-6:1.0:0.5:20:0:1:3:11.50|8.50:0|0:11.09:-0.43:5:0.0:-24|1;-6|1;0|4:-6|1;0|1 +1 1975421 STR_1073 CACACACACACAC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1975421;END=1975433;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=56;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:56:0:0:1:28.00|28.00:0|0:.:0.0:.:0.0:0|47:0|45 +1 1975445 STR_1074 CACACACACACA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1975445;END=1975456;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=58;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:58:0:0:2:29.00|29.00:0|0:.:0.0:.:0.0:-8|1;0|49:0|47 +1 1975581 STR_1075 CACACACACACA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1975581;END=1975592;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=37;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:37:0:0:3:18.50|18.50:0|0:.:0.0:.:0.0:0|30:0|28 +1 1975606 STR_1076 ACACACACACACA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1975606;END=1975618;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=33;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:33:0:1:1:16.50|16.50:0|0:.:0.0:.:0.0:-2|1;0|25:-2|1;0|25 +1 1975666 STR_1077 ACACACACACAGATACACACAGAAAGCTATACACACACACACACACACACATACACAC ACACACACACAGATACACACAGAAAGCTATACACACACACACACACACATACACAC . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-2;START=1975666;END=1975723;PERIOD=2;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=65;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-2:1.0:0.5:65:0:0:2:28.54|36.46:0|0:24.19:-0.58:51:-0.25:-8|1;-2|19;0|11;19|1:-2|17;0|11 +1 1976980 STR_1078 AAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1976980;END=1976994;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1980605 STR_1079 AAAAAAAAGAAAAAGAAAGAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1980605;END=1980630;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=32;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:32:0:0:2:15.00|17.00:0|0:.:0.0:.:0.0:-17|1;0|19:0|17 +1 1984555 STR_1080 TTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1984555;END=1984568;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1986010 STR_1081 AAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1986010;END=1986022;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=34;DSNP=0;DSTUTTER=3;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:34:0:3:2:17.00|17.00:0|0:.:0.0:.:0.0:-20|1;-1|2;0|24:-1|3;0|20 +1 1986381 STR_1082 TTTTTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-2;START=1986381;END=1986399;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=33;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-2:1.0:0.5:33:0:1:2:22.38|10.62:0|0:2.49:-2.12:18:-0.61:-11|1;-8|1;-2|3;0|10;1|1:-2|3;0|7;1|1 +1 1988169 STR_1083 TTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1988169;END=1988185;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=29;DSNP=0;DSTUTTER=3;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:29:0:3:3:14.50|14.50:0|0:.:0.0:.:0.0:-14|1;-3|1;0|11;1|1:-3|1;0|8 +1 1989311 STR_1084 TTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1989311;END=1989325;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1989746 STR_1085 TTTTTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1989746;END=1989768;PERIOD=1;AN=0;REFAC=0;NSKIP=1;NFILT=0;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 1993922 STR_1086 TTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1993922;END=1993939;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=38;DSNP=0;DSTUTTER=5;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:38:0:5:2:19.00|19.00:0|0:.:0.0:.:0.0:-10|1;-3|2;-1|2;0|15:-3|2;-1|2;0|11 +1 1995285 STR_1087 TTTTTTTTTTTTTTTTTTG TTTTTTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=1995285;END=1995302;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=25;DSNP=0;DSTUTTER=2;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:0.99:0.49:25:0:2:1:13.55|11.45:0|0:1.88:-0.1:14:-0.27:-4|1;-3|1;-1|1;0|9;1|1:-1|1;0|8 +1 1997112 STR_1088 TGTCTCAAAAAAAAAAAAAAAAAAAAAAAA TTTCCCAAAAAAAAAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=1997118;END=1997141;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=29;DSNP=0;DSTUTTER=1;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:0.94:0.47:29:0:1:4:21.96|7.04:0|0:1.21:-3.14:19:0.0:-1|1;0|6:-2|1;-1|1;0|2 +1 1997788 STR_1089 TCTCTTTCTTTCTCTCTCTCTCTGTCTGTCTCTCT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=1997788;END=1997822;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=57;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:57:0:0:2:28.50|28.50:0|0:.:0.0:.:0.0:-21|1;-16|1;0|28:0|25 +1 2006302 STR_1090 AAAAAAAAAAACAACAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2006302;END=2006322;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=24;DSNP=0;DSTUTTER=3;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:24:0:3:1:12.00|12.00:0|0:.:0.0:.:0.0:-1|2;0|15;1|2:-1|1;0|13;1|2 +1 2008182 STR_1091 AAAAAAAAAAAAAAA AAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=2008182;END=2008196;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=43;DSNP=0;DSTUTTER=5;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:43:0:5:4:25.59|17.41:0|0:16.98:-0.79:33:-0.15:-4|2;-1|9;0|19;1|3:-4|2;-1|7;0|15;1|1 +1 2010284 STR_1092 TTTTTTTTTTTTTTTTGAGAT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2010284;END=2010299;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2016446 STR_1093 AAAAAAAGAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2016446;END=2016465;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=27;DSNP=0;DSTUTTER=3;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:27:0:3:4:13.50|13.50:0|0:.:0.0:.:0.0:-1|1;0|14;1|1:-1|1;0|9;1|1 +1 2017495 STR_1094 TTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2017495;END=2017513;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=27;DSNP=0;DSTUTTER=1;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:27:0:1:3:13.50|13.50:0|0:.:0.0:.:0.0:-14|1;0|11;1|1:0|11 +1 2020371 STR_1095 TTTTGTTTTATTTTGTTTTGTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2020371;END=2020394;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=42;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:42:0:0:1:21.00|21.00:0|0:.:0.0:.:0.0:0|20:0|19 +1 2030088 STR_1097 TTTTGTTTGTTTTCGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2030088;END=2030136;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=50;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:50:0:0:2:25.00|25.00:0|0:.:0.0:.:0.0:-23|1;0|14:0|14 +1 2030761 STR_1098 TCATTCATTCATTCATTCAT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2030761;END=2030780;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=32;DSNP=0;DSTUTTER=1;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:32:0:1:0:16.00|16.00:0|0:.:0.0:.:0.0:-4|1;0|21:-4|1;0|20 +1 2032459 STR_1099 AAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2032459;END=2032477;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2032959 STR_1100 TTCATTCATTCATTCATTCAT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2032959;END=2032979;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=43;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:43:0:0:2:21.50|21.50:0|0:.:0.0:.:0.0:0|36:0|33 +1 2033756 STR_1101 TTTTTTTTTGTTTGTTTTGTTTTGTTTTGTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2033756;END=2033788;PERIOD=5;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2035153 STR_1102 AGAGAAAGAGAGAGAG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2035153;END=2035168;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=41;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:41:0:0:3:20.50|20.50:0|0:.:0.0:.:0.0:-12|1;-7|1;0|30:0|27 +1 2046212 STR_1103 AAAAAAAAAAGAAAAAGAAAAAGAAAAAG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2046212;END=2046240;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=42;DSNP=0;DSTUTTER=1;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:42:0:1:3:21.00|21.00:0|0:.:0.0:.:0.0:0|15;1|1:0|16 +1 2048807 STR_1104 TTTTTTTTTTTTT TTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=2048807;END=2048819;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=4;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:31:0:4:4:15.16|15.84:0|0:9.55:0.0:24:0.0:-2|1;-1|10;0|9;1|2;2|1:-2|1;-1|10;0|8;1|2;2|1 +1 2049438 STR_1105 TTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2049438;END=2049453;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2049776 STR_1106 TTTTTGTTTTTTTTTTTTT TTTTTGTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1;START=2049776;END=2049794;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=29;DSNP=0;DSTUTTER=2;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|1:1.0:0.5:29:0:2:4:14.91|14.09:0|0:5.96:-0.0:17:-1.3:-11|1;-9|2;0|8;1|6:-1|1;0|5;1|4 +1 2050147 STR_1107 CAGCTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGA CAGCTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT,CCGCTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=4,6;START=2050153;END=2050194;PERIOD=2;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=2;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:4|6:1.0:0.5:31:0:2:2:19.56|11.44:0|0:8.06:-0.55:31:-0.83:-13|1;2|1;4|11;6|4:2|1;4|10;6|3 +1 2050653 STR_1108 TTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2050653;END=2050670;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2051206 STR_1109 TTCTTTTTATTTCTTTTCTTTTCTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2051206;END=2051240;PERIOD=5;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2051733 STR_1110 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2051733;END=2051761;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2052279 STR_1111 TTTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=2052279;END=2052295;PERIOD=1;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=33;DSNP=0;DSTUTTER=4;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:-1|-1:1.0:1.0:33:0:4:2:16.50|16.50:0|0:3.27:0.0:.:0.0:-4|1;-3|1;-2|2;-1|10;0|1:-3|1;-2|2;-1|9 +1 2061332 STR_1112 TTTTGTTTGTTTGTTTTGTTTTGTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2061332;END=2061358;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=44;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:44:0:1:2:22.00|22.00:0|0:.:0.0:.:0.0:0|19;9|1:0|19 +1 2063554 STR_1113 GTTTGTTTGTTTGTTTTTTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2063554;END=2063573;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=43;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:43:0:0:1:21.50|21.50:0|0:.:0.0:.:0.0:0|28:0|28 +1 2071027 STR_1114 CAAAACAACACAAAACAAAAACAAAACAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2071027;END=2071055;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=42;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:42:0:0:2:21.00|21.00:0|0:.:0.0:.:0.0:0|26;2|1:0|26 +1 2074465 STR_1115 TTTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2074465;END=2074485;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=15;DSNP=0;DSTUTTER=2;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:15:0:2:1:7.50|7.50:0|0:.:0.0:.:0.0:-9|1;0|2:0|1;1|1 +1 2078394 STR_1116 TCCATCCATCCACCACCTATCCATCTATCCACGATCCATCCATCTCGTCATCCAGCCAGCCAGCCAGCCATCCTCCACCCACCCATCCTCCA TCCATCCATCCACCACCTATCCATCTATCCACGATCCATCCATCTCGTCAGCCAGCCAGCCAGCCAGCCATCCTCCACCCACCCATCCACCA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=2078394;END=2078485;PERIOD=4;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=75;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:75:0:0:1:37.04|37.96:0|0:151.82:-0.0:75:-0.19:0|12:0|12 +1 2081442 STR_1117 AAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2081442;END=2081454;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=30;DSNP=0;DSTUTTER=3;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:30:0:3:4:15.00|15.00:0|0:.:0.0:.:0.0:-15|1;-2|1;-1|1;0|16;1|2:-2|1;-1|1;0|13;1|1 +1 2081601 STR_1118 AAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2081601;END=2081621;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2086537 STR_1119 GATGATGGTGATGATGATGGTGACAATGATGGTGACGATGATGGTGATGATGGTGATGATG GATGATGGTGATGATGATGGTGACGATGATGGTGACGATGATGGTGATGATGGTGATGATG . