From 21f16d556f66867e55100cea0546116315f64fa2 Mon Sep 17 00:00:00 2001 From: ldgauthier Date: Mon, 17 Sep 2018 08:49:56 -0400 Subject: [PATCH] Fixed ref conf calculation upstream of indel (#5172) Improve hom ref GQs near indels in GVCFs. Also consider bases on either side of indels informative if local assembly has been performed --- .../HaplotypeCallerEngine.java | 2 +- .../ReferenceConfidenceModel.java | 68 +- .../walkers/rnaseq/SplitNCigarReads.java | 7 +- .../hellbender/utils/Nucleotide.java | 10 + .../utils/clipping/ReadClipper.java | 4 +- .../hellbender/utils/read/AlignmentUtils.java | 48 + .../hellbender/utils/read/CigarUtils.java | 44 +- .../HaplotypeCallerSparkIntegrationTest.java | 4 +- .../HaplotypeCallerIntegrationTest.java | 26 +- .../ReferenceConfidenceModelUnitTest.java | 94 +- .../utils/read/CigarUtilsUnitTest.java | 10 +- .../funcotator_dataSources/achilles/hg38 | 4 +- .../cancer_gene_census/hg38 | 4 +- .../dna_repair_genes/hg38 | 4 +- .../funcotator_dataSources/familial/hg38 | 4 +- .../funcotator_dataSources/hgnc/hg38 | 4 +- .../simple_uniprot/hg38 | 4 +- ...testGenomicsDBImportWithNonDiploidData.vcf | 905 ++++++------------ ...GenomicsDBImportWithNonDiploidData.vcf.idx | Bin 40777 -> 40774 bytes ...0000-10150000.postIndelRefConfUpdate.g.vcf | 656 +++++++++++++ ...ed.testGVCFMode.gatk4.alleleSpecific.g.vcf | 780 +++++---------- .../expected.testGVCFMode.gatk4.g.vcf | 780 +++++---------- .../expected.testGVCFMode.gatk4.g.vcf.idx | Bin 843 -> 40765 bytes 23 files changed, 1692 insertions(+), 1770 deletions(-) create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.CEUTrio.HiSeq.WGS.b37.NA12878.CONTAMINATED.WITH.HCC1143.NORMALS.15PCT.20.10100000-10150000.postIndelRefConfUpdate.g.vcf diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java index 709d3aa5169..ce6fb85cf9d 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java @@ -474,7 +474,7 @@ public ActivityProfileState isActive( final AlignmentContext context, final Refe for( final Map.Entry sample : splitContexts.entrySet() ) { // The ploidy here is not dictated by the sample but by the simple genotyping-engine used to determine whether regions are active or not. final int activeRegionDetectionHackishSamplePloidy = activeRegionEvaluationGenotyperEngine.getConfiguration().genotypeArgs.samplePloidy; - final double[] genotypeLikelihoods = referenceConfidenceModel.calcGenotypeLikelihoodsOfRefVsAny(activeRegionDetectionHackishSamplePloidy,sample.getValue().getBasePileup(), ref.getBase(), hcArgs.minBaseQualityScore, averageHQSoftClips).genotypeLikelihoods; + final double[] genotypeLikelihoods = referenceConfidenceModel.calcGenotypeLikelihoodsOfRefVsAny(activeRegionDetectionHackishSamplePloidy,sample.getValue().getBasePileup(), ref.getBase(), hcArgs.minBaseQualityScore, averageHQSoftClips, false).genotypeLikelihoods; genotypes.add( new GenotypeBuilder(sample.getKey()).alleles(noCall).PL(genotypeLikelihoods).make() ); } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java index ecc6f03e940..82aa9221b13 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java @@ -13,10 +13,7 @@ import org.broadinstitute.hellbender.engine.AssemblyRegion; import org.broadinstitute.hellbender.tools.walkers.genotyper.PloidyModel; import org.broadinstitute.hellbender.tools.walkers.variantutils.PosteriorProbabilitiesUtils; -import org.broadinstitute.hellbender.utils.MathUtils; -import org.broadinstitute.hellbender.utils.QualityUtils; -import org.broadinstitute.hellbender.utils.SimpleInterval; -import org.broadinstitute.hellbender.utils.Utils; +import org.broadinstitute.hellbender.utils.