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=2086537;END=2086597;PERIOD=3;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=68;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:68:0:0:2:39.48|28.52:0|0:69.77:-0.77:53:-1.25:0|30;17|1:0|30 +1 2086885 STR_1120 TGATGGTGGTGGTGATGGTGATGATGACGGTGGTGATGAAGGTGATGGT TGGTGGTGGTGATGGTGATGATGACGGTGGTGATGAAGGTGATGGT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-3;START=2086885;END=2086933;PERIOD=6;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=50;DSNP=0;DSTUTTER=1;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-3:1.0:0.5:50:0:1:3:21.51|28.49:0|0:57.19:-0.53:33:-0.34:-3|14;0|7;3|1:-3|14;0|7 +1 2086973 STR_1121 TGGTGATGGTGGTGGTGGTGATGGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2086973;END=2086998;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=45;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:45:0:0:2:22.50|22.50:0|0:.:0.0:.:0.0:-9|1;0|36:0|36 +1 2087238 STR_1122 TGGTGGTGGTGGTGGTAGAGGTGGGGTGGATGGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2087238;END=2087272;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=47;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:47:0:0:1:23.50|23.50:0|0:.:0.0:.:0.0:-1|1;0|22:0|19 +1 2088361 STR_1123 GTGTGTGTGTGTGTGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2088361;END=2088376;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=56;DSNP=0;DSTUTTER=3;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:56:0:3:2:28.00|28.00:0|0:.:0.0:.:0.0:-2|2;0|44;2|1:-2|2;0|43;2|1 +1 2088844 STR_1124 TTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2088844;END=2088854;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=55;DSNP=0;DSTUTTER=3;DFLANKINDEL=6 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:55:0:3:6:27.50|27.50:0|0:.:0.0:.:0.0:-2|1;-1|1;0|49;1|1:-2|1;-1|1;0|44;1|1 +1 2089152 STR_1125 TTTTTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1;START=2089152;END=2089170;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=37;DSNP=0;DSTUTTER=4;DFLANKINDEL=5 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|1:1.0:0.5:37:0:4:5:16.67|20.33:0|0:3.73:-0.32:18:-1.18:-34|1;-32|1;-1|1;0|8;1|6;2|2;3|1:-1|1;0|5;1|4;2|1;3|1 +1 2090371 STR_1126 TTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2090371;END=2090382;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=12;DSNP=0;DSTUTTER=1;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:12:0:1:0:6.00|6.00:0|0:.:0.0:.:0.0:-1|1;0|9:-1|1;0|8 +1 2091672 STR_1127 GTGTGCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT GTGTGCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-4;START=2091672;END=2091711;PERIOD=2;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=43;DSNP=0;DSTUTTER=1;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-4:1.0:0.5:43:0:1:0:20.62|22.38:0|0:22.37:0.0:27:-0.15:-4|13;-2|1;0|7:-4|12;-2|1;0|6 +1 2093571 STR_1128 TTTTCTTTTCTTTTCTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2093571;END=2093588;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=52;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:52:0:0:2:26.00|26.00:0|0:.:0.0:.:0.0:0|37;24|1:0|37 +1 2094048 STR_1129 ATTATTATTATTATTATT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2094048;END=2094065;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=25;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:25:0:0:2:12.50|12.50:0|0:.:0.0:.:0.0:0|16:0|14 +1 2095174 STR_1130 AAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2095174;END=2095188;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2095338 STR_1131 AAAAAAAAGAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2095338;END=2095356;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=38;DSNP=0;DSTUTTER=1;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:38:0:1:3:19.00|19.00:0|0:.:0.0:.:0.0:-14|1;-10|1;0|20;1|1:0|18 +1 2098175 STR_1132 CCCCCACCCCCACCCCCA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2098175;END=2098192;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=37;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:37:0:0:0:18.50|18.50:0|0:.:0.0:.:0.0:0|31:0|31 +1 2102781 STR_1133 AAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2102781;END=2102797;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2106808 STR_1135 CCCAACCCCCATCCCAACCCCAACCCCAATATT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2106808;END=2106836;PERIOD=6;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2114302 STR_1136 GAGTGAGTGAGCCAGTGAATGAGTGAGTGAGCAGGAGTGGGTTAGAGAGCGAGGGAGTGAGTGAATGAGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2114302;END=2114372;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=42;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:42:0:1:2:21.00|21.00:0|0:.:0.0:.:0.0:-40|1;0|12;12|1:0|11 +1 2114663 STR_1137 CAAAACAAAAACAAAAAACAAAA CCGTCTCAAAACAAAAACAAAAAACAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=6;START=2114664;END=2114685;PERIOD=6;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=48;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|6:1.0:0.5:48:0:0:3:19.38|28.62:0|0:17.92:-0.76:35:-0.31:-19|1;-4|1;0|9;5|1;6|10:0|8;6|10 +1 2114852 STR_1138 GAGTGAGTGAGTGAATGAGTGA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2114852;END=2114873;PERIOD=4;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2118720 STR_1139 TTTTCTTTTTTTTTTTCTTTTTCTTTTTTTTTTCTTTTTTTTG TTTTCTTTTTTTTTTTCTTTTTCTTTTTTTTTTCTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=0;START=2118720;END=2118761;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=25;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|0:1.0:0.5:25:0:1:1:15.99|9.01:0|0:4.61:-0.93:15:-0.64:-7|1;0|9:0|6 +1 2119129 STR_1140 CCCTGCCCTGCCCGTCCTGCCCTGCCC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2119129;END=2119155;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=53;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:53:0:0:1:26.50|26.50:0|0:.:0.0:.:0.0:-3|1;0|39:0|39 +1 2120444 STR_1141 AAAAAAGAAAAAAAAAAAAAAAAACAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2120444;END=2120473;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2120771 STR_1142 AAAAAAAAAAAAACAAAAAAAAAA AAAAAAAAAAAAAACAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1;START=2120771;END=2120794;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=21;DSNP=0;DSTUTTER=3;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|1:1.0:0.5:21:0:3:1:11.39|9.61:0|0:5.69:-0.12:10:0.0:0|6;1|4;2|1:0|5;1|3;2|1 +1 2123180 STR_1143 AAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=2;START=2123180;END=2123194;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=16;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|2:1.0:0.5:16:0:1:1:11.04|4.96:0|0:3.16:-0.84:12:-0.74:-1|1;0|10;2|1:-1|1;0|8;2|1 +1 2124346 STR_1144 TTGTTGTTGTTGTTGTTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2124346;END=2124363;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=52;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:52:0:0:0:26.00|26.00:0|0:.:0.0:.:0.0:0|37:0|37 +1 2126221 STR_1145 CCCCGCCCCCGCCCCTCCAGGCCCCGCCCCCGCCCCGGCCCCGCCT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2126221;END=2126262;PERIOD=6;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2127980 STR_1146 AAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2127980;END=2127994;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2128438 STR_1147 CTCCTGCCTCCTCCTCCTC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2128438;END=2128456;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=47;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:47:0:0:0:23.50|23.50:0|0:.:0.0:.:0.0:0|35:0|35 +1 2129485 STR_1148 GGTGCTGGTGATGGTGATGGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2129485;END=2129506;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=59;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:59:0:0:1:29.50|29.50:0|0:.:0.0:.:0.0:-1|1;0|42:0|42 +1 2130831 STR_1149 CCCAGCCCAGCCCAGCCCAGCCCAGCCCAG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2130831;END=2130860;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=45;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:45:0:0:1:22.50|22.50:0|0:.:0.0:.:0.0:0|30:0|30 +1 2131835 STR_1150 AAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2131835;END=2131851;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2133456 STR_1151 AAAAAAAAAAAAAAAAGAAGAAGAAGAAGAAAAAGAAAAAG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2133456;END=2133496;PERIOD=6;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2133902 STR_1152 TTTATTTTATTTATTTATT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2133902;END=2133920;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=32;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:32:0:0:0:16.00|16.00:0|0:.:0.0:.:0.0:0|15:0|15 +1 2134072 STR_1153 TTTTGTTTTGTTTTGTTTTGT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2134072;END=2134092;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=34;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:34:0:0:2:17.00|17.00:0|0:.:0.0:.:0.0:0|23:0|22 +1 2138270 STR_1154 AAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2138270;END=2138287;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2139349 STR_1155 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT GTGTGTGCGTGTGTGTGTGTGTGTGT,GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-20,6;START=2139349;END=2139394;PERIOD=2;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=41;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:-20|6:1.0:0.5:41:0:1:2:18.56|22.44:0|0:47.32:-0.21:36:-0.75:-22|1;-20|10;-11|1;0|3;6|8;9|1:-20|8;6|8 +1 2142642 STR_1156 TTTTCTTTTCTTTTTCTTTCTTTCTTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2142642;END=2142685;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=18;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:18:0:1:1:9.00|9.00:0|0:.:0.0:.:0.0:-39|1;2|1:. +1 2143340 STR_1157 TTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2143340;END=2143359;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2147566 STR_1158 GTGGCGTGGCGTGGCGTGGTGTGGC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2147566;END=2147590;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=48;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:48:0:0:2:24.00|24.00:0|0:.:0.0:.:0.0:-16|1;0|29:0|29 +1 2148750 STR_1159 AAAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2148750;END=2148771;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2149071 STR_1160 AAAAAAAAAAAAAAA AAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=2149071;END=2149085;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=29;DSNP=0;DSTUTTER=3;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:29:0:3:1:20.94|8.06:0|0:14.03:-2.18:24:-0.25:-4|2;-1|3;0|17;1|1:-4|2;-1|2;0|16;1|1 +1 2149369 STR_1161 AAAAAAAAAAACAAAAAAAAAA AAAAAAAAAAAACAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=2;START=2149369;END=2149390;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=25;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|2:1.0:0.5:25:0:0:1:22.94|2.06:0|0:4.39:-5.24:23:0.0:0|19;2|1:0|18;2|1 +1 2151291 STR_1162 AAAACAAAACAAAACAAAACAAAA AAAACAAAACAAAACAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-5;START=2151291;END=2151314;PERIOD=5;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=33;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:-5|-5:1.0:1.0:33:0:0:1:16.50|16.50:0|0:4.34:0.0:.:0.0:-15|1;-5|17:-5|17 +1 2151611 STR_1163 AAAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2151611;END=2151631;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2151912 STR_1164 TCAAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2151914;END=2151932;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2152772 STR_1165 CCTCCCTCCCTCCCTC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2152772;END=2152787;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=36;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:36:0:0:1:18.00|18.00:0|0:.:0.0:.:0.0:0|27:0|26 +1 2153544 STR_1166 TTTTTTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2153544;END=2153567;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2155135 STR_1167 AATAAAATAAAATAAAGTAAAATAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2155135;END=2155161;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=49;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:49:0:0:3:24.50|24.50:0|0:.:0.0:.:0.0:-21|1;0|24:0|24 +1 2155513 STR_1168 AAACAAAAACAAAAACAAAACAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2155513;END=2155537;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=56;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:56:0:0:0:28.00|28.00:0|0:.:0.0:.:0.0:0|39:0|39 +1 2155689 STR_1169 GCAGGGCAGGGCAAGGCAGGG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2155689;END=2155709;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=37;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:37:0:0:3:18.50|18.50:0|0:.:0.0:.:0.0:0|25;1|1:0|25 +1 2156907 STR_1170 TTTTTTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=2156907;END=2156926;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=23;DSNP=0;DSTUTTER=2;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:0.98:0.49:23:0:2:1:9.27|13.73:0|0:1.78:-0.57:13:0.0:-9|1;-2|1;-1|6;0|1;2|1:-2|1;-1|4;0|1;2|1 +1 2157218 STR_1171 TTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2157218;END=2157230;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2157510 STR_1172 TTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2157510;END=2157522;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2157692 STR_1173 AAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2157692;END=2157702;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=39;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:39:0:0:2:19.50|19.50:0|0:.:0.0:.:0.0:-11|1;0|33:0|31 +1 2159391 STR_1174 GGGGCGGGGCCGGCGCGGGGCGGAGCGGGCGGCGCGGGGCGGGGCGGCGCGGCGGCGG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2159391;END=2159448;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=11;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:11:0:0:1:5.50|5.50:0|0:.:0.0:.:0.0:-9|1:. +1 2159584 STR_1175 CGGGCGGGCGGGCCGCGGAGCCGGCGGGCGGGCGGGCCGGGGGCCGGCGGCGGGCG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2159584;END=2159639;PERIOD=4;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2162403 STR_1177 TGTGTGTGTGCATGTGTGTGTTTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2162403;END=2162432;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=43;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:43:0:0:1:21.50|21.50:0|0:.:0.0:.:0.0:0|22:0|19 +1 2167853 STR_1179 TTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2167853;END=2167863;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=41;DSNP=0;DSTUTTER=3;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:41:0:3:1:20.50|20.50:0|0:.:0.0:.:0.0:-2|2;-1|1;0|34:-2|2;-1|1;0|31 +1 2173389 STR_1180 TGTGTGTGTGTGTGTGTGTGTGCCTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2173389;END=2173420;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=41;DSNP=0;DSTUTTER=1;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:41:0:1:0:20.50|20.50:0|0:.:0.0:.:0.0:0|22;2|1:0|21;2|1 +1 2175396 STR_1181 TTTCTTTCTTTCTTTCTTTCTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2175396;END=2175418;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=34;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:34:0:0:1:17.00|17.00:0|0:.:0.0:.:0.0:0|25:0|24 +1 2177228 STR_1182 TTTTTTTTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2177228;END=2177253;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2178658 STR_1183 AAAAAAACAAAAAACAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2178658;END=2178678;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=47;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:47:0:0:1:23.50|23.50:0|0:.:0.0:.:0.0:0|28:0|26 +1 2181348 STR_1184 CACAGTTTTTTTTTTT CTCCGTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1;START=2181353;END=2181363;PERIOD=1;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=29;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|1:0.9:0.45:29:0:1:2:26.50|2.50:0|0:0.94:-6.09:26:-0.41:0|22;1|2:0|19;1|2 +1 2182725 STR_1185 TTTATTTATTTATTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2182725;END=2182739;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=52;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:52:0:0:1:26.00|26.00:0|0:.:0.0:.:0.0:0|35:0|33 +1 2183548 STR_1186 GAGGAGGAGGAGGAGGA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2183548;END=2183564;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=36;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:36:0:0:1:18.00|18.00:0|0:.:0.0:.:0.0:0|33:0|32 +1 2184535 STR_1187 AAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2184535;END=2184550;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2186173 STR_1188 GTGTGTGTGTGTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2186173;END=2186189;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=50;DSNP=0;DSTUTTER=4;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:50:0:4:2:25.00|25.00:0|0:.:0.0:.:0.0:-4|1;-2|3;0|38:-4|1;-2|3;0|37 +1 2189158 STR_1189 TTTATATATTTATTTATTTACTTATTTATTTATTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2189158;END=2189192;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=23;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:23:0:0:1:11.50|11.50:0|0:.:0.0:.:0.0:0|7:0|7 +1 2189943 STR_1190 TTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2189943;END=2189958;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2189991 STR_1191 TTTTTTTTTGTTTTTGTTTTTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2189991;END=2190012;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=1;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:35:0:1:0:17.50|17.50:0|0:.:0.0:.:0.0:0|23:0|23 +1 2191969 STR_1192 TTTTTCTTTTTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2191969;END=2191997;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=14;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:14:0:0:2:7.00|7.00:0|0:.:0.0:.:0.0:-26|1:. +1 2194333 STR_1193 TTTGTTTTTTTTTGTTTTTGTTTTTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2194333;END=2194358;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=51;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:51:0:0:2:25.50|25.50:0|0:.:0.0:.:0.0:0|32:0|31 +1 2194674 STR_1194 TTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2194674;END=2194693;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2195301 STR_1195 ATCTCAAAAAAAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2195306;END=2195323;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2195453 STR_1196 AAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2195453;END=2195464;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=35;DSNP=0;DSTUTTER=3;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:35:0:3:2:17.50|17.50:0|0:.:0.0:.:0.0:-1|3;0|25:-1|3;0|19 +1 2195701 STR_1197 TTTAATTTAATTTAATTTATTTA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2195701;END=2195723;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=51;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:51:0:0:0:25.50|25.50:0|0:.:0.0:.:0.0:0|28:0|28 +1 2196238 STR_1198 TTCTTTTTTTCTTTCTTTC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2196238;END=2196256;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=34;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:34:0:0:0:17.00|17.00:0|0:.:0.0:.:0.0:0|23:0|23 +1 2200289 STR_1199 TCCCTCCCTCCCTCCCT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2200289;END=2200305;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=50;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:50:0:0:2:25.00|25.00:0|0:.:0.0:.:0.0:0|36;1|1:0|34 +1 2210096 STR_1200 TTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2210096;END=2210106;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=27;DSNP=0;DSTUTTER=1;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:27:0:1:3:13.50|13.50:0|0:.:0.0:.:0.0:-1|1;0|18:-1|1;0|14 +1 2211645 STR_1201 AAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2211645;END=2211657;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=32;DSNP=0;DSTUTTER=4;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:32:0:4:3:16.00|16.00:0|0:.:0.0:.:0.0:-2|1;0|20;1|3:-2|1;0|19;1|3 +1 2211815 STR_1202 AAAAAAAAAAAAA AAAAAAAAAAAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1;START=2211815;END=2211827;PERIOD=1;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=34;DSNP=0;DSTUTTER=3;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:1|1:1.0:1.0:34:0:3:1:17.00|17.00:0|0:3.87:0.0:.:0.0:-12|1;-10|1;0|4;1|21:0|1;1|19 +1 2216992 STR_1203 GTTTTGTTTTGTTGTTTTTGTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2216992;END=2217019;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=28;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:28:0:0:2:14.00|14.00:0|0:.:0.0:.:0.0:0|15:0|15 +1 2217310 STR_1204 TTTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2217310;END=2217330;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2218778 STR_1205 TTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTTT,TTTTTTTTTTTTTTTTTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=1,2;START=2218778;END=2218793;PERIOD=1;AN=2;REFAC=0;AC=1,1;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=2;DFLANKINDEL=4 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|2:1|2:1.0:0.5:31:0:2:4:10.87|20.13:0|0:2.41:-1.28:22:-0.75:-23|1;-21|1;-17|1;-16|1;-5|2;0|4;1|3;2|10:0|1;1|3;2|9 +1 2219412 STR_1206 TTTTCTTTTCTTTCTTTTTTTTTTTTCTT TTTTCTTTTCTTTCTTTTTTTTTTTCTT . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=2219412;END=2219440;PERIOD=5;AN=2;REFAC=1;AC=1;NSKIP=0;NFILT=0;DP=38;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|1:0|-1:1.0:0.5:38:0:0:3:27.00|11.00:0|0:8.94:-3.84:18:0.0:-30|1;-1|1;0|9:-1|1;0|9 +1 2222104 STR_1207 AGGAGGAGGAGGAGGAAGAGG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2222104;END=2222124;PERIOD=3;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=33;DSNP=0;DSTUTTER=1;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:33:0:1:2:15.52|17.48:0|0:.:0.0:.:0.0:-3|1;0|20:-3|1;0|20 +1 2227656 STR_1208 AAAAAAAACAAAAAAAAAAAAACAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2227656;END=2227684;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2231510 STR_1209 GCCCAGCCCTGCCCTGCCCTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2231510;END=2231530;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=48;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:48:0:0:1:24.00|24.00:0|0:.:0.0:.:0.0:0|40:0|40 +1 2236569 STR_1210 CACAGACACACACACAC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2236569;END=2236585;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=47;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:47:0:0:1:23.50|23.50:0|0:.:0.0:.:0.0:0|42:0|39 +1 2246709 STR_1212 GGGGGCGGGGGCGGGGGCGGGGGCGG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2246709;END=2246734;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=46;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:46:0:0:2:23.00|23.00:0|0:.:0.0:.:0.0:-24|1;0|24:0|25 +1 2250040 STR_1213 TTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2250040;END=2250052;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2253996 STR_1214 AAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2253996;END=2254006;PERIOD=1;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=30;DSNP=0;DSTUTTER=1;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:30:0:1:3:15.00|15.00:0|0:.:0.0:.:0.0:0|21;1|2:0|15;1|1 +1 2256545 STR_1215 TTCCTTCCCTTCCTTCCCTTCCTTCCTTCCCTCCCTCCCTCCCTTCCTTCCCTCCCTTCCTTCCTTTCCTTCCTTCCCTTCCTTCACTTCCTTC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2256545;END=2256638;PERIOD=4;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2256681 STR_1216 CTCTCTCTCTCTCCTCTCTCTCTCTGCCTCTCTTTCTCTCTCTCTCCTCTCTCTCTCTCTCTCT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2256681;END=2256744;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=27;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:27:0:1:1:13.50|13.50:0|0:.:0.0:.:0.0:-2|1;0|14:0|11 +1 2257082 STR_1217 TTTTTTTTTTTTTTTTTTTTTT . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2257082;END=2257103;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2258892 STR_1218 AACACAAACACAGAAACACAGAAACACACAGAAACAGAAACACAGAAACAAACACAGAGACACAGACACA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2258892;END=2258961;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=58;DSNP=0;DSTUTTER=0;DFLANKINDEL=3 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:58:0:0:3:27.40|30.60:0|0:.:0.0:.:0.0:0|18:0|20 +1 2266787 STR_1219 CACACTCACACTCACACTCAC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2266787;END=2266807;PERIOD=6;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=53;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:53:0:0:1:26.50|26.50:0|0:.:0.0:.:0.0:0|39:0|41 +1 2267268 STR_1220 AGCCCAGCCCAGCCCAGC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2267268;END=2267285;PERIOD=5;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=39;DSNP=0;DSTUTTER=0;DFLANKINDEL=2 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:39:0:0:2:19.50|19.50:0|0:.:0.0:.:0.0:0|24;3|1:0|23 +1 2269083 STR_1221 CACACACACACA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2269083;END=2269094;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=31;DSNP=0;DSTUTTER=0;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:31:0:0:1:15.50|15.50:0|0:.:0.0:.:0.0:0|25:0|25 +1 2273132 STR_1222 AAAAAAAAAAAAAAAAAAGAAAAAGAAAA AAAAAAAAAAAGAAAAAGAAAAAGAAAA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-1;START=2273132;END=2273160;PERIOD=1;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=32;DSNP=0;DSTUTTER=1;DFLANKINDEL=1 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:-1|-1:1.0:1.0:32:0:1:1:16.00|16.00:0|0:6.32:0.0:.:0.0:-2|1;-1|11;0|1:-1|9 +1 2274263 STR_1223 TATTTTATTTTATTTTATATTTTATTTTATTTTATTTTATTTTATTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2274263;END=2274355;PERIOD=5;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2277269 STR_1224 CACACACACACACACACACACACACAG CACACACACACACACACACA . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;BPDIFFS=-7;START=2277269;END=2277294;PERIOD=2;AN=2;REFAC=0;AC=2;NSKIP=0;NFILT=0;DP=27;DSNP=0;DSTUTTER=2;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 1|1:-7|-7:1.0:1.0:27:0:2:0:13.50|13.50:0|0:6.02:0.0:.:0.0:-9|2;-7|18:-9|2;-7|17 +1 2278791 STR_1225 GTGTGTGTGCTGTGTG . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2278791;END=2278806;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=60;DSNP=0;DSTUTTER=1;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:60:0:1:0:30.00|30.00:0|0:.:0.0:.:0.0:0|43:0|42 +1 2280058 STR_1226 GCACGCACGCACACACGCACCTGCGCAGGCACGCACACACGCACGCAC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2280058;END=2280105;PERIOD=4;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=60;DSNP=0;DSTUTTER=2;DFLANKINDEL=7 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:60:0:2:7:30.00|30.00:0|0:.:0.0:.:0.0:-36|1;0|28;2|1;16|1:-8|1;0|28 +1 2280127 STR_1227 CACACACACGCACGCACACGCACAC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2280127;END=2280151;PERIOD=2;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. +1 2280255 STR_1228 CACACACACGCACGCACACGCACAC . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2280255;END=2280279;PERIOD=2;AN=2;REFAC=2;NSKIP=0;NFILT=0;DP=63;DSNP=0;DSTUTTER=0;DFLANKINDEL=7 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS 0|0:0|0:1.0:1.0:63:0:0:7:31.50|31.50:0|0:.:0.0:.:0.0:-10|1;0|45:0|36 +1 2291322 STR_1229 AAAAAAAAAAAAA . . . INFRAME_PGEOM=0.95;INFRAME_UP=0.05;INFRAME_DOWN=0.05;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=2291322;END=2291334;PERIOD=1;AN=0;REFAC=0;NSKIP=0;NFILT=1;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0 GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:. diff --git a/tests/data/test_multitype.vcf b/tests/data/test_multitype.vcf new file mode 100644 index 0000000..814bd82 --- /dev/null +++ b/tests/data/test_multitype.vcf @@ -0,0 +1,14 @@ +##fileformat=VCFv4.3 +##source=adVNTR ver. 1.3.3 +##command=GangSTR-2.4.2.12-9da7 --bam /scratch/bams/drive3/4512-JFI-0366_BXD196_phased_possorted_bam.bam --regions /scratch/regions/0705_mm10.bed --ref /scratch/ref/mm10.fa --str-info /scratch/strinfo/100519_mm10_strinfo_wo_stutt_recalc_many_samples.bed --chrom chr1 --trim-to-readlength 128 --drop-dupes --out result/4512-JFI-0366_BXD196/res_chr1 +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CSTB_2_5_testdata.bam +chr21 45196323 . GCGCGGGGCGGGGCGCGGGGCGGGGCGCGGGGCGGG GCGCGGGGCGGGGCGCGGGGCGGG,GCGCGGGGCGGGGCGCGGGGCGGGGCGCGGGGCGGGGCGCGGGGCGGGGCGCGGGGCGGG . . END=45196359;VID=301645;RU=GCGCGGGGCGGG;RC=3 GT:DP:SR:FR:ML 1/2:60:39:21:1.0 diff --git a/tests/data/test_popstr.vcf b/tests/data/test_popstr.vcf new file mode 100644 index 0000000..fa2d3f3 --- /dev/null +++ b/tests/data/test_popstr.vcf @@ -0,0 +1,124 @@ +##fileformat=VCFv4.2 +##FILTER= +##fileDate=20191025 +##source=PopSTR +##source_bin=/nfs/odinn/users/snaedisk/code/popSTR/computeReadAttributes +##source_bin=/nfs/odinn/users/snaedisk/code/popSTR/computePnSlippage +##source_bin=/nfs/odinn/users/snaedisk/code/popSTR/msGenotyperDefault +##reference=/odinn/data/reference/Homo_sapiens-deCODE-hg38/Sequence/WholeGenomeFasta/genome.fa +##contig= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##bcftools_viewVersion=1.10.2+htslib-1.10.2 +##bcftools_viewCommand=view -O v -o trtools/testsupport/sample_vcfs/test_popstr2.vcf -r chr21:0-6200000 trtools/testsupport/sample_vcfs/test_popstr.vcf.gz; Date=Thu Jul 2 17:58:46 2020 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 NA12891 NA12892 +chr21 5020351 chr21:5020351:M GGGGGGGCGGGGGGGGGG <14>,<17> . . RefLen=18;Motif=G GT:AD:DP:PL 0/2:5,0,11:17:152,197,255,0,90,44 1/2:1,11,6:18:255,84,131,255,0,255 0/0:14,0,0:15:0,44,255,44,255,255 +chr21 5024618 chr21:5024618:M TTTTTTTTTTTTTTTTTTTT <19> . . RefLen=20;Motif=T GT:AD:DP:PL 0/1:1,4:5:57,1,3 0/1:5,5:11:61,0,53 0/0:11,1:13:0,12,166 +chr21 5031126 chr21:5031126:M TTTTTTTTTTTTTTTTTTTTTT <21> . . RefLen=22;Motif=T GT:AD:DP:PL 1/1:0,3:3:51,9,0 1/1:0,4:4:66,12,0 0/0:3,0:3:0,9,50 +chr21 5040718 chr21:5040718:M TTTTTTTTTTT <10> . . RefLen=11;Motif=T GT:AD:DP:PL 0/1:11,24:35:255,0,105 0/1:12,13:25:160,0,141 0/0:18,0:19:0,56,255 +chr21 5042862 chr21:5042862:M AAAAAAAAAAAA <13> . . RefLen=12;Motif=A GT:AD:DP:PL 0/1:8,9:18:116,0,106 0/1:11,6:17:56,0,145 0/0:14,0:16:0,46,255 +chr21 5051279 chr21:5051279:M TCACTCACTCATTCATCCCACATTCACTCACTCA <1.8> . . RefLen=34;Motif=TCAC GT:AD:DP:PL 0/1:8,3:11:43,0,165 0/1:4,7:11:142,0,66 0/1:5,7:13:147,0,85 +chr21 5051299 chr21:5051299:M CATTCACTCACTCATTCATTCATCCCACATTCACTCATTCATTCAT <4.8> . . RefLen=46;Motif=CATT GT:AD:DP:PL 0/0:2,0:2:0,6,52 0/1:6,3:9:76,0,130 0/1:3,1:4:22,0,67 +chr21 5058258 chr21:5058258:M TTTTTTTGTTTTTTTTTTTTTT <21> . . RefLen=22;Motif=T GT:AD:DP:PL 0/1:2,6:8:86,0,12 0/1:6,6:12:68,0,69 0/0:5,0:5:0,15,89 +chr21 5067052 chr21:5067052:M AAAAAAAAAAAAAAAA <14> . . RefLen=16;Motif=A GT:AD:DP:PL 1/1:0,6:7:163,18,0 0/1:8,5:13:99,0,175 0/1:1,1:2:21,0,20 +chr21 5103483 chr21:5103483:M AAAAAAAAAAAAAAAAAGAAAAAAAAAA <27> . . RefLen=28;Motif=A GT:AD:DP:PL 0/0:9,0:10:0,29,166 0/0:8,2:12:0,1,119 0/1:4,13:17:174,0,19 +chr21 5103759 chr21:5103759:M ACACACACACACACACACACACACACACACACACACACACACACACA <24.5>,<25.5>,<26.5> . . RefLen=47;Motif=AC GT:AD:DP:PL 1/2:1,11,5,0:17:255,68,36,141,0,152,255,72,198,255 2/3:0,1,5,3:9:207,144,125,47,33,23,82,52,0,67 1/1:2,12,0,0:14:169,7,0,175,41,227,208,42,255,255 +chr21 5124343 chr21:5124343:M AAAAAAAAAAAAAAAAA <16> . . RefLen=17;Motif=A GT:AD:DP:PL 0/1:2,6:8:84,0,12 0/1:8,3:11:19,0,104 0/1:7,2:11:6,0,104 +chr21 5224724 chr21:5224724:M AAACAAACAAA <2.5> . . RefLen=11;Motif=AAAC GT:AD:DP:PL 0/1:180,60:256:61,0,255 0/1:172,46:242:27,0,255 0/1:156,91:272:255,0,255 +chr21 5229746 chr21:5229746:M TTGTTGTTGTTGTT <4.3> . . RefLen=14;Motif=TTG GT:AD:DP:PL 0/0:64,30:101:0,1,130 0/1:34,37:82:82,0,20 0/0:59,12:80:0,28,167 +chr21 5230609 chr21:5230609:M ACACACACACACACACACACACACACACACACAC <15>,<20>,<22>,<23> . . RefLen=34;Motif=AC GT:AD:DP:PL 0/2:15,0,14,5,7:45:255,255,255,0,190,200,26,236,139,255,100,255,131,255,255 1/4:6,9,0,2,12:30:255,255,255,255,255,255,111,72,255,255,39,0,244,242,223 0/3:27,0,13,17,7:67:255,255,255,152,255,255,0,255,255,255,142,255,255,255,255 +chr21 5230670 chr21:5230670:M AAAAAAGAAAAAACAAAAAAA <13> . . RefLen=21;Motif=A GT:AD:DP:PL 0/1:79,43:122:255,0,255 0/1:72,45:117:255,0,255 0/1:99,20:119:192,0,255 +chr21 5240627 chr21:5240627:M TTTTTTTTTTTTTTTTTT <16>,<17> . . RefLen=18;Motif=T GT:AD:DP:PL 1/2:13,21,20:63:255,32,137,136,0,102 1/2:6,11,26:52:255,124,153,110,0,39 1/2:13,26,35:77:255,128,231,140,0,66 +chr21 5242046 chr21:5242046:M TCTCTCTCTCTCTCTCTCTCTTTCTCTCTCTCT <12.5>,<17.5> . . RefLen=33;Motif=TC GT:AD:DP:PL 1/2:1,33,6:45:255,44,50,255,0,255 1/2:0,16,11:33:255,95,225,255,0,255 1/2:3,31,7:66:255,19,81,255,0,255 +chr21 5242078 chr21:5242078:M TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT <20.5> . . RefLen=37;Motif=TG GT:AD:DP:PL 0/1:18,12:39:77,0,170 1/1:2,10:22:115,4,0 0/1:24,15:56:110,0,240 +chr21 5245137 chr21:5245137:M GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCTGTGT <14> . . RefLen=40;Motif=GT GT:AD:DP:PL 0/1:12,28:82:255,0,255 0/1:19,28:77:255,0,237 0/1:12,44:94:255,0,255 +chr21 5247825 chr21:5247825:M TTTATTTATTT <2.5>,<3.2> . . RefLen=11;Motif=TTTA GT:AD:DP:PL 1/2:1,28,9:45:124,41,19,144,0,255 1/2:0,39,16:57:198,101,81,183,0,255 1/2:0,29,15:48:170,101,98,138,0,255 +chr21 5247833 chr21:5247833:M TTTTTTTTTTTT <11> . . RefLen=12;Motif=T GT:AD:DP:PL 1/1:11,57:76:255,86,0 1/1:7,35:52:255,65,0 1/1:8,80:90:255,154,0 +chr21 5260390 chr21:5260390:M ATATATATATATATAT <7>,<9> . . RefLen=16;Motif=AT GT:AD:DP:PL 1/2:5,15,15:36:255,197,255,188,0,255 0/2:4,0,8:12:101,135,255,0,57,33 0/1:23,12,0:35:108,0,255,208,255,255 +chr21 5261573 chr21:5261573:M TTTCTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTTCTTTCTTTCTTTCTTT <16.5>,<17.8> . . RefLen=77;Motif=TTTC GT:AD:DP:PL 0/2:0,0,5:16:67,22,68,0,11,16 1/1:0,0,0:5:0,0,0,0,0,0 1/2:0,9,2:30:211,4,92,48,0,46 +chr21 5296708 chr21:5296708:M ATAATAATAATAATAATAA <4.7>,<5.3> . . RefLen=19;Motif=ATA GT:AD:DP:PL 1/2:0,4,20:24:255,255,255,84,0,16 1/1:0,4,0:4:116,12,0,96,12,87 2/2:0,3,43:46:255,255,255,134,72,0 +chr21 5327591 chr21:5327591:M AGTGGAGTGGAGTGGAGTGGAGTTGATCAGAGTGCAGTGGAATTGAATGGAATGGACTGGAATGGAATAGAGTGGAGTGGAGGGGAGTGG <27> . . RefLen=90;Motif=AGTGG GT:AD:DP:PL 1/1:0,3:3:36,8,0 0/1:1,3:4:25,0,14 1/1:1,9:10:83,2,0 +chr21 5329879 chr21:5329879:M GAATGGAATGGAATGGAGTGGAGTGGA <27> . . RefLen=27;Motif=GAATG GT:AD:DP:PL 1/1:0,101:101:255,255,0 1/1:0,89:89:255,247,0 1/1:1,106:107:255,255,0 +chr21 5329940 chr21:5329940:M AATGGAGTGGAATGGAAT <27> . . RefLen=18;Motif=AATGG GT:AD:DP:PL 0/1:17,101:118:255,0,130 0/1:17,89:106:255,0,167 0/1:17,105:122:255,0,119 +chr21 5329969 chr21:5329969:M GAGTGGACTGGAGTGGAGTGGAGTTTAGTGGAGTG <27> . . RefLen=35;Motif=GAGTG GT:AD:DP:PL 0/1:13,20:33:153,0,247 0/1:4,19:23:169,0,40 0/1:14,26:40:208,0,254 +chr21 5334486 chr21:5334486:M TTTTTTTTTGTTTGTTTGTTTGTTTTTTT <28> . . RefLen=29;Motif=T GT:AD:DP:PL ./.:0,0:0:0,0,0 0/0:1,0:1:0,3,18 1/1:0,17:17:255,50,0 +chr21 5370146 chr21:5370146:M AAATAATAAATAAATAAATAAATAAA <7.5> . . RefLen=26;Motif=AAAT GT:AD:DP:PL 0/0:8,1:12:0,19,139 0/1:0,3:6:26,0,20 0/0:9,0:9:0,26,130 +chr21 5448587 chr21:5448587:M TTTTTTTTTTTTT <12>,<16> . . RefLen=13;Motif=T GT:AD:DP:PL 0/2:10,5,8:24:159,138,224,0,63,255 0/1:17,13,3:33:78,0,129,94,142,255 1/2:9,13,7:29:160,58,111,50,0,255 +chr21 5505757 chr21:5505757:M TGTGTGTGTCTGTCTGTGTGTGTGT <11.5> . . RefLen=25;Motif=TG GT:AD:DP:PL 0/1:9,2:11:3,0,125 0/1:14,4:18:15,0,181 1/1:0,4:4:69,12,0 +chr21 5511978 chr21:5511978:M ACACACACACACACACACACACACACACACACACACACACACACA <14.5>,<25.5> . . RefLen=45;Motif=AC GT:AD:DP:PL 1/2:0,1,3:7:132,92,101,46,0,32 1/2:1,3,1:7:106,33,63,60,0,69 1/2:0,0,5:8:144,124,143,32,0,14 +chr21 5515734 chr21:5515734:M AAAAAAAAAAAAAGAAAAAAGAAAAAAAA <28> . . RefLen=29;Motif=A GT:AD:DP:PL 1/1:4,17:24:248,2,0 0/1:10,8:19:83,0,106 1/1:0,21:22:255,64,0 +chr21 5520202 chr21:5520202:M TGTGTGTGTGTGTGTGTGTGTGTGATGTGTTTGTGTGTG <20.5> . . RefLen=39;Motif=TG GT:AD:DP:PL 0/1:2,1:3:2,0,12 0/1:6,3:11:1,0,46 ./.:0,0:0:0,0,0 +chr21 5520833 chr21:5520833:M TTTTTTTCTTTTCTTTTCTTTTTCTTTTTTTTTTTTTT <37>,<40> . . RefLen=38;Motif=T GT:AD:DP:PL 1/1:1,4,0:7:47,8,0,67,20,153 1/2:2,3,4:10:57,51,78,10,0,69 1/1:0,5,0:6:47,13,0,62,15,133 +chr21 5534983 chr21:5534983:M CTCTCTCTCTCCCTCTCTCTCTCTCT <13.5> . . RefLen=26;Motif=CT GT:AD:DP:PL 1/1:0,1:1:5,2,0 0/0:5,2:7:0,3,14 1/1:0,3:3:14,5,0 +chr21 5535008 chr21:5535008:M TTTTTTTTTTTT <16> . . RefLen=12;Motif=T GT:AD:DP:PL 1/1:0,3:3:87,9,0 0/1:5,4:9:87,0,119 0/1:1,1:3:32,0,21 +chr21 5536014 chr21:5536014:M ACACACAAACACACCACACACACACACACACACACACA <17> . . RefLen=38;Motif=AC GT:AD:DP:PL 1/1:0,11:12:220,33,0 1/1:0,9:11:178,27,0 1/1:0,28:29:255,86,0 +chr21 5550856 chr21:5550856:M AAAAAAAAAAAAA <14> . . RefLen=13;Motif=A GT:AD:DP:PL 1/1:1,5:6:68,1,0 0/0:5,0:5:0,15,81 0/0:1,0:1:0,3,17 +chr21 5552200 chr21:5552200:M CACACACACACA <7.5> . . RefLen=12;Motif=CA GT:AD:DP:PL 1/1:1,18:20:255,20,0 0/1:2,2:5:29,0,36 1/1:0,24:25:255,57,0 +chr21 5552591 chr21:5552591:M GAAGAAGGAGAAGAAGAAGAGGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA <45> . . RefLen=92;Motif=GAA GT:AD:DP:PL 1/1:0,3:4:35,8,0 1/1:0,5:7:58,14,0 1/1:0,5:6:58,14,0 +chr21 5555313 chr21:5555313:M TTTTTTTTTTTT <10>,<11> . . RefLen=12;Motif=T GT:AD:DP:PL 1/2:6,11,13:34:130,5,112,9,0,12 0/1:20,7,3:32:32,0,255,27,153,136 0/1:3,17,3:29:210,0,72,114,44,119 +chr21 5557399 chr21:5557399:M AAAAAAAAAAATAAAAAAAAAAA <26> . . RefLen=23;Motif=A GT:AD:DP:PL 0/1:6,7:16:158,0,108 0/1:4,6:10:119,0,72 1/1:1,10:12:240,11,0 +chr21 5557715 chr21:5557715:M TTTTTTTGTTTTTTTCTTTT <14> . . RefLen=20;Motif=T GT:AD:DP:PL 0/1:16,5:21:78,0,255 0/0:14,1:15:0,18,255 0/1:7,6:15:131,0,151 +chr21 5562461 chr21:5562461:M TTTTTTTTTTTTTTTT <14> . . RefLen=16;Motif=T GT:AD:DP:PL 0/1:6,9:15:162,0,96 1/1:1,10:14:218,12,0 0/1:2,10:12:196,0,11 +chr21 5563477 chr21:5563477:M TGTTGTTGTTGTTGTTGTTGT <10> . . RefLen=21;Motif=TGT GT:AD:DP:PL 0/1:13,4:18:64,0,255 0/1:13,3:16:31,0,255 0/1:7,6:15:107,0,154 +chr21 5563948 chr21:5563948:M TTTTTTTTTTTTTTTTTT <15> . . RefLen=18;Motif=T GT:AD:DP:PL 0/1:3,2:5:38,0,65 0/1:2,1:6:81,0,49 0/1:2,3:6:91,0,38 +chr21 5564112 chr21:5564112:M TTTTTTTTTTT <12> . . RefLen=11;Motif=T GT:AD:DP:PL 0/1:11,10:21:93,0,108 0/1:13,6:20:43,0,135 1/1:3,15:19:191,9,0 +chr21 5580885 chr21:5580885:M TCTCTCTCTTTCTTTCTTTCCTTCTCTCTCTCT <4.5>,<5.5> . . RefLen=33;Motif=TC GT:AD:DP:PL 0/2:5,0,3:8:57,35,159,0,132,124 0/2:13,1,3:17:83,23,255,0,255,255 1/1:0,4,1:5:215,15,0,51,2,36 +chr21 5582877 chr21:5582877:M AAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAA <5.2> . . RefLen=43;Motif=AAAT GT:AD:DP:PL 1/1:0,3:3:88,9,0 0/1:0,3:5:74,0,4 1/1:0,1:1:30,3,0 +chr21 5589529 chr21:5589529:M AAAAGAAAAACAAAAA <2.8> . . RefLen=16;Motif=AAAACA GT:AD:DP:PL 0/0:19,0:19:0,53,252 0/1:16,8:24:39,0,145 0/0:15,2:17:0,21,172 +chr21 5592304 chr21:5592304:M AAAAAAAAAAAAA <11> . . RefLen=13;Motif=A GT:AD:DP:PL 0/1:5,4:18:38,0,58 0/0:7,0:13:0,26,145 0/1:0,6:10:73,0,17 +chr21 5598766 chr21:5598766:M AAAAAGAAAAAAAAAA <15> . . RefLen=16;Motif=A GT:AD:DP:PL 0/1:17,12:33:81,0,197 0/0:26,5:31:0,18,255 0/1:21,14:39:90,0,234 +chr21 5613671 chr21:5613671:M TTATGATTATGATTATGATTATGATTATGATTATGATTATGATTAT <6.7> . . RefLen=46;Motif=TTATGA GT:AD:DP:PL 0/1:2,6:19:81,0,11 0/1:4,6:14:73,0,9 1/1:0,10:16:96,1,0 +chr21 5614254 chr21:5614254:M AGAGAGAGAGAGAGA <14.5> . . RefLen=15;Motif=AG GT:AD:DP:PL 0/1:13,3:16:27,0,255 0/0:15,0:16:0,31,255 0/1:6,3:10:46,0,126 +chr21 5624629 chr21:5624629:M ATATATATATATAT <9> . . RefLen=14;Motif=AT GT:AD:DP:PL 0/1:5,9:17:200,0,52 0/1:4,5:13:140,0,43 0/1:6,14:20:234,0,63 +chr21 5625184 chr21:5625184:M ATTTATTTATTTATTTATTTATTT <7> . . RefLen=24;Motif=ATTT GT:AD:DP:PL 0/0:21,1:22:0,47,194 0/0:21,6:27:0,12,143 0/1:17,9:26:20,0,97 +chr21 5687702 chr21:5687702:M ATATATATATATAT <9> . . RefLen=14;Motif=AT GT:AD:DP:PL 0/1:10,13:30:255,0,118 0/1:11,15:27:252,0,144 0/1:9,9:18:140,0,132 +chr21 5688257 chr21:5688257:M ATTTATTTATTTATTTATTTATTT <7> . . RefLen=24;Motif=ATTT GT:AD:DP:PL 0/0:16,5:21:0,6,106 0/0:17,5:22:0,9,114 0/1:20,8:28:5,0,120 +chr21 5693908 chr21:5693908:M ATTTATTTATTT <2.5> . . RefLen=12;Motif=ATTT GT:AD:DP:PL 0/1:7,7:16:31,0,16 0/1:7,8:16:31,0,16 1/1:1,11:12:76,20,0 +chr21 5698851 chr21:5698851:M AAAAAAAAAAAAAAAA <15> . . RefLen=16;Motif=A GT:AD:DP:PL 0/0:36,2:41:0,66,255 0/1:16,7:27:25,0,128 0/0:30,10:47:0,5,255 +chr21 5711871 chr21:5711871:M TTTCTTTCTTTCTTTCCTTTTCTGTCTTCTTTCTTTCTCTCTTTCTTTCCTTCTTTCTTTCTCTCTTCTTTTTTCTTTCTTTCTTT <15.2> . . RefLen=86;Motif=TTTC GT:AD:DP:PL 1/1:0,4:4:124,12,0 1/1:0,4:4:119,12,0 1/1:0,4:4:123,12,0 +chr21 5717129 chr21:5717129:M TTTTTTTTTTTTTTTTTTTTTTT <16>,<20> . . RefLen=23;Motif=T GT:AD:DP:PL 0/1:1,0,1:4:27,0,20,6,0,22 1/2:0,1,3:5:102,66,65,37,0,27 1/2:0,5,2:9:187,47,30,134,0,125 +chr21 5738430 chr21:5738430:M AAAAAAAAAAAAAAAAAAA <20> . . RefLen=19;Motif=A GT:AD:DP:PL 0/0:5,2:9:0,4,36 0/0:8,0:13:0,28,96 1/1:0,4:7:41,12,0 +chr21 5745954 chr21:5745954:M CACACACACACACACACACACACACAC <14.5>,<15.5> . . RefLen=27;Motif=CA GT:AD:DP:PL 0/0:19,2,0:21:0,34,207,57,255,255 0/0:15,4,0:19:0,4,131,45,182,255 1/2:2,5,3:10:77,12,9,24,0,55 +chr21 5757052 chr21:5757052:M TTTTTTTTTTT <12> . . RefLen=11;Motif=T GT:AD:DP:PL 0/0:18,5:25:0,11,166 0/1:7,12:22:73,0,48 0/1:16,7:23:16,0,115 +chr21 5758152 chr21:5758152:M AGAAGAAGAAGA <3> . . RefLen=12;Motif=AGA GT:AD:DP:PL 0/1:31,10:41:28,0,255 0/0:34,1:35:0,85,255 0/1:31,11:42:37,0,255 +chr21 5762970 chr21:5762970:M AAAAAAAAAAA <12> . . RefLen=11;Motif=A GT:AD:DP:PL 0/1:11,6:18:19,0,86 0/0:19,1:20:0,43,199 0/1:22,8:30:9,0,165 +chr21 5772988 chr21:5772988:M