*; import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods; import org.broadinstitute.hellbender.utils.genotyper.SampleList; import org.broadinstitute.hellbender.utils.haplotype.Haplotype; @@ -26,6 +23,7 @@ import org.broadinstitute.hellbender.utils.pileup.ReadPileup; import org.broadinstitute.hellbender.utils.read.AlignmentUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; +import org.broadinstitute.hellbender.utils.read.ReadCoordinateComparator; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils; import org.broadinstitute.hellbender.utils.variant.HomoSapiensConstants; @@ -292,7 +290,7 @@ private VariantContext makeReferenceConfidenceVariantContext(final int ploidy, // Assume infinite population on a single sample. final int refOffset = offset + globalRefOffset; final byte refBase = ref[refOffset]; - final RefVsAnyResult homRefCalc = calcGenotypeLikelihoodsOfRefVsAny(ploidy, pileup, refBase, BASE_QUAL_THRESHOLD, null); + final RefVsAnyResult homRefCalc = calcGenotypeLikelihoodsOfRefVsAny(ploidy, pileup, refBase, BASE_QUAL_THRESHOLD, null, true); final Allele refAllele = Allele.create(refBase, true); final List refSiteAlleles = Arrays.asList(refAllele, Allele.NON_REF_ALLELE); @@ -405,7 +403,8 @@ public RefVsAnyResult calcGenotypeLikelihoodsOfRefVsAny(final int ploidy, final ReadPileup pileup, final byte refBase, final byte minBaseQual, - final MathUtils.RunningAverage hqSoftClips) { + final MathUtils.RunningAverage hqSoftClips, + final boolean readsWereRealigned) { final int likelihoodCount = ploidy + 1; final double log10Ploidy = MathUtils.log10(ploidy); @@ -418,7 +417,7 @@ public RefVsAnyResult calcGenotypeLikelihoodsOfRefVsAny(final int ploidy, continue; } readCount++; - applyPileupElementRefVsNonRefLikelihoodAndCount(refBase, likelihoodCount, log10Ploidy, result, p, qual, hqSoftClips); + applyPileupElementRefVsNonRefLikelihoodAndCount(refBase, likelihoodCount, log10Ploidy, result, p, qual, hqSoftClips, readsWereRealigned); } final double denominator = readCount * log10Ploidy; for (int i = 0; i < likelihoodCount; i++) { @@ -427,9 +426,8 @@ public RefVsAnyResult calcGenotypeLikelihoodsOfRefVsAny(final int ploidy, return result; } - private void applyPileupElementRefVsNonRefLikelihoodAndCount(final byte refBase, final int likelihoodCount, final double log10Ploidy, final RefVsAnyResult result, final PileupElement element, final byte qual, final MathUtils.RunningAverage hqSoftClips) { - final boolean isAlt = element.getBase() != refBase || element.isDeletion() || element.isBeforeDeletionStart() - || element.isAfterDeletionEnd() || element.isBeforeInsertion() || element.isAfterInsertion() || element.isNextToSoftClip(); + private void applyPileupElementRefVsNonRefLikelihoodAndCount(final byte refBase, final int likelihoodCount, final double log10Ploidy, final RefVsAnyResult result, final PileupElement element, final byte qual, final MathUtils.RunningAverage hqSoftClips, final boolean readsWereRealigned) { + final boolean isAlt = readsWereRealigned ? isAltAfterAssembly(element, refBase) : isAltBeforeAssembly(element, refBase); final double referenceLikelihood; final double nonRefLikelihood; if (isAlt) { @@ -456,6 +454,15 @@ private void applyPileupElementRefVsNonRefLikelihoodAndCount(final byte refBase, } } + private boolean isAltBeforeAssembly(final PileupElement element, final byte refBase){ + return element.getBase() != refBase || element.isDeletion() || element.isBeforeDeletionStart() + || element.isAfterDeletionEnd() || element.isBeforeInsertion() || element.isAfterInsertion() || element.isNextToSoftClip(); + } + + private boolean isAltAfterAssembly(final PileupElement element, final byte refBase){ + return element.getBase() != refBase || element.isDeletion(); //we shouldn't have soft clips after assembly + } + /** * Get a list of pileups that span the entire active region span, in order, one for each position */ @@ -468,7 +475,8 @@ private List getPileupsOverReference(final Haplotype refHaplotype, Utils.validateArg(calledHaplotypes.contains(refHaplotype), "calledHaplotypes must contain the refHaplotype"); Utils.validateArg(readLikelihoods.numberOfSamples() == 1, () -> "readLikelihoods must contain exactly one sample but it contained " + readLikelihoods.numberOfSamples()); - final List reads = activeRegion.getReads(); + final List reads = new ArrayList<>(readLikelihoods.sampleReads(0)); + reads.sort(new ReadCoordinateComparator(activeRegion.getHeader())); //because we updated the reads based on the local realignments we have to re-sort or the pileups will be... unpredictable final LocusIteratorByState libs = new LocusIteratorByState(reads.iterator(), LocusIteratorByState.NO_DOWNSAMPLING, false, samples.asSetOfSamples(), activeRegion.getHeader(), true); @@ -547,7 +555,7 @@ int sumMismatchingQualities(final byte[] readBases, for ( int i = 0; i < n; i++ ) { final byte readBase = readBases[readStart + i]; final byte refBase = refBases[refStart + i]; - if ( readBase != refBase ) { + if ( !Nucleotide.intersect(readBase, refBase) && !(readBase == AlignmentUtils.GAP_CHARACTER)) { sum += readQuals[readStart + i]; if ( sum > maxSum ) { // abort early return sum; @@ -562,7 +570,7 @@ int sumMismatchingQualities(final byte[] readBases, * Compute whether a read is informative to eliminate an indel of size <= maxIndelSize segregating at readStart/refStart * * @param read the read - * @param readStart the starting position of the read (i.e., that aligns it to a position in the reference) + * @param readStart the index with respect to @{param}refBases where the read starts * @param refBases the reference bases * @param refStart the offset into refBases that aligns to the readStart position in readBases * @param maxIndelSize the max indel size to consider for the read to be informative @@ -582,8 +590,9 @@ boolean isReadInformativeAboutIndelsOfSize(final GATKRead read, // We are safe to use the faster no-copy versions of getBases and getBaseQualities here, // since we're not modifying the returned arrays in any way. This makes a small difference // in the HaplotypeCaller profile, since this method is a major hotspot. - final byte[] readBases = read.getBasesNoCopy(); - final byte[] readQuals = read.getBaseQualitiesNoCopy(); + final byte[] readBases = AlignmentUtils.getBasesAlignedOneToOne(read); //calls getBasesNoCopy if CIGAR is all match + final byte[] readQuals = AlignmentUtils.getBaseQualsAlignedOneToOne(read); + final int baselineMMSum = sumMismatchingQualities(readBases, readQuals, readStart, refBases, refStart, Integer.MAX_VALUE); @@ -607,7 +616,7 @@ boolean isReadInformativeAboutIndelsOfSize(final GATKRead read, * Calculate the number of indel informative reads at pileup * * @param pileup a pileup - * @param pileupOffsetIntoRef the position of the pileup in the reference + * @param pileupOffsetIntoRef index along the reference corresponding to the pileup * @param ref the ref bases * @param maxIndelSize maximum indel size to consider in the informativeness calculation * @return an integer >= 0 @@ -616,16 +625,14 @@ boolean isReadInformativeAboutIndelsOfSize(final GATKRead read, int calcNIndelInformativeReads(final ReadPileup pileup, final int pileupOffsetIntoRef, final byte[] ref, final int maxIndelSize) { int nInformative = 0; for ( final PileupElement p : pileup ) { - final GATKRead read = p.getRead(); - final int offset = p.getOffset(); - // doesn't count as evidence if ( p.isBeforeDeletionStart() || p.isBeforeInsertion() || p.isDeletion() ) { continue; } - // todo -- this code really should handle CIGARs directly instead of relying on the above tests - if ( isReadInformativeAboutIndelsOfSize(read, offset, ref, pileupOffsetIntoRef, maxIndelSize) ) { + final int offset = getCigarModifiedOffset(p); + + if ( isReadInformativeAboutIndelsOfSize(p.getRead(), offset, ref, pileupOffsetIntoRef, maxIndelSize) ) { nInformative++; if( nInformative > MAX_N_INDEL_INFORMATIVE_READS ) { return MAX_N_INDEL_INFORMATIVE_READS; @@ -635,6 +642,25 @@ int calcNIndelInformativeReads(final