AAACAAAACAAAACAAAACAAAACAAAACAAAACAAAACA <7> . . RefLen=40;Motif=AAACA GT:AD:DP:PL 1/1:2,8:11:82,1,0 1/1:3,12:15:119,2,0 1/1:0,17:17:229,48,0 +chr21 5774011 chr21:5774011:M AAAAAAAAAAAAAA <13> . . RefLen=14;Motif=A GT:AD:DP:PL 0/1:8,10:18:127,0,91 0/1:8,12:20:147,0,78 0/1:6,15:21:203,0,44 +chr21 5784132 chr21:5784132:M TTTTTTTTTTTTTTTTTT <19> . . RefLen=18;Motif=T GT:AD:DP:PL 0/1:4,1:7:7,0,36 0/0:6,0:7:0,8,63 0/1:6,3:9:13,0,51 +chr21 5790769 chr21:5790769:M TTTTTTTTTTTTTTTTT <16> . . RefLen=17;Motif=T GT:AD:DP:PL 0/0:28,1:29:0,68,255 0/1:9,5:14:42,0,109 0/0:23,2:25:0,39,255 +chr21 5794367 chr21:5794367:M TTTTTTTTTTTT <13> . . RefLen=12;Motif=T GT:AD:DP:PL 0/1:29,13:45:80,0,255 0/1:17,16:38:172,0,176 0/0:30,3:33:0,48,255 +chr21 5859014 chr21:5859014:M AAAAAAAAAAAAAAAAAAA <18>,<20> . . RefLen=19;Motif=A GT:AD:DP:PL 0/0:11,0,1:15:0,26,98,16,76,77 0/1:2,3,0:5:12,0,4,24,13,53 0/2:6,0,3:11:1,16,65,0,29,33 +chr21 5866538 chr21:5866538:M CACACACACACACACACACACACACAC <14.5> . . RefLen=27;Motif=CA GT:AD:DP:PL 0/1:13,4:17:1,0,110 0/0:17,2:21:0,33,198 0/1:3,4:9:44,0,12 +chr21 5877636 chr21:5877636:M TTTTTTTTTTT <12> . . RefLen=11;Motif=T GT:AD:DP:PL 0/0:12,3:15:0,7,100 0/1:7,7:16:34,0,53 0/1:16,6:22:7,0,117 +chr21 5878736 chr21:5878736:M AGAAGAAGAAGA <3> . . RefLen=12;Motif=AGA GT:AD:DP:PL 0/1:21,9:30:44,0,218 0/0:33,3:36:0,60,255 0/1:24,12:36:69,0,240 +chr21 5881133 chr21:5881133:M TAAAATAAAATAAAACAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATA <10.4> . . RefLen=57;Motif=TAAAA GT:AD:DP:PL 0/1:2,4:6:32,0,8 0/1:3,1:4:1,0,25 ./.:0,0:0:0,0,0 +chr21 5883554 chr21:5883554:M AAAAAAAAAAA <12> . . RefLen=11;Motif=A GT:AD:DP:PL 0/1:8,5:13:22,0,56 0/0:28,4:34:0,47,255 0/1:22,10:33:24,0,169 +chr21 5893572 chr21:5893572:M AAACAAAACAAAACAAAACAAAACAAAACAAAACAAAACA <7> . . RefLen=40;Motif=AAACA GT:AD:DP:PL 1/1:2,15:17:176,21,0 1/1:2,14:17:158,19,0 1/1:0,14:14:187,39,0 +chr21 5894595 chr21:5894595:M AAAAAAAAAAAAAA <13> . . RefLen=14;Motif=A GT:AD:DP:PL 0/1:8,4:13:33,0,115 0/1:6,12:18:152,0,49 0/1:6,9:16:119,0,59 +chr21 5904716 chr21:5904716:M TTTTTTTTTTTTTTTTTT <19> . . RefLen=18;Motif=T GT:AD:DP:PL 0/0:8,0:9:0,25,113 0/0:5,0:5:0,14,62 0/1:8,4:13:14,0,76 +chr21 5910071 chr21:5910071:M GGGAGGGGGGAGGGA <3.5> . . RefLen=15;Motif=GGGA GT:AD:DP:PL 0/0:19,2:21:0,10,255 0/1:8,3:11:43,0,171 0/0:17,0:17:0,51,255 +chr21 5914951 chr21:5914951:M TTTTTTTTTTTT <13>,<14> . . RefLen=12;Motif=T GT:AD:DP:PL 0/1:22,10,0:33:68,0,255,135,255,255 0/2:12,9,9:31:187,22,124,0,68,255 0/0:40,0,0:41:0,119,255,123,255,255 +chr21 5972367 chr21:5972367:M TTTTGTTTTTTTTTTTTTTT <21> . . RefLen=20;Motif=T GT:AD:DP:PL 0/0:10,0:10:0,29,180 0/0:3,0:5:0,14,74 0/1:5,3:8:29,0,64 +chr21 5980542 chr21:5980542:M TTTTTTTTTTTTTTTTTTTT <21> . . RefLen=20;Motif=T GT:AD:DP:PL 1/1:1,11:12:185,17,0 0/1:2,12:16:163,0,11 1/1:1,8:9:127,8,0 +chr21 5981384 chr21:5981384:M TTTTTTTTTTTTTTTTT <16> . . RefLen=17;Motif=T GT:AD:DP:PL 0/1:4,3:7:34,0,52 0/1:6,1:9:3,0,89 0/0:9,1:13:0,5,140 +chr21 5983797 chr21:5983797:M TTTTTTTTTTTTTTTT <18>,<19> . . RefLen=16;Motif=T GT:AD:DP:PL 0/1:5,4,0:10:85,0,115,70,132,199 0/1:1,2,1:5:55,0,16,18,12,44 0/2:2,0,3:5:69,49,92,0,52,45 +chr21 5990439 chr21:5990439:M TTTTTTTTTTTGTTGTTGTTTTTTTTT <28> . . RefLen=27;Motif=T GT:AD:DP:PL 0/1:7,9:17:119,0,91 0/1:6,13:19:174,0,50 0/1:9,3:12:20,0,129 +chr21 5990535 chr21:5990535:M TTTTTTTTTTTTTTTT <22> . . RefLen=16;Motif=T GT:AD:DP:PL 0/1:7,6:15:156,0,174 0/1:3,0:5:13,0,86 0/0:7,0:9:0,9,189 +chr21 5996445 chr21:5996445:M TTTTTTTTTTTTTTTTTT <15>,<17> . . RefLen=18;Motif=T GT:AD:DP:PL 1/2:0,6,6:14:255,111,133,160,0,135 0/1:4,10,2:17:253,0,86,230,33,255 1/2:0,12,3:18:255,60,40,255,0,255 +chr21 6005386 chr21:6005386:M TTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTT <7.8> . . RefLen=35;Motif=TTTG GT:AD:DP:PL 0/1:9,9:18:124,0,121 0/1:9,8:17:98,0,113 0/1:7,14:21:207,0,70 +chr21 6020382 chr21:6020382:M TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCTTTGTGTGTG <21> . . RefLen=50;Motif=TG GT:AD:DP:PL 1/1:0,3:3:95,9,0 0/1:4,5:9:131,0,86 0/1:4,3:8:72,0,102 +chr21 6040905 chr21:6040905:M AAAAAAAAAAAAA <14> . . RefLen=13;Motif=A GT:AD:DP:PL 0/1:11,15:26:203,0,128 0/1:10,6:17:65,0,127 0/1:12,10:23:115,0,161 +chr21 6070033 chr21:6070033:M TGTGTGTGAGGTGTGTGGTGTGTGTG <67.5> . . RefLen=26;Motif=TG GT:AD:DP:PL 0/1:19,14:33:71,0,255 0/1:30,12:42:19,0,255 0/1:26,16:42:68,0,255 +chr21 6070105 chr21:6070105:M TGTGTGTGTAGTGTATGTGGTTGTGTG <67.5> . . RefLen=27;Motif=TG GT:AD:DP:PL 0/1:22,14:36:66,0,255 0/1:27,12:39:31,0,255 0/1:30,16:46:60,0,255 +chr21 6071721 chr21:6071721:M GGGGGGGGGGG <12> . . RefLen=11;Motif=G GT:AD:DP:PL 0/1:1,3:4:40,0,5 1/1:0,1:1:17,3,0 1/1:0,3:3:51,9,0 +chr21 6072175 chr21:6072175:M TTTTTTTTTTTTTTTTTTTT <21> . . RefLen=20;Motif=T GT:AD:DP:PL 0/1:6,4:10:42,0,78 0/0:2,0:2:0,6,34 1/1:0,1:1:18,3,0 +chr21 6073138 chr21:6073138:M CCCCCCCACCCCCCCCC <16>,<18> . . RefLen=17;Motif=C GT:AD:DP:PL 1/1:0,16,0:16:216,45,0,255,48,255 1/2:0,3,1:4:41,12,12,38,0,61 1/2:0,3,3:6:62,39,55,39,0,56 +chr21 6075369 chr21:6075369:M TTTTTTTTTTAGTTTTTTAGTTTTTGTTTTTTTTGCTTTTTTTTTTTTT <50> . . RefLen=49;Motif=T GT:AD:DP:PL 0/1:4,3:7:33,0,52 0/0:4,0:4:0,12,69 0/1:1,1:2:12,0,12 +chr21 6097940 chr21:6097940:M CACACACACACACACACACACACACA <14> . . RefLen=26;Motif=CA GT:AD:DP:PL 0/0:28,0:28:0,82,255 0/1:16,8:26:62,0,220 0/0:31,1:33:0,79,255 +chr21 6100222 chr21:6100222:M AAAAAAAAAAAAAAAA <17>,<18> . . RefLen=16;Motif=A GT:AD:DP:PL 1/2:1,13,7:21:255,105,63,177,0,180 0/2:22,1,6:31:93,94,255,0,255,255 1/1:2,18,3:23:255,32,0,242,15,255 +chr21 6109896 chr21:6109896:M GTGTGTGTGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT <24>,<27>,<29> . . RefLen=44;Motif=GT GT:AD:DP:PL 2/3:0,0,5,4:10:255,255,255,108,108,88,143,142,0,128 1/2:0,3,4,0:9:211,130,120,81,0,66,209,127,84,209 3/3:0,0,0,6:6:184,184,184,179,179,175,18,18,18,0 +chr21 6132994 chr21:6132994:M ATATATATATATATATATATATATATA <12.5>,<17.5> . . RefLen=27;Motif=AT GT:AD:DP:PL 0/2:2,0,5:8:137,143,168,0,31,35 1/2:0,6,1:7:97,23,6,90,0,156 0/0:9,0,0:10:0,29,151,30,178,255 diff --git a/tests/dataloader.py b/tests/dataloader.py new file mode 100644 index 0000000..d767db9 --- /dev/null +++ b/tests/dataloader.py @@ -0,0 +1,23 @@ +import os + +import pytest +from pathlib import Path + +DATADIR = Path(__file__).parent.joinpath("data") + +# functions that all pytests have access to +# Not for use in runtime code! + + +# Usage based on this documentation +# https://docs.pytest.org/en/latest/example/simple.html#pass-different-values-to-a-test-function-depending-on-command-line-options +def pytest_addoption(parser): + default = os.path.dirname(os.path.abspath(__file__)) + parser.addoption( + "--datadir", default=default, help="Directory containing sample data files" + ) + + +@pytest.fixture() +def vcfdir(request): + return DATADIR diff --git a/tests/test_logging.py b/tests/test_logging.py new file mode 100755 index 0000000..849ec75 --- /dev/null +++ b/tests/test_logging.py @@ -0,0 +1,49 @@ +import logging + +from core.logging import getLogger + + +def test_getLogger(caplog): + logger = getLogger() + assert isinstance(logger, logging.Logger) + + # capture any messages that get logged to the Logger + with caplog.at_level(logging.ERROR): + logger.error("Error message") + + # check that we properly logged the message + assert "Error message" in caplog.text + + +def test_getLogger_with_name(): + logger_name = "test_logger" + logger = getLogger(name=logger_name) + assert logger.name == "core.test_logger" + + +def test_getLogger_with_level(): + logger = getLogger(level="DEBUG") + assert logger.level == logging.DEBUG + logger = getLogger(level=logging.DEBUG) + assert logger.level == logging.DEBUG + + +def test_getLogger_with_exact_time(): + logger = getLogger() + formatter = logger.handlers[0].formatter + assert "%(msecs)" not in formatter._fmt + + +def test_getLogger_with_index_name(): + log = getLogger(name="index") + log.setLevel(logging.ERROR) + assert isinstance(log, logging.Logger) + assert log.name == "core.index" + + +def test_getLogger_with_default_parameters(): + logger = getLogger() + assert isinstance(logger, logging.Logger) + assert logger.name == "core" + # by default, the log level should be "ERROR" + assert logger.level == logging.ERROR diff --git a/tests/test_trharmonizer.py b/tests/test_trharmonizer.py new file mode 100644 index 0000000..f2b472e --- /dev/null +++ b/tests/test_trharmonizer.py @@ -0,0 +1,1168 @@ +import os +import types + +# from typing import List + +import cyvcf2 +import pytest +import numpy as np +from pytest import approx + +import core.tr_harmonizer as trh + +# pylint: disable=C0116,C0103 + +#### Test TRRecord using dummy info #### + +# TODO add tests that check this for quality scores? + + +class DummyCyvcf2Record: + def __init__( + self, + gts, # arraylike (n x 2). All entries in a row should contain -1s for no calls + # For calls with different ploidy, the array should + # contain columns equal to the greatest ploidy and lower + # ploidy calls should be padded with -1s + # if this is a vcf with no samples in it (just loci + # descriptions) then this should be None + ref, + alt, + ): + self.POS = 42 + self.CHROM = "1984" + self.FORMAT = {} + self.INFO = {} + self.ALT = list(alt) + self.REF = ref + + if gts is not None: + self.genotype = types.SimpleNamespace() + self._gts = np.array(gts) + if len(self._gts) > 0: + self._gts = np.concatenate( + (self._gts, np.zeros((self._gts.shape[0], 1))), axis=1 + ) # add the phasing axis, we're not testing that here + self.genotype.array = lambda: self._gts + self.genotype.n_samples = len(gts) + else: + self.genotype = None + + def format(self, key): + return self.FORMAT.get(key, None) + + +# Set up dummy VCF records which are just lists of genotypes +dummy_record_gts = [[0, 1], [1, 1], [1, 1], [1, 2], [2, 2], [0, -1]] + + +def get_dummy_record(): + return DummyCyvcf2Record( + gts=dummy_record_gts, # last sample is haploid + ref="CAGCAGCAG", + alt=("CAGCAGCAGCAG", "CAGCAGCAGCAGCAGCAG"), + ) + + +def get_dummy_record_empty(): + return DummyCyvcf2Record( + gts=[], ref="CAGCAGCAG", alt=("CAGCAGCAGCAG", "CAGCAGCAGCAGCAGCAG") + ) + + +dummy_record_diploid = [[0, 1], [1, 1], [1, 1], [1, 2], [2, 2], [0, 0]] + + +def get_dummy_record_diploid(): + return DummyCyvcf2Record( + gts=dummy_record_diploid, # last sample is haploid + ref="CAGCAGCAG", + alt=("CAGCAGCAGCAG", "CAGCAGCAGCAGCAGCAG"), + ) + + +dummy_record_gts_allsamelen = [[0, 0], [0, 0], [0, 1], [1, 1]] + + +def get_dummy_record_gts_allsamelen(): + return DummyCyvcf2Record( + gts=dummy_record_gts_allsamelen, ref="CAGCAGCAG", alt=["CAGCAACAG"] + ) + + +dummy_record_gts_monomorphic = [[0, 0], [0, 0], [0, 0], [0, 0]] + + +def get_dummy_record_gts_monomorphic(): + return DummyCyvcf2Record(gts=dummy_record_gts_monomorphic, ref="CAGCAGCAG", alt=[]) + + +triploid_gts = np.array([[0, 0, -2], [0, 0, -2], [0, 0, -2], [0, 0, 0]]) + + +def get_triploid_record(): + return DummyCyvcf2Record(gts=triploid_gts, ref="CAGCAGCAG", alt=[]) + + +def get_nocall_record(): + return DummyCyvcf2Record(gts=[[-1, -1]], ref="CAGCAGCAG", alt=[]) + + +def get_record_with_nosamples(): + return DummyCyvcf2Record( + gts=None, ref="CAGCAGCAG", alt=["CAGCAGCAGCAG", "CAGCAGCAGCAGCAGCAG"] + ) + + +def test_unexpected_vcf_type(): + with pytest.raises(ValueError): + trh._UnexpectedTypeError(trh.VcfTypes.gangstr) # pylint: disable=W0212 + + +def test_TRRecord_print(): + ref = "ABC" + alt = ["DEF", "GHI"] + motif = "foo" + ID = "bar" + test_rec = DummyCyvcf2Record(None, ref, alt) + + # default format + record = trh.TRRecord(test_rec, ref, alt, motif, ID, None) + assert str(record) == "{} {} {} {},{}".format(ID, motif, ref, alt[0], alt[1]) + + # having a quality field doesn't change the format + record = trh.TRRecord(test_rec, ref, alt, motif, ID, "some_field") + assert str(record) == "{} {} {} {},{}".format(ID, motif, ref, alt[0], alt[1]) + + # use CHROM:POS if records do not have Ids + record = trh.TRRecord(test_rec, ref, alt, motif, None, None) + assert str(record) == "{}:{} {} {} {},{}".format( + test_rec.CHROM, test_rec.POS, motif, ref, alt[0], alt[1] + ) + + # full alleles are printed over short alleles when present + record = trh.TRRecord( + test_rec, "B", ["E", "H"], motif, ID, None, full_alleles=(ref, alt) + ) + assert str(record) == "{} {} {} {},{}".format(ID, motif, ref, alt[0], alt[1]) + + # alt allele lens are printed when seqs are not present + record = trh.TRRecord( + test_rec, ref, None, motif, ID, None, alt_allele_lengths=[3, 5.5] + ) + assert str(record) == "{} {} {} n_reps:3,n_reps:5.5".format(ID, motif, ref) + + # ref allele len is printed when seq is not present + record = trh.TRRecord( + test_rec, + None, + None, + motif, + ID, + None, + ref_allele_length=7, + alt_allele_lengths=[3, 5.5], + ) + assert str(record) == "{} {} n_reps:7 n_reps:3,n_reps:5.5".format(ID, motif) + + +def test_TRRecord_output_shape(): + rec = get_dummy_record() + record = trh.TRRecord(rec, rec.REF, rec.ALT, "CAG", "STR1", None) + assert record.GetGenotypeIndicies().shape == rec.genotype.array().shape + + +def test_TRRecord_allele_seqs_from_lens(): + rec = get_record_with_nosamples() + ref_allele = rec.REF + alt_alleles = rec.ALT + motif = "CAG" + ID = "BAR" + + # alt alleles + # confirm cannot use alt_allele_lengths and alt_allele sequences at the same time + with pytest.raises(ValueError): + trh.TRRecord( + rec, + ref_allele, + alt_alleles, + motif, + ID, + "some_field", + alt_allele_lengths=[4, 6], + ) + + # confirm accessing fabricated alt_alleles from lengths + record = trh.TRRecord( + rec, ref_allele, None, motif, ID, "some_field", alt_allele_lengths=[4, 5.5] + ) + assert record.alt_alleles == [motif * 4, motif * 5 + "C"] + + # ref allele + # confirm cannot use ref_allele_length and ref_allele sequence at the same time + with pytest.raises(ValueError): + trh.TRRecord(rec, ref_allele, alt_alleles, motif, ID, None, ref_allele_length=5) + + # confirm cannot use ref_allele_length and alt_allele sequences at the same time + with pytest.raises(ValueError): + trh.TRRecord(rec, None, alt_alleles, motif, ID, None, ref_allele_length=5) + + # confirm accessing fabricated ref_allele from length + record = trh.TRRecord( + rec, + None, + None, + motif, + ID, + None, + ref_allele_length=5.5, + alt_allele_lengths=[4, 5.5], + ) + assert record.ref_allele == motif * 5 + "C" + + +def test_TRRecord_unique_lengths(): + alts = ["ACGAAGACG", "ACGACGACGACG", "ACGACGACAACG"] + ref = "ACGACGACG" + test_rec = DummyCyvcf2Record(None, ref, alts) + record = trh.TRRecord(test_rec, ref, alts, "ACG", "ACG-repeat", None) + + assert record.UniqueLengthGenotypes() == {0, 2} + assert record.UniqueLengthGenotypeMapping() == {0: 0, 1: 0, 2: 2, 3: 2} + + +def test_TRRecord_full_alleles(): + full_ref = "TCAGCAGCAGA" + full_alts = [ + "ACAGCAGCAGCAGC", + "ACAGCAGCAGCAGCAGCAGG", + "ACAGCAGCAGCAGG", + "ACAGCAGCAGG", + "TCAGCAGG", + ] + ref_allele = full_ref[1:-1] + alt_alleles = [] + for allele in full_alts: + alt_alleles.append(allele[1:-1]) + motif = "CAG" + ID = "STR1" + test_rec = DummyCyvcf2Record(None, full_ref, full_alts) + + # confirm that you need to set ref_allele if you wish to set full alleles + with pytest.raises(ValueError): + trh.TRRecord( + test_rec, + None, + alt_alleles, + motif, + ID, + None, + full_alleles=(full_ref, full_alts), + ) + # confirm that you need to set alt_alleles if you wish to set full alleles + with pytest.raises(ValueError): + trh.TRRecord( + test_rec, + ref_allele, + None, + motif, + ID, + None, + full_alleles=(full_ref, full_alts), + ) + # confirm that each allele in full_alleles must contain its corresponding + # non-full allele as a substring + with pytest.raises(ValueError): + trh.TRRecord( + test_rec, + ref_allele, + alt_alleles, + motif, + ID, + None, + full_alleles=(["CAGCAGCAQQQQQQQQQQQQQQQ"], full_alts), + ) + with pytest.raises(ValueError): + bad_alts = ["CAGCAGCAQQQQQQQQQQQQQQQ", full_alts[1]] + trh.TRRecord( + test_rec, + ref_allele, + alt_alleles, + motif, + ID, + None, + full_alleles=(ref_allele, bad_alts), + ) + + record = trh.TRRecord( + test_rec, + ref_allele, + alt_alleles, + motif, + ID, + None, + full_alleles=(ref_allele, alt_alleles), + ) + + assert record.UniqueStringGenotypes() == {0, 1, 2, 5} + assert record.UniqueStringGenotypeMapping() == {0: 0, 1: 1, 2: 2, 3: 1, 4: 0, 5: 5} + + +def test_TRRecord_GetGenotypes_Dosages(): + dummy_record = get_dummy_record() + # Test good example + ref_allele = dummy_record.REF + alt_alleles = dummy_record.ALT + rec = trh.TRRecord(dummy_record, ref_allele, alt_alleles, "CAG", "", None) + true_gts = [ + [ref_allele, alt_alleles[0]], + [alt_alleles[0], alt_alleles[0]], + [alt_alleles[0], alt_alleles[0]], + [alt_alleles[0], alt_alleles[1]], + [alt_alleles[1], alt_alleles[1]], + [ref_allele, "."], + ] + true_gts = np.array(true_gts) + true_len_gts = np.array([[3, 4], [4, 4], [4, 4], [4, 6], [6, 6], [3, -1]]) + true_bestguess_dosages = np.array([7, 8, 8, 10, 12, 3]) + true_bestguess_norm_dosages = 2 * np.array([1 / 6, 1 / 3, 1 / 3, 2 / 3, 1, np.nan]) + assert np.all(rec.GetGenotypeIndicies()[:, :-1] == np.array(dummy_record_gts)) + assert np.all(rec.GetLengthGenotypes()[:, :-1] == true_len_gts) + assert np.all(rec.GetStringGenotypes()[:, :-1] == true_gts) + assert np.all(rec.GetDosages() == true_bestguess_dosages) + assert np.all( + rec.GetDosages(dosagetype=trh.TRDosageTypes.bestguess) == true_bestguess_dosages + ) + + # Test empty + empty_record = get_dummy_record_empty() + rec = trh.TRRecord( + empty_record, empty_record.REF, empty_record.ALT, "CAG", "", None + ) + assert rec.GetDosages() is None + + # Test all ref + allsamelen_record = get_dummy_record_gts_allsamelen() + allsamelen_record.FORMAT["AP1"] = np.array([[0], [0], [0], [0]]) + allsamelen_record.FORMAT["AP2"] = np.array([[0], [0], [0], [0]]) + rec = trh.TRRecord( + allsamelen_record, allsamelen_record.REF, allsamelen_record.ALT, "CAG", "", None + ) + true_bestguess_norm_dosages = np.array([0, 0, 0, 0], dtype=np.float32) + assert np.all( + rec.GetDosages(dosagetype=trh.TRDosageTypes.bestguess_norm) + == true_bestguess_norm_dosages + ) + true_bestguess_dosages = np.array([6, 6, 6, 6]) + assert np.all( + rec.GetDosages(dosagetype=trh.TRDosageTypes.bestguess) == true_bestguess_dosages + ) + true_beagle_norm_dosages = np.array([0, 0, 0, 0]) + assert np.all( + rec.GetDosages(dosagetype=trh.TRDosageTypes.beagleap_norm) + == true_beagle_norm_dosages + ) + + monomorphic_record = get_dummy_record_gts_monomorphic() + monomorphic_record.FORMAT["AP1"] = np.array([[]]) + monomorphic_record.FORMAT["AP2"] = np.array([[]]) + rec = trh.TRRecord(monomorphic_record, monomorphic_record.REF, [], "CAG", "", None) + true_bestguess_norm_dosages = np.array([0, 0, 0, 0], dtype=np.float32) + assert np.all( + rec.GetDosages(dosagetype=trh.TRDosageTypes.bestguess_norm) + == true_bestguess_norm_dosages + ) + true_beagleap_dosages = np.array([6, 6, 6, 6], dtype=np.float32) + assert np.all( + rec.GetDosages(dosagetype=trh.TRDosageTypes.beagleap) == true_beagleap_dosages + ) + + # Test regular diploid record - Example with bestguess same as AP-based dosage + diploid_record = get_dummy_record_diploid() + diploid_record.FORMAT["AP1"] = np.array( + [[0, 0], [1, 0], [1, 0], [1, 0], [0, 1], [0, 0]] + ) + diploid_record.FORMAT["AP2"] = np.array( + [[1, 0], [1, 0], [1, 0], [0, 1], [0, 1], [0, 0]] + ) + rec = trh.TRRecord( + diploid_record, diploid_record.REF, diploid_record.ALT, "CAG", "", None + ) + true_bestguess_dosages = np.array([7, 8, 8, 10, 12, 6]) + true_bestguess_dosages_norm = 2 * np.array( + [1 / 6, 1 / 3, 1 / 3, 2 / 3, 1, 0], dtype=np.float32 + ) + assert np.all( + rec.GetDosages(dosagetype=trh.TRDosageTypes.bestguess) == true_bestguess_dosages + ) + assert np.all( + rec.GetDosages(dosagetype=trh.TRDosageTypes.beagleap) == true_bestguess_dosages + ) + assert np.all( + rec.GetDosages(dosagetype=trh.TRDosageTypes.bestguess_norm) + == true_bestguess_dosages_norm + ) + assert np.all( + rec.GetDosages(dosagetype=trh.TRDosageTypes.beagleap_norm) + == true_bestguess_dosages_norm + ) + # Test if bestguess doesn't match AP + diploid_record.FORMAT["AP1"] = np.array( + [[0.5, 0.5], [1, 0], [1, 0], [1, 0], [0, 1], [0, 0]] + ) + diploid_record.FORMAT["AP2"] = np.array( + [[1, 0], [1, 0], [1, 0], [0.25, 0.75], [0, 1], [0, 0]] + ) + true_beagleap_dosages = np.array([9, 8, 8, 9.5, 12, 6]) + assert np.all( + rec.GetDosages(dosagetype=trh.TRDosageTypes.beagleap) == true_beagleap_dosages + ) + # Test if beagle APs add up to more than 1 or are negative + diploid_record.FORMAT["AP1"] = np.array( + [[10, 0.5], [1, 0], [1, 0], [1, 0], [0, 1], [0, 0]] + ) + with pytest.raises(ValueError): + rec.GetDosages(dosagetype=trh.TRDosageTypes.beagleap) + diploid_record.FORMAT["AP1"] = np.array( + [[-0.5, 0.5], [1, 0], [1, 0], [1, 0], [0, 1], [0, 0]] + ) + with pytest.raises(ValueError): + rec.GetDosages(dosagetype=trh.TRDosageTypes.beagleap) + + # Test triploid example where alt=[] + triploid_record = get_triploid_record() + rec = trh.TRRecord(triploid_record, ref_allele, [], "CAG", "", None) + true_len_gts = [[3, 3, -2], [3, 3, -2], [3, 3, -2], [3, 3, 3]] + true_len_gts = np.array(true_len_gts) + true_idx_gts = [[0, 0, -2], [0, 0, -2], [0, 0, -2], [0, 0, 0]] + true_idx_gts = np.array(true_idx_gts) + true_gts = [ + [ref_allele, ref_allele, ","], + [ref_allele, ref_allele, ","], + [ref_allele, ref_allele, ","], + [ref_allele, ref_allele, ref_allele], + ] + true_gts = np.array(true_gts) + true_bestguess_dosages = np.array([6, 6, 6, 9]) + assert np.all(rec.GetGenotypeIndicies()[:, :-1] == true_idx_gts) + assert np.all(rec.GetLengthGenotypes()[:, :-1] == true_len_gts) + assert np.all(rec.GetStringGenotypes()[:, :-1] == true_gts) + assert np.all(rec.GetDosages() == true_bestguess_dosages) + # Try to get beagle-based dosages when missing AP1/AP2 fields + with pytest.raises(ValueError): + rec.GetDosages(dosagetype=trh.TRDosageTypes.beagleap) + with pytest.raises(ValueError): + rec.GetDosages(dosagetype=trh.TRDosageTypes.beagleap_norm) + + # Test example with fewer alt_alleles than the max genotype index + with pytest.raises(ValueError): + trh.TRRecord(dummy_record, ref_allele, [], "CAG", "", None) + + +def _dicts_equal(dict1, dict2): + return all(k in dict2 and v == dict2[k] for k, v in dict1.items()) and len( + dict1 + ) == len(dict2) + + +def test_GetGenotypeCounts(): + # Test working example, no sample_index, + # also a call with a missing haplotype + dummy_record = get_dummy_record() + ref_allele = dummy_record.REF + alt_alleles = dummy_record.ALT + rec = trh.TRRecord(dummy_record, ref_allele, alt_alleles, "CAG", "", None) + true_idx_gt_counts = {(0, 1): 1, (1, 1): 2, (1, 2): 1, (2, 2): 1} + true_gt_counts = { + (ref_allele, alt_alleles[0]): 1, + (alt_alleles[0], alt_alleles[0]): 2, + (alt_alleles[0], alt_alleles[1]): 1, + (alt_alleles[1], alt_alleles[1]): 1, + } + true_len_gt_counts = {(3, 4): 1, (4, 4): 2, (4, 6): 1, (6, 6): 1} + + gt_counts_uselength = rec.GetGenotypeCounts() + gt_counts_nolength = rec.GetGenotypeCounts(uselength=False) + gt_counts_idx = rec.GetGenotypeCounts(index=True) + assert _dicts_equal(true_idx_gt_counts, gt_counts_idx) + assert _dicts_equal(true_len_gt_counts, gt_counts_uselength) + assert _dicts_equal(true_gt_counts, gt_counts_nolength) + + # Test example where alt=[] + triploid_record = get_triploid_record() + rec = trh.TRRecord(triploid_record, ref_allele, [], "CAG", "", None) + true_idx_gt_counts = {(0, 0, 0): 1, (-2, 0, 0): 3} + true_len_gt_counts = {(3, 3, 3): 1, (-2, 3, 3): 3} + true_gt_counts = { + (ref_allele, ref_allele, ref_allele): 1, + (",", ref_allele, ref_allele): 3, + } + gt_counts_idx = rec.GetGenotypeCounts(index=True) + gt_counts_uselength = rec.GetGenotypeCounts() + gt_counts_nolength = rec.GetGenotypeCounts(uselength=False) + assert _dicts_equal(true_idx_gt_counts, gt_counts_idx) + assert _dicts_equal(true_len_gt_counts, gt_counts_uselength) + assert _dicts_equal(true_gt_counts, gt_counts_nolength) + + # Test example where there are no samples + rec = trh.TRRecord(get_nocall_record(), ref_allele, [], "CAG", "", None) + # expect a entry for counting no-calls + assert len(rec.GetGenotypeCounts(index=True)) == 0 + assert len(rec.GetGenotypeCounts()) == 0 + assert len(rec.GetGenotypeCounts(uselength=True)) == 0 + assert len(rec.GetGenotypeCounts(index=True, include_nocalls=True)) == 1 + assert len(rec.GetGenotypeCounts(include_nocalls=True)) == 1 + assert len(rec.GetGenotypeCounts(uselength=True, include_nocalls=True)) == 1 + + # Test working example with sample_index + true_idx_gt_counts_sindex = {(0, 1): 1, (1, 1): 1} + true_gt_counts_sindex = { + (ref_allele, alt_alleles[0]): 1, + (alt_alleles[0], alt_alleles[0]): 1, + } + true_len_gt_counts_sindex = {(3, 4): 1, (4, 4): 1} + sindex = [0, 2, 5] + dummy_record = get_dummy_record() + rec = trh.TRRecord(dummy_record, ref_allele, alt_alleles, "CAG", "", None) + gt_counts_idx_sindex = rec.GetGenotypeCounts(sample_index=sindex, index=True) + gt_counts_uselength_sindex = rec.GetGenotypeCounts(sample_index=sindex) + gt_counts_nolength_sindex = rec.GetGenotypeCounts( + sample_index=sindex, uselength=False + ) + assert _dicts_equal(true_idx_gt_counts_sindex, gt_counts_idx_sindex) + assert _dicts_equal(true_len_gt_counts_sindex, gt_counts_uselength_sindex) + assert _dicts_equal(true_gt_counts_sindex, gt_counts_nolength_sindex) + + +def test_GetAlleleCounts(): + # Test working example, no sample_index + dummy_record = get_dummy_record() + ref_allele = dummy_record.REF + alt_alleles = dummy_record.ALT + rec = trh.TRRecord(dummy_record, ref_allele, alt_alleles, "CAG", "", None) + true_al_counts = {ref_allele: 2, alt_alleles[0]: 6, alt_alleles[1]: 3} + true_len_al_counts = {3: 2, 4: 6, 6: 3} + true_idx_al_counts = {0: 2, 1: 6, 2: 3} + + al_counts_uselength = rec.GetAlleleCounts() + al_counts_nolength = rec.GetAlleleCounts(uselength=False) + al_counts_idx = rec.GetAlleleCounts(index=True) + assert _dicts_equal(true_idx_al_counts, al_counts_idx) + assert _dicts_equal(true_len_al_counts, al_counts_uselength) + assert _dicts_equal(true_al_counts, al_counts_nolength) + + # Test example where alt=[] + rec = trh.TRRecord(get_triploid_record(), ref_allele, [], "CAG", "", None) + true_len_al_counts = {3: 9} + true_idx_al_counts = {0: 9} + true_al_counts = {ref_allele: 9} + al_counts_idx = rec.GetAlleleCounts(index=True) + al_counts_uselength = rec.GetAlleleCounts() + al_counts_nolength = rec.GetAlleleCounts(uselength=False) + assert _dicts_equal(true_idx_al_counts, al_counts_idx) + assert _dicts_equal(true_len_al_counts, al_counts_uselength) + assert _dicts_equal(true_al_counts, al_counts_nolength) + + # Test example where there are no samples + rec = trh.TRRecord(get_nocall_record(), ref_allele, [], "CAG", "", None) + assert len(rec.GetAlleleCounts(index=True)) == 0 + assert len(rec.GetAlleleCounts()) == 0 + assert len(rec.GetAlleleCounts(uselength=True)) == 0 + + # Test working example with sample_index + true_idx_al_counts_sindex = {0: 2, 1: 3} + true_len_al_counts_sindex = {3: 2, 4: 3} + true_al_counts_sindex = {ref_allele: 2, alt_alleles[0]: 3} + sindex = [0, 2, 5] + rec = trh.TRRecord(dummy_record, ref_allele, alt_alleles, "CAG", "", None) + al_counts_idx_sindex = rec.GetAlleleCounts(sample_index=sindex, index=True) + al_counts_uselength_sindex = rec.GetAlleleCounts(sample_index=sindex) + al_counts_nolength_sindex = rec.GetAlleleCounts( + sample_index=sindex, uselength=False + ) + assert _dicts_equal(true_idx_al_counts_sindex, al_counts_idx_sindex) + assert _dicts_equal(true_len_al_counts_sindex, al_counts_uselength_sindex) + assert _dicts_equal(true_al_counts_sindex, al_counts_nolength_sindex) + + +def test_GetAlleleFreqs(): + # Test working example, no sample_index + dummy_record = get_dummy_record() + ref_allele = dummy_record.REF + alt_alleles = dummy_record.ALT + rec = trh.TRRecord(dummy_record, ref_allele, alt_alleles, "CAG", "", None) + true_al_freqs = { + ref_allele: 0.1818181, + alt_alleles[0]: 0.5454545, + alt_alleles[1]: 0.2727272, + } + true_len_al_freqs = {3: 0.1818181, 4: 0.5454545, 6: 0.2727272} + true_idx_al_freqs = {0: 0.1818181, 1: 0.5454545, 2: 0.2727272} + + al_freqs_uselength = rec.GetAlleleFreqs() + al_freqs_nolength = rec.GetAlleleFreqs(uselength=False) + al_freqs_idx = rec.GetAlleleFreqs(index=True) + assert all( + v == approx(true_idx_al_freqs[k]) for k, v in al_freqs_idx.items() + ) and len(al_freqs_idx) == len(true_idx_al_freqs) + assert all( + v == approx(true_len_al_freqs[k]) for k, v in al_freqs_uselength.items() + ) and len(al_freqs_uselength) == len(true_len_al_freqs) + assert all( + v == approx(true_al_freqs[k]) for k, v in al_freqs_nolength.items() + ) and len(al_freqs_nolength) == len(true_al_freqs) + + # Test example where alt=[] + rec = trh.TRRecord(get_triploid_record(), ref_allele, [], "CAG", "", None) + true_len_al_freq = {3: 1} + true_idx_al_freq = {0: 1} + true_al_freq = {ref_allele: 1} + al_freq_idx = rec.GetAlleleFreqs(index=True) + al_freq_uselength = rec.GetAlleleFreqs() + al_freq_nolength = rec.GetAlleleFreqs(uselength=False) + assert all(v == true_idx_al_freq[k] for k, v in al_freq_idx.items()) and len( + al_freq_idx + ) == len(true_idx_al_freq) + assert all(v == true_len_al_freq[k] for k, v in al_freq_uselength.items()) and len( + al_freq_uselength + ) == len(true_len_al_freq) + assert all(v == true_al_freq[k] for k, v in al_freq_nolength.items()) and len( + al_freq_nolength + ) == len(true_al_freq) + + # Test example where there are no samples + rec = trh.TRRecord(get_nocall_record(), ref_allele, [], "CAG", "", None) + assert len(rec.GetAlleleFreqs(index=True)) == 0 + assert len(rec.GetAlleleFreqs()) == 0 + assert len(rec.GetAlleleFreqs(uselength=True)) == 0 + + # Test working example with sample_index + true_idx_al_freqs_sindex = {0: 0.4, 1: 0.6} + true_len_al_freqs_sindex = {3: 0.4, 4: 0.6} + true_al_freqs_sindex = {ref_allele: 0.4, alt_alleles[0]: 0.6} + sindex = [0, 2, 5] + rec = trh.TRRecord(dummy_record, ref_allele, alt_alleles, "CAG", "", None) + al_freqs_idx_sindex = rec.GetAlleleFreqs(sample_index=sindex, index=True) + al_freqs_uselength_sindex = rec.GetAlleleFreqs(sample_index=sindex) + al_freqs_nolength_sindex = rec.GetAlleleFreqs(sample_index=sindex, uselength=False) + assert all( + v == true_idx_al_freqs_sindex[k] for k, v in al_freqs_idx_sindex.items() + ) and len(al_freqs_idx_sindex) == len(true_idx_al_freqs_sindex) + assert all( + v == true_len_al_freqs_sindex[k] for k, v in al_freqs_uselength_sindex.items() + ) and len(al_freqs_uselength_sindex) == len(true_len_al_freqs_sindex) + assert all( + v == true_al_freqs_sindex[k] for k, v in al_freqs_nolength_sindex.items() + ) and len(al_freqs_nolength_sindex) == len(true_al_freqs_sindex) + + +def test_GetMaxAllele(): + # Test working example + dummy_record = get_dummy_record() + ref_allele = dummy_record.REF + alt_alleles = dummy_record.ALT + rec = trh.TRRecord(dummy_record, ref_allele, alt_alleles, "CAG", "", None) + true_al_max = 6 + al_max = rec.GetMaxAllele() + assert al_max == true_al_max + + # Test example where alt=[] + rec = trh.TRRecord(get_triploid_record(), ref_allele, [], "CAG", "", None) + true_al_max = 3 + al_max = rec.GetMaxAllele() + assert al_max == true_al_max + + # Test example where there are no called samples + rec = trh.TRRecord(get_nocall_record(), ref_allele, [], "CAG", "", None) + true_al_max = np.nan + al_max = rec.GetMaxAllele() + assert np.isnan(al_max) + + # Test working example with sample_index + sindex = [0, 2, 5] + true_al_max_sindex = 4 + rec = trh.TRRecord(dummy_record, ref_allele, alt_alleles, "CAG", "", None) + al_max_sindex = rec.GetMaxAllele(sample_index=sindex) + assert al_max_sindex == true_al_max_sindex + + +def test_GetCalledSamples(): + dummy_record = get_dummy_record() + ref_allele = dummy_record.REF + alt_alleles = dummy_record.ALT + rec = trh.TRRecord(dummy_record, ref_allele, alt_alleles, "CAG", "", None) + assert np.all(rec.GetCalledSamples() == [True] * 5 + [False]) + assert np.all(rec.GetCalledSamples(strict=False)) + + # Test differences in ploidy + rec = trh.TRRecord(get_triploid_record(), ref_allele, [], "CAG", "", None) + assert np.all(rec.GetCalledSamples(strict=True)) + + # Test a true no call + rec = trh.TRRecord(get_nocall_record(), ref_allele, [], "CAG", "", None) + assert np.all(~rec.GetCalledSamples()) + + +def test_GetSamplePloidies(): + # All samples have the same ploidy + # even a partial nocall + dummy_record = get_dummy_record() + ref_allele = dummy_record.REF + alt_alleles = dummy_record.ALT + rec = trh.TRRecord(dummy_record, ref_allele, alt_alleles, "CAG", "", None) + assert np.all(rec.GetSamplePloidies() == 2) + + # Test differences in ploidy + rec = trh.TRRecord(get_triploid_record(), ref_allele, [], "CAG", "", None) + assert np.all(rec.GetSamplePloidies() == [2, 2, 2, 3]) + + # Test a no call, sample ploidy should not change + rec = trh.TRRecord(get_nocall_record(), ref_allele, [], "CAG", "", None) + assert np.all(rec.GetSamplePloidies() == 2) + + +def test_GetCallRate(): + dummy_record = get_dummy_record() + ref_allele = dummy_record.REF + alt_alleles = dummy_record.ALT + rec = trh.TRRecord(dummy_record, ref_allele, alt_alleles, "CAG", "", None) + assert rec.GetCallRate() == pytest.approx(5 / 6) + assert rec.GetCalledSamples(strict=False) == pytest.approx(1) + + # Test differences in ploidy + rec = trh.TRRecord(get_triploid_record(), ref_allele, [], "CAG", "", None) + assert rec.GetCalledSamples(strict=True) == pytest.approx(1) + + # Test a true no call + rec = trh.TRRecord(get_nocall_record(), ref_allele, [], "CAG", "", None) + assert rec.GetCalledSamples(strict=False) == pytest.approx(0) + + +#### Test TRRecordHarmonizer on different files #### + + +def reset_vcfs(vcfdir): + global gangstr_vcf, hipstr_vcf, popstr_vcf, advntr_vcf, eh_vcf, snps_vcf + gangstr_vcf = cyvcf2.VCF(os.path.join(vcfdir, "test_gangstr.vcf")) + hipstr_vcf = cyvcf2.VCF(os.path.join(vcfdir, "test_hipstr.vcf")) + popstr_vcf = cyvcf2.VCF(os.path.join(vcfdir, "test_popstr.vcf")) + advntr_vcf = cyvcf2.VCF(os.path.join(vcfdir, "test_advntr.vcf")) + eh_vcf = cyvcf2.VCF(os.path.join(vcfdir, "test_ExpansionHunter.vcf")) + snps_vcf = cyvcf2.VCF(os.path.join(vcfdir, "snps.vcf")) + + +def test_multitype_vcf(vcfdir): + with pytest.raises(TypeError): + reader = cyvcf2.VCF(os.path.join(vcfdir, "test_multitype.vcf")) + trh.TRRecordHarmonizer(reader) + + +def test_trh_init_and_type_infer(vcfdir): + reset_vcfs(vcfdir) + + # Test example with a meaningless VCF type given + with pytest.raises(ValueError): + trh.TRRecordHarmonizer(gangstr_vcf, vcftype="unknownvcf") + # Test example with unsupported VCF + with pytest.raises(TypeError): + trh.TRRecordHarmonizer(snps_vcf) + + # Test methods not passing in a vcftype + with pytest.raises(ValueError): + trh.MayHaveImpureRepeats("foo") + with pytest.raises(ValueError): + trh.HasLengthRefGenotype("foo") + with pytest.raises(ValueError): + trh.HasLengthAltGenotypes("foo") + with pytest.raises(TypeError): + trh.MayHaveImpureRepeats({}) # give a meaningless argument type + + # Test examples with correct preset VCF type + gangstr_trh = trh.TRRecordHarmonizer(gangstr_vcf, vcftype="gangstr") + assert gangstr_trh.vcftype == trh.VcfTypes.gangstr + gangstr_trh = trh.TRRecordHarmonizer(gangstr_vcf, vcftype=trh.VcfTypes.gangstr) + assert gangstr_trh.vcftype == trh.VcfTypes.gangstr + assert trh.InferVCFType(gangstr_vcf) == trh.VcfTypes.gangstr + assert not gangstr_trh.MayHaveImpureRepeats() and not trh.MayHaveImpureRepeats( + trh.VcfTypes.gangstr + ) + assert not gangstr_trh.HasLengthRefGenotype() and not trh.HasLengthRefGenotype( + trh.VcfTypes.gangstr + ) + assert not gangstr_trh.HasLengthAltGenotypes() and not trh.HasLengthAltGenotypes( + trh.VcfTypes.gangstr + ) + assert not gangstr_trh.IsBeagleVCF() + + hipstr_trh = trh.TRRecordHarmonizer(hipstr_vcf, vcftype="hipstr") + assert hipstr_trh.vcftype == trh.VcfTypes.hipstr + hipstr_trh = trh.TRRecordHarmonizer(hipstr_vcf, vcftype=trh.VcfTypes.hipstr) + assert hipstr_trh.vcftype == trh.VcfTypes.hipstr + assert trh.InferVCFType(hipstr_vcf) == trh.VcfTypes.hipstr + assert hipstr_trh.MayHaveImpureRepeats() and trh.MayHaveImpureRepeats( + trh.VcfTypes.hipstr + ) + assert not hipstr_trh.HasLengthRefGenotype() and not trh.HasLengthRefGenotype( + trh.VcfTypes.hipstr + ) + assert not hipstr_trh.HasLengthAltGenotypes() and not trh.HasLengthAltGenotypes( + trh.VcfTypes.hipstr + ) + assert not hipstr_trh.IsBeagleVCF() + + popstr_trh = trh.TRRecordHarmonizer(popstr_vcf, vcftype="popstr") + assert popstr_trh.vcftype == trh.VcfTypes.popstr + popstr_trh = trh.TRRecordHarmonizer(popstr_vcf, vcftype=trh.VcfTypes.popstr) + assert popstr_trh.vcftype == trh.VcfTypes.popstr + assert trh.InferVCFType(popstr_vcf) == trh.VcfTypes.popstr + assert popstr_trh.MayHaveImpureRepeats() and trh.MayHaveImpureRepeats( + trh.VcfTypes.popstr + ) + assert not popstr_trh.HasLengthRefGenotype() and not trh.HasLengthRefGenotype( + trh.VcfTypes.popstr + ) + assert popstr_trh.HasLengthAltGenotypes() and trh.HasLengthAltGenotypes( + trh.VcfTypes.popstr + ) + + advntr_trh = trh.TRRecordHarmonizer(advntr_vcf, vcftype="advntr") + assert advntr_trh.vcftype == trh.VcfTypes.advntr + advntr_trh = trh.TRRecordHarmonizer(advntr_vcf, vcftype=trh.VcfTypes.advntr) + assert advntr_trh.vcftype == trh.VcfTypes.advntr + assert trh.InferVCFType(advntr_vcf) == trh.VcfTypes.advntr + assert advntr_trh.MayHaveImpureRepeats() and trh.MayHaveImpureRepeats( + trh.VcfTypes.advntr + ) + assert not advntr_trh.HasLengthRefGenotype() and not trh.HasLengthRefGenotype( + trh.VcfTypes.advntr + ) + assert not advntr_trh.HasLengthAltGenotypes() and not trh.HasLengthAltGenotypes( + trh.VcfTypes.advntr + ) + assert not advntr_trh.IsBeagleVCF() + + eh_trh = trh.TRRecordHarmonizer(eh_vcf, vcftype="eh") + assert eh_trh.vcftype == trh.VcfTypes.eh + eh_trh = trh.TRRecordHarmonizer(eh_vcf, vcftype=trh.VcfTypes.eh) + assert eh_trh.vcftype == trh.VcfTypes.eh + assert trh.InferVCFType(eh_vcf) == trh.VcfTypes.eh + assert not eh_trh.MayHaveImpureRepeats() and not trh.MayHaveImpureRepeats( + trh.VcfTypes.eh + ) + assert eh_trh.HasLengthRefGenotype() and trh.HasLengthRefGenotype(trh.VcfTypes.eh) + assert eh_trh.HasLengthAltGenotypes() and trh.HasLengthAltGenotypes(trh.VcfTypes.eh) + assert not eh_trh.IsBeagleVCF() + + +def test_imputed_vcf_types(vcfdir): + imputed_gangstr_trh = trh.TRRecordHarmonizer( + cyvcf2.VCF(os.path.join(vcfdir, "beagle/gangstr_imputed.vcf.gz")), + vcftype="gangstr", + ) + assert imputed_gangstr_trh.vcftype == trh.VcfTypes.gangstr + assert imputed_gangstr_trh.IsBeagleVCF() + assert not next(imputed_gangstr_trh).HasQualityScores() + + imputed_advntr_trh = trh.TRRecordHarmonizer( + cyvcf2.VCF(os.path.join(vcfdir, "beagle/advntr_imputed.vcf.gz")), + vcftype="advntr", + ) + assert imputed_advntr_trh.vcftype == trh.VcfTypes.advntr + assert imputed_advntr_trh.IsBeagleVCF() + assert not next(imputed_advntr_trh).HasQualityScores() + + imputed_hipstr_trh = trh.TRRecordHarmonizer( + cyvcf2.VCF(os.path.join(vcfdir, "beagle/hipstr_imputed.vcf.gz")), + vcftype="hipstr", + ) + assert imputed_hipstr_trh.vcftype == trh.VcfTypes.hipstr + assert imputed_hipstr_trh.IsBeagleVCF() + assert not next(imputed_hipstr_trh).HasQualityScores() + + imputed_eh_trh = trh.TRRecordHarmonizer( + cyvcf2.VCF(os.path.join(vcfdir, "beagle/eh_imputed.vcf.gz")), vcftype="eh" + ) + assert imputed_eh_trh.vcftype == trh.VcfTypes.eh + assert imputed_eh_trh.IsBeagleVCF() + assert not next(imputed_eh_trh).HasQualityScores() + + +def test_missing_infos_imputed_vcfs_fail(vcfdir): + missing_infos_imputed_gangstr_trh = trh.TRRecordHarmonizer( + cyvcf2.VCF(os.path.join(vcfdir, "beagle/gangstr_imputed_missing_infos.vcf.gz")), + vcftype="gangstr", + ) + with pytest.raises(TypeError): + next(missing_infos_imputed_gangstr_trh) + + missing_infos_imputed_advntr_trh = trh.TRRecordHarmonizer( + cyvcf2.VCF(os.path.join(vcfdir, "beagle/advntr_imputed_missing_infos.vcf.gz")), + vcftype="advntr", + ) + with pytest.raises(TypeError): + next(missing_infos_imputed_advntr_trh) + + missing_infos_imputed_hipstr_trh = trh.TRRecordHarmonizer( + cyvcf2.VCF(os.path.join(vcfdir, "beagle/hipstr_imputed_missing_infos.vcf.gz")), + vcftype="hipstr", + ) + with pytest.raises(TypeError): + next(missing_infos_imputed_hipstr_trh) + + missing_infos_imputed_eh_trh = trh.TRRecordHarmonizer( + cyvcf2.VCF(os.path.join(vcfdir, "beagle/eh_imputed_missing_infos.vcf.gz")), + vcftype="eh", + ) + with pytest.raises(TypeError): + next(missing_infos_imputed_eh_trh) + + +def test_string_or_vcftype(vcfdir): + assert trh.HasLengthAltGenotypes("gangstr") == trh.HasLengthAltGenotypes( + trh.VcfTypes.gangstr + ) + assert