ReadPileup pileup, final int pileupOffsetIn return nInformative; } + /** + * Calculate the index of the current pileup position against the reference-aligned read + * This offset should be representative of the "IGV view" for the read where insertions are collapsed and deletions + * are padded so that we can easily count the mismatches against the reference + * @param p the PileupElement containing the offset as an index into the read base sequence + * @return the new reference-aligned index/offset + */ + @VisibleForTesting + protected int getCigarModifiedOffset (final PileupElement p){ + final GATKRead read = p.getRead(); + int offset = (p.getCurrentCigarElement().getOperator().consumesReferenceBases() || p.getCurrentCigarElement().getOperator() == CigarOperator.S)? p.getOffsetInCurrentCigar() : 0; + for (final CigarElement elem : read.getCigar().getCigarElements().subList(0, p.getCurrentCigarOffset())) { + if (elem.getOperator().consumesReferenceBases() || elem.getOperator() == CigarOperator.S) { + offset += elem.getLength(); + } + } + return offset; + } + /** * Create a reference haplotype for an active region * diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/SplitNCigarReads.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/SplitNCigarReads.java index 0bcc1277a84..7f75fdb6e0b 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/SplitNCigarReads.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/SplitNCigarReads.java @@ -23,7 +23,6 @@ import org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.hellbender.utils.read.*; -import java.io.File; import java.io.FileNotFoundException; import java.io.IOException; import java.util.ArrayList; @@ -303,12 +302,12 @@ private static GATKRead splitReadBasedOnCigar(final GATKRead read, final int cig // we keep only the section of the read that is aligned to the reference between startRefIndex and stopRefIndex (inclusive). // the other sections of the read are clipped: - final int startRefIndex = read.getUnclippedStart() + CigarUtils.countRefBasesBasedOnCigar(read, 0, cigarFirstIndex); //goes through the prefix of the cigar (up to cigarStartIndex) and move the reference index. - final int stopRefIndex = startRefIndex + CigarUtils.countRefBasesBasedOnCigar(read,cigarFirstIndex,cigarSecondIndex)-1; //goes through a consecutive non-N section of the cigar (up to cigarEndIndex) and move the reference index. + final int startRefIndex = read.getUnclippedStart() + CigarUtils.countRefBasesBasedOnUnclippedAlignment(read, 0, cigarFirstIndex); //goes through the prefix of the cigar (up to cigarStartIndex) and move the reference index. + final int stopRefIndex = startRefIndex + CigarUtils.countRefBasesBasedOnUnclippedAlignment(read,cigarFirstIndex,cigarSecondIndex)-1; //goes through a consecutive non-N section of the cigar (up to cigarEndIndex) and move the reference index. if ( forSplitPositions != null ) { final String contig = read.getContig(); - final int splitStart = startRefIndex + CigarUtils.countRefBasesBasedOnCigar(read,cigarFirstIndex,cigarEndIndex); //we use cigarEndIndex instead of cigarSecondIndex so we won't take into account the D's at the end. + final int splitStart = startRefIndex + CigarUtils.countRefBasesBasedOnUnclippedAlignment(read,cigarFirstIndex,cigarEndIndex); //we use cigarEndIndex instead of cigarSecondIndex so we won't take into account the D's at the end. final int splitEnd = splitStart + read.getCigarElement(cigarEndIndex).getLength() - 1; forSplitPositions.addSplicePosition(contig, splitStart, splitEnd); } diff --git a/src/main/java/org/broadinstitute/hellbender/utils/Nucleotide.java b/src/main/java/org/broadinstitute/hellbender/utils/Nucleotide.java index 49a21fc6947..437ee9913ea 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/Nucleotide.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/Nucleotide.java @@ -368,6 +368,16 @@ public Nucleotide intersect(final Nucleotide other) { return maskToValue[mask & other.mask]; } + /** + * Checks whether two nucleotides intersect given their byte encodings. + * @param a first nucleotide. + * @param b second nucleotide. + * @return {@code true} iff the input nucleotides intersect. + */ + public static boolean intersect(final byte a, final byte b) { + return (baseToValue[0xFF & a].mask & baseToValue[0xFF & b].mask) != 0; + } + /** * Checks whether two base encodings make reference to the same {@link #Nucleotide} * instance regardless of their case. diff --git a/src/main/java/org/broadinstitute/hellbender/utils/clipping/ReadClipper.java b/src/main/java/org/broadinstitute/hellbender/utils/clipping/ReadClipper.java index 97e81b0fe30..5fa39b80951 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/clipping/ReadClipper.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/clipping/ReadClipper.java @@ -357,7 +357,7 @@ public static GATKRead hardClipToRegion( final GATKRead read, final int refStart */ public static GATKRead hardClipToRegionIncludingClippedBases( final GATKRead read, final int refStart, final int refStop ) { final int start = read.getUnclippedStart(); - final int stop = start + CigarUtils.countRefBasesBasedOnCigar(read, 0, read.numCigarElements()) - 1; + final int stop = start + CigarUtils.countRefBasesBasedOnUnclippedAlignment(read, 0, read.numCigarElements()) - 1; return hardClipToRegion(read, refStart, refStop, start, stop); } @@ -519,7 +519,7 @@ protected GATKRead clipByReferenceCoordinates(final int refStart, final int refS */ public static GATKRead softClipToRegionIncludingClippedBases( final GATKRead read, final int refStart, final int refStop ) { final int start = read.getUnclippedStart(); - final int stop = start + CigarUtils.countRefBasesBasedOnCigar(read, 0, read.numCigarElements()) - 1; + final int stop = start + CigarUtils.countRefBasesBasedOnUnclippedAlignment(read, 0, read.numCigarElements()) - 1; if (start <= refStop && stop >= refStart) { if (start < refStart && stop > refStop) { diff --git a/src/main/java/org/broadinstitute/hellbender/utils/read/AlignmentUtils.java b/src/main/java/org/broadinstitute/hellbender/utils/read/AlignmentUtils.java index 8baf6073333..4347941cf10 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/read/AlignmentUtils.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/read/AlignmentUtils.java @@ -6,6 +6,7 @@ import org.broadinstitute.gatk.nativebindings.smithwaterman.SWOverhangStrategy; import org.broadinstitute.hellbender.exceptions.GATKException; import org.broadinstitute.hellbender.utils.BaseUtils; +import org.broadinstitute.hellbender.utils.Nucleotide; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.haplotype.Haplotype; import org.broadinstitute.hellbender.utils.pileup.PileupElement; @@ -13,12 +14,14 @@ import org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAlignment; import java.util.*; +import java.util.function.Function; public final class AlignmentUtils { private static final EnumSet ALIGNED_TO_GENOME_OPERATORS = EnumSet.of(CigarOperator.M, CigarOperator.EQ, CigarOperator.X); private static final EnumSet ALIGNED_TO_GENOME_PLUS_SOFTCLIPS = EnumSet.of(CigarOperator.M, CigarOperator.EQ, CigarOperator.X, CigarOperator.S); public final static String HAPLOTYPE_TAG = "HC"; + public final static byte GAP_CHARACTER = (byte)'-'; // cannot be instantiated private AlignmentUtils() { } @@ -197,6 +200,51 @@ public static byte[] getBasesCoveringRefInterval(final int refStart, final int r return Arrays.copyOfRange(bases, basesStart, basesStop + 1); } + public static byte[] getBasesAlignedOneToOne(final GATKRead read) { + return getSequenceAlignedOneToOne(read, r -> r.getBasesNoCopy(), GAP_CHARACTER); + } + + public static byte[] getBaseQualsAlignedOneToOne(final GATKRead read) { + return getSequenceAlignedOneToOne(read, r -> r.getBaseQualitiesNoCopy(), (byte)0); + } + + public static byte[] getSequenceAlignedOneToOne(final GATKRead read, final Function bytesProvider, final byte padWith) { + Utils.nonNull(read); + Utils.nonNull(bytesProvider); + final Cigar cigar = read.getCigar(); + final byte[] sequence = bytesProvider.apply(read); + + if (!cigar.containsOperator(CigarOperator.DELETION) && !cigar.containsOperator(CigarOperator.INSERTION)) { + return sequence; + } + else { + final byte[] paddedBases = new byte[CigarUtils.countRefBasesIncludingSoftClips(read, 0, cigar.numCigarElements())]; + int literalPos = 0; + int paddedPos = 0; + for ( int i = 0; i < cigar.numCigarElements(); i++ ) { + final CigarElement ce = cigar.getCigarElement(i); + final CigarOperator co = ce.getOperator(); + if (co.consumesReadBases()) { + if (!co.consumesReferenceBases()) { + literalPos += ce.getLength(); //skip inserted bases + } + else { + System.arraycopy(sequence, literalPos, paddedBases, paddedPos, ce.getLength()); + literalPos += ce.getLength(); + paddedPos += ce.getLength(); + } + } + else if (co.consumesReferenceBases()) { + for ( int j = 0; j < ce.getLength(); j++ ) { //pad deleted bases + paddedBases[paddedPos] = padWith; + paddedPos++; + } + } + } + return paddedBases; + } + } + /** * Get the number of bases at which refSeq and readSeq differ, given their alignment * diff --git a/src/main/java/org/broadinstitute/hellbender/utils/read/CigarUtils.java b/src/main/java/org/broadinstitute/hellbender/utils/read/CigarUtils.java index fb07b4848ff..33e7a8d0ebc 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/read/CigarUtils.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/read/CigarUtils.java @@ -85,16 +85,11 @@ public static Cigar invertCigar (final Cigar cigar) { /** * Compute the number of reference bases between the start (inclusive) and end (exclusive) cigar elements. - * Note: The method does NOT use CigarOperator.consumesReferenceBases, since it checks something different. - * The idea is you remove some elements from the beginning of the cigar string, - * and want to recalculate what if the new starting reference position, - * you want to count all the elements that indicate existing bases in the reference - * (everything but I and P). + * Reference bases are counted as the number of positions w.r.t. the reference spanned by an alignment to that reference. * For example original position = 10. cigar: 2M3I2D1M. If you remove the 2M the new starting position is 12. * If you remove the 2M3I it is still 12. If you remove 2M3I2D (not reasonable cigar), you will get position 14. */ - @SuppressWarnings("fallthru") - public static int countRefBasesBasedOnCigar(final GATKRead read, final int cigarStartIndex, final int cigarEndIndex){ + public static int countRefBasesBasedOnUnclippedAlignment(final GATKRead read, final int cigarStartIndex, final int cigarEndIndex){ if (read == null){ throw new IllegalArgumentException("null read"); } @@ -105,21 +100,26 @@ public static int countRefBasesBasedOnCigar(final GATKRead read, final int cigar int result = 0; for(int i = cigarStartIndex; i < cigarEndIndex; i++){ final CigarElement cigarElement = elems.get(i); - switch (cigarElement.getOperator()) { - case M: - case D: - case N: - case EQ: - case X: - case S: - case H: - result += cigarElement.getLength(); - break; - case I: - case P: //for these two, nothing happens. - break; - default: - throw new GATKException("Unsupported cigar operator: " + cigarElement.getOperator()); + final CigarOperator operator = cigarElement.getOperator(); + if (operator.consumesReferenceBases() || operator.isClipping()) { + result += cigarElement.getLength(); + } + } + return result; + } + + public static int countRefBasesIncludingSoftClips(final GATKRead read, final int cigarStartIndex, final int cigarEndIndex){ + Utils.nonNull(read, "null read"); + final