trh.HasLengthRefGenotype("gangstr") == trh.HasLengthRefGenotype( + trh.VcfTypes.gangstr + ) + assert trh.MayHaveImpureRepeats("gangstr") == trh.MayHaveImpureRepeats( + trh.VcfTypes.gangstr + ) + reset_vcfs(vcfdir) + assert trh.HarmonizeRecord("gangstr", next(gangstr_vcf)).GetMaxAllele() == len( + "tctgtctgtctg" + ) / len("tctg") + assert trh.HarmonizeRecord( + trh.VcfTypes.gangstr, next(gangstr_vcf) + ).GetMaxAllele() == len("aaaacaaaacaaaacaaaac") / len("aaaac") + + +def all_types(): + for vcftype in trh.VcfTypes: + yield vcftype + yield "snps" + + +def get_vcf(vcftype): + if vcftype == trh.VcfTypes.gangstr: + return gangstr_vcf + if vcftype == trh.VcfTypes.hipstr: + return hipstr_vcf + if vcftype == trh.VcfTypes.popstr: + return popstr_vcf + if vcftype == trh.VcfTypes.advntr: + return advntr_vcf + if vcftype == trh.VcfTypes.eh: + return eh_vcf + if vcftype == "snps": + return snps_vcf + raise ValueError("Unexpected vcftype") + # TODO add Beagle + + +def test_wrong_vcftype(vcfdir): + # an iterator that includes both tr caller types + # and error file types + for correct_type in trh.VcfTypes: + reset_vcfs(vcfdir) + for incorrect_type in all_types(): + if incorrect_type == correct_type: + # make sure the incorrect_type is actually incorrect + continue + + invcf = get_vcf(incorrect_type) + with pytest.raises(TypeError): + trh.TRRecordHarmonizer(invcf, vcftype=correct_type) + + reset_vcfs(vcfdir) + for incorrect_type in all_types(): + if incorrect_type == correct_type: + # make sure the incorrect_type is actually incorrect + continue + + invcf = get_vcf(incorrect_type) + record = next(invcf) + with pytest.raises(TypeError): + trh.HarmonizeRecord(correct_type, record) + + +def test_HarmonizeRecord(vcfdir): + reset_vcfs(vcfdir) + + # Unknown type + with pytest.raises(ValueError): + trh.HarmonizeRecord("foo", next(snps_vcf)) + + # Gangstr + gangstr_trh = trh.TRRecordHarmonizer(gangstr_vcf) + + tr_rec1 = next(iter(gangstr_trh)) + assert tr_rec1.ref_allele == "tctgtctgtctg".upper() + assert tr_rec1.alt_alleles == [] + assert tr_rec1.motif == "tctg".upper() + assert not tr_rec1.HasFullStringGenotypes() + assert not tr_rec1.HasFabricatedRefAllele() + assert not tr_rec1.HasFabricatedAltAlleles() + tr_rec2 = next(iter(gangstr_trh)) + tr_rec3 = next(iter(gangstr_trh)) + assert ( + tr_rec3.ref_allele + == "tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg".upper() + ) + assert tr_rec3.alt_alleles == [ + "tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg".upper() + ] + assert tr_rec3.motif == "tg".upper() + assert tr_rec3.ref_allele_length == 26 + assert tr_rec3.alt_allele_lengths == [24] + + # hipstr + hipstr_trh = trh.TRRecordHarmonizer(hipstr_vcf) + + str_iter = iter(hipstr_trh) + tr_rec1 = next(str_iter) + assert tr_rec1.ref_allele == "GGTGGTGGTGGGGGCGGTGGGGGTGGTG" + assert tr_rec1.alt_alleles == ["GGTGGTGGTGGGGGCGGTGGTGGTGCTG"] + assert tr_rec1.motif == "GGT" + assert tr_rec1.record_id == "STR_2" + assert not tr_rec1.HasFullStringGenotypes() + assert not tr_rec1.HasFabricatedRefAllele() + assert not tr_rec1.HasFabricatedAltAlleles() + assert tr_rec1.pos == tr_rec1.full_alleles_pos + tr_rec2 = next(str_iter) + tr_rec3 = next(str_iter) + assert tr_rec3.ref_allele == "TTTTTTTTTTTTTTT" + assert tr_rec3.alt_alleles == [] + assert tr_rec3.motif == "T".upper() + assert tr_rec3.record_id == "STR_4" + record = next(str_iter) + while record.record_id != "STR_125": + record = next(str_iter) + assert record.HasFullStringGenotypes() + # record in the test file has flanking bp at the start of the ref. allele + assert record.pos > record.full_alleles_pos + # TODO this isn't really the correct behavior - + # we're trimming off an extra repeat from the alt allele + assert record.full_alleles == ( + "TGCATATATGTATAATATATATTATATATGGA", + ["TCCATATATGCATAATATATATTATATATATG"], + ) + assert record.ref_allele == "ATATATGTATAATATATATTATATAT" + assert record.alt_alleles == ["ATATATGCATAATATATATTATATAT"] + + # popstr + popstr_trh = trh.TRRecordHarmonizer(popstr_vcf) + + tr_rec1 = next(iter(popstr_trh)) + assert tr_rec1.ref_allele == "GGGGGGGCGGGGGGGGGG" + assert tr_rec1.alt_alleles == ["G" * 14, "G" * 17] + assert tr_rec1.motif == "G" + assert tr_rec1.record_id == "chr21:5020351:M" + assert not tr_rec1.HasFullStringGenotypes() + assert not tr_rec1.HasFabricatedRefAllele() + assert tr_rec1.HasFabricatedAltAlleles() + tr_rec2 = next(iter(popstr_trh)) + tr_rec3 = next(iter(popstr_trh)) + assert tr_rec3.ref_allele == "TTTTTTTTTTTTTTTTTTTTTT" + assert tr_rec3.alt_alleles == ["T" * 21] + assert tr_rec3.motif == "T" + assert tr_rec3.record_id == "chr21:5031126:M" + + # advntr + advntr_trh = trh.TRRecordHarmonizer(advntr_vcf) + + tr_rec1 = next(iter(advntr_trh)) + assert tr_rec1.ref_allele == "GCGCGGGGCGGGGCGCGGGGCGGGGCGCGGGGCGGG" + assert tr_rec1.alt_alleles == [ + "GCGCGGGGCGGGGCGCGGGGCGGG", + "GCGCGGGGCGGGGCGCGGGGCGGGGCGCGGGGCGGGGCGCGGGGCGGGGCGCGGGGCGGG", + ] + assert tr_rec1.motif == "GCGCGGGGCGGG" + assert not tr_rec1.HasFullStringGenotypes() + assert not tr_rec1.HasFabricatedRefAllele() + assert not tr_rec1.HasFabricatedAltAlleles() + + # advntr + eh_trh = trh.TRRecordHarmonizer(eh_vcf) + + tr_rec1 = next(iter(eh_trh)) + motif = "CAG" + assert tr_rec1.ref_allele == motif * 19 + assert tr_rec1.alt_alleles == [motif * 16, motif * 18] + assert tr_rec1.motif == motif + assert tr_rec1.record_id == "HTT" + assert not tr_rec1.HasFullStringGenotypes() + assert tr_rec1.HasFabricatedRefAllele() + assert tr_rec1.HasFabricatedAltAlleles() + + +def assertFEquals(f1: float, f2: float): + epsilon = 1e-6 + assert abs(f1 - f2) < epsilon + + +# def test_PHREDtoProb(): +# # pylint: disable=W0212 +# assertFEquals(trh._PHREDtoProb(0), 1) +# assertFEquals(trh._PHREDtoProb(20), .01) +# assertFEquals(trh._PHREDtoProb(2), 0.63095734448) + +# def test_ConvertPLToQualityProb(): +# # pylint: disable=W0212 +# assertFEquals(trh._ConvertPLtoQualityProb([0]), 1) +# assertFEquals(trh._ConvertPLtoQualityProb([10]), .1) +# assertFEquals(trh._ConvertPLtoQualityProb([255, 10, 246]), .1) +# assertFEquals(trh._ConvertPLtoQualityProb([10, 0, 10]), .8) +# # confirm that PHRED scores of 0 don't drop below phred +# # score of 1 despite our rebinning approach +# assertFEquals(trh._ConvertPLtoQualityProb([0, 1, 1, 1]), +# trh._PHREDtoProb(1)) + + +def _getVariantFromHarominzer(harmonizer, nvar=1): + itr = iter(harmonizer) + while nvar > 0: + nvar -= 1 + var = next(itr) + return var + + +def test_TRRecord_Quality(vcfdir): + reset_vcfs(vcfdir) + + gangstr_trh = trh.TRRecordHarmonizer(gangstr_vcf) + assert gangstr_trh.HasQualityScore() + var = _getVariantFromHarominzer(gangstr_trh) + assert var.HasQualityScores() + assert var.GetQualityScores()[0] == 0.999912 + + gangstr_vcf_noqual = cyvcf2.VCF(os.path.join(vcfdir, "test_gangstr_noqual.vcf")) + gangstr_trh_noqual = trh.TRRecordHarmonizer(gangstr_vcf_noqual) + assert not gangstr_trh_noqual.HasQualityScore() + var = _getVariantFromHarominzer(gangstr_trh_noqual) + assert not var.HasQualityScores() + with pytest.raises(TypeError): + var.GetQualityScores() + + hipstr_trh = trh.TRRecordHarmonizer(hipstr_vcf) + assert hipstr_trh.HasQualityScore() + var = _getVariantFromHarominzer(hipstr_trh, nvar=18) + assert var.HasQualityScores() + assert var.GetQualityScores()[0] == 0.93 + + popstr_trh = trh.TRRecordHarmonizer(popstr_vcf) + assert not popstr_trh.HasQualityScore() + var = _getVariantFromHarominzer(popstr_trh) + assert not var.HasQualityScores() + + advntr_trh = trh.TRRecordHarmonizer(advntr_vcf) + assert advntr_trh.HasQualityScore() + var = _getVariantFromHarominzer(advntr_trh) + assert var.HasQualityScores() + assert var.GetQualityScores()[0] == 0.863 + + eh_trh = trh.TRRecordHarmonizer(eh_vcf) + assert not eh_trh.HasQualityScore() + var = _getVariantFromHarominzer(eh_trh) + assert not var.HasQualityScores() + with pytest.raises(TypeError): + var.GetQualityScores() diff --git a/tests/test_utils.py b/tests/test_utils.py new file mode 100644 index 0000000..f535847 --- /dev/null +++ b/tests/test_utils.py @@ -0,0 +1,169 @@ +# import os, sys + +# import pytest +# import numpy as np + +import core.utils as utils + + +# # LoadSingleReader +# def test_LoadSingleReader(monkeypatch, vcfdir): +# file1 = utils.LoadSingleReader(os.path.join(vcfdir, "few_samples_few_loci.vcf.gz")) +# assert file1 is not None +# file2 = utils.LoadSingleReader( +# os.path.join(vcfdir, "test_gangstr.vcf"), checkgz=False +# ) +# assert file2 is not None +# file3 = utils.LoadSingleReader( +# os.path.join(vcfdir, "nonexistent.vcf"), checkgz=False +# ) +# assert file3 is None + + +# # ValidateAlleleFreqs +# def test_ValidateAlleleFreqs(): +# afreqs = {0: 1} +# assert utils.ValidateAlleleFreqs(afreqs) +# afreqs = {0: 0.5, 1: 0.5} +# assert utils.ValidateAlleleFreqs(afreqs) +# afreqs = {} +# assert not utils.ValidateAlleleFreqs(afreqs) +# afreqs = {0: 0.5} +# assert not utils.ValidateAlleleFreqs(afreqs) +# afreqs = {-1: 1, 1: 1} +# assert not utils.ValidateAlleleFreqs(afreqs) + + +# # GetHeterozygosity +# def test_GetHeterozygosity(): +# afreqs = {0: 1} +# assert utils.GetHeterozygosity(afreqs) == 0 +# afreqs = {0: 0.5, 1: 0.5} +# assert utils.GetHeterozygosity(afreqs) == 0.5 +# afreqs = {0: 0.5, 1: 0.2, 2: 0.3} +# assert utils.GetHeterozygosity(afreqs) == 0.62 +# afreqs = {} +# assert np.isnan(utils.GetHeterozygosity(afreqs)) + + +# def test_GetEntropy(): +# afreqs = {0: 1} +# assert utils.GetEntropy(afreqs) == 0 +# afreqs = {0: 0.5, 1: 0.5} +# assert utils.GetEntropy(afreqs) == 1 +# afreqs = {0: 0.5, 1: 0.2, 2: 0.3} +# assert abs(utils.GetEntropy(afreqs) - 1.48) < 0.01 +# afreqs = {} +# assert np.isnan(utils.GetEntropy(afreqs)) + + +# # GetMean +# def test_GetMean(): +# afreqs = {0: 1} +# assert utils.GetMean(afreqs) == 0 +# afreqs = {0: 0.5, 1: 0.5} +# assert utils.GetMean(afreqs) == 0.5 +# afreqs = {0: 0.5, 1: 0.2, 2: 0.3} +# assert utils.GetMean(afreqs) == 0.8 +# afreqs = {} +# assert np.isnan(utils.GetMean(afreqs)) + + +# # GetMode +# def test_GetMode(): +# afreqs = {0: 1} +# assert utils.GetMode(afreqs) == 0 +# afreqs = {0: 0.49, 1: 0.51} +# assert utils.GetMode(afreqs) == 1 +# afreqs = {0: 0.1, 1: 0.1, 2: 0.3, 3: 0.5} +# assert utils.GetMode(afreqs) == 3 +# afreqs = {} +# assert np.isnan(utils.GetMode(afreqs)) + + +# # GetVariance +# def test_GetVariance(): +# afreqs = {0: 1} +# assert utils.GetVariance(afreqs) == 0 +# afreqs = {0: 0.5, 1: 0.5} +# assert utils.GetVariance(afreqs) == 0.25 +# afreqs = {} +# assert np.isnan(utils.GetVariance(afreqs)) + + +# # GetHardyWeinbergBinomialTest +# def test_GetHardyWeinbergBinomialTest(): +# # Try examples that should work +# afreqs = {0: 0.5, 1: 0.2, 2: 0.3} +# gcounts = {(0, 1): 10, (0, 0): 20, (1, 2): 5} +# assert round(utils.GetHardyWeinbergBinomialTest(afreqs, gcounts), 2) == 0.02 +# gcounts = {(0, 0): 20} +# assert round(utils.GetHardyWeinbergBinomialTest(afreqs, gcounts), 2) == 0.0 +# gcounts = {(0, 1): 20} +# assert round(utils.GetHardyWeinbergBinomialTest(afreqs, gcounts), 2) == 0.0 +# # Try with genotypes whose alleles not in afreqs +# gcounts = {(3, 3): 6} +# assert np.isnan(utils.GetHardyWeinbergBinomialTest(afreqs, gcounts)) +# gcounts = {(0, 3): 6} +# assert np.isnan(utils.GetHardyWeinbergBinomialTest(afreqs, gcounts)) +# # Try invalid afreqs +# afreqs = {} +# assert np.isnan(utils.GetHardyWeinbergBinomialTest(afreqs, gcounts)) + + +# # GetHomopolymerRun +# def test_GetHomopolymerRun(): +# assert utils.GetHomopolymerRun("AATAAAAAAAAT") == 8 +# assert utils.GetHomopolymerRun("AATAAAAAAT") == 6 +# assert utils.GetHomopolymerRun("AATAAAAAAAATTTTTTTTT") == 9 +# assert utils.GetHomopolymerRun("AATAAAAAAAAGGGGGGGGGGTTTTTTTTT") == 10 +# assert utils.GetHomopolymerRun("") == 0 + + +# # GetCanonicalMotif +# def test_GetCanonicalMotif(): +# assert utils.GetCanonicalMotif("AGC") == "AGC" +# assert utils.GetCanonicalMotif("CAG") == "AGC" +# assert utils.GetCanonicalMotif("TG") == "AC" +# assert utils.GetCanonicalMotif("AT") == "AT" +# assert utils.GetCanonicalMotif("T") == "A" +# assert utils.GetCanonicalMotif("TTGTT") == "AAAAC" +# assert utils.GetCanonicalMotif("") == "" +# assert utils.GetCanonicalMotif("cag") == "AGC" + + +# GetCanonicalOneStrand +def test_GetCanonicalOneStrand(): + assert utils.GetCanonicalOneStrand("AGC") == "AGC" + assert utils.GetCanonicalOneStrand("CAG") == "AGC" + assert utils.GetCanonicalOneStrand("TG") == "GT" + assert utils.GetCanonicalOneStrand("AT") == "AT" + assert utils.GetCanonicalOneStrand("T") == "T" + assert utils.GetCanonicalOneStrand("TTGTT") == "GTTTT" + assert utils.GetCanonicalOneStrand("") == "" + assert utils.GetCanonicalOneStrand("at") == "AT" + + +# # ReverseComplement +# def test_ReverseComplement(): +# assert utils.ReverseComplement("CGAT") == "ATCG" +# assert utils.ReverseComplement("") == "" +# assert utils.ReverseComplement("CGNT") == "ANCG" +# assert utils.ReverseComplement("ccga") == "TCGG" + + +# InferRepeatSequence +def test_InferRepeatSequence(): + assert utils.InferRepeatSequence("ATATATATATA", 2) == "AT" + assert utils.InferRepeatSequence("ATATATACATA", 2) == "AT" + assert utils.InferRepeatSequence("ATATATACATAAAAAAAAAAAAAAA", 1) == "A" + assert utils.InferRepeatSequence("ATATAT", 10) == "NNNNNNNNNN" + + +# # LongestPerfectRepeat +# def test_LongestPerfectRepeat(): +# assert utils.LongestPerfectRepeat("ACACAC", "AC") == 6 +# assert utils.LongestPerfectRepeat("ACACACA", "AC") == 7 +# assert utils.LongestPerfectRepeat("ACACACA", "CA") == 7 +# assert utils.LongestPerfectRepeat("ACACACA", "TG") == 7 +# assert utils.LongestPerfectRepeat("ACACACA", "TG", check_reverse=False) == 0