List elems = read.getCigarElements(); + if (cigarStartIndex < 0 || cigarEndIndex > elems.size() || cigarStartIndex > cigarEndIndex){ + throw new IllegalArgumentException("invalid index:" + 0 + " -" + elems.size()); + } + int result = 0; + for(int i = cigarStartIndex; i < cigarEndIndex; i++){ + final CigarElement cigarElement = elems.get(i); + final CigarOperator operator = cigarElement.getOperator(); + if (operator.consumesReferenceBases() || operator == CigarOperator.S) { + result += cigarElement.getLength(); } } return result; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/HaplotypeCallerSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/HaplotypeCallerSparkIntegrationTest.java index 41bd2765c93..09788920539 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/HaplotypeCallerSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/HaplotypeCallerSparkIntegrationTest.java @@ -100,7 +100,7 @@ public void testVCFModeIsConcordantWithGATK3_8ResultsAlleleSpecificAnnotations() /* * Test that in GVCF mode we're >= 99% concordant with GATK3 results */ - @Test + @Test(enabled=false) //disabled after reference confidence change in #5172 public void testGVCFModeIsConcordantWithGATK3_8Results() throws Exception { Utils.resetRandomGenerator(); @@ -157,7 +157,7 @@ public static Object[][] gvcfCases() { }; } - @Test(dataProvider = "gvcfCases") + @Test(dataProvider = "gvcfCases", enabled=false) //disabled after reference confidence change in #5172 public void testGVCFModeIsConcordantWithGATK3_8AlelleSpecificResults(String extension) throws Exception { Utils.resetRandomGenerator(); final File output = createTempFile("testGVCFModeIsConcordantWithGATK3_8AlelleSpecificResults", extension); diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java index d4c0b91eec2..2977f358ea6 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java @@ -236,7 +236,7 @@ public void testGVCFModeIsConsistentWithPastResults_AlleleSpecificAnnotations(fi /* * Test that in GVCF mode we're >= 99% concordant with GATK3 results */ - @Test(dataProvider="HaplotypeCallerTestInputs") + @Test(dataProvider="HaplotypeCallerTestInputs", enabled=false) //disabled after reference confidence change in #5172 public void testGVCFModeIsConcordantWithGATK3_8Results(final String inputFileName, final String referenceFileName) throws Exception { Utils.resetRandomGenerator(); @@ -265,7 +265,7 @@ public void testGVCFModeIsConcordantWithGATK3_8Results(final String inputFileNam Assert.assertTrue(concordance >= 0.99, "Concordance with GATK 3.8 in GVCF mode is < 99% (" + concordance + ")"); } - @Test(dataProvider="HaplotypeCallerTestInputs") + @Test(dataProvider="HaplotypeCallerTestInputs", enabled=false) //disabled after reference confidence change in #5172 public void testGVCFModeIsConcordantWithGATK3_8AlelleSpecificResults(final String inputFileName, final String referenceFileName) throws Exception { Utils.resetRandomGenerator(); final File output = createTempFile("testGVCFModeIsConcordantWithGATK3_8AlelleSpecificResults", ".g.vcf"); @@ -677,10 +677,8 @@ public Object[][] getContaminationCorrectionTestData() { // java -jar target/GenomeAnalysisTK.jar -T HaplotypeCaller -I ../hellbender/src/test/resources/large/contaminated_bams/CEUTrio.HiSeq.WGS.b37.NA12878.CONTAMINATED.WITH.HCC1143.NORMALS.AT.15PERCENT.bam -R ../hellbender/src/test/resources/large/human_g1k_v37.20.21.fasta -L 20:10100000-10150000 -contamination 0.15 -o ../hellbender/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.CEUTrio.HiSeq.WGS.b37.NA12878.CONTAMINATED.WITH.HCC1143.NORMALS.15PCT.20.10100000-10150000.gatk3.8-1-1-gdde23f56a6.vcf final String expectedGATK3ContaminationCorrectedCallsVCF = TEST_FILES_DIR + "expected.CEUTrio.HiSeq.WGS.b37.NA12878.CONTAMINATED.WITH.HCC1143.NORMALS.15PCT.20.10100000-10150000.gatk3.8-1-1-gdde23f56a6.vcf"; - // Expected calls from GATK 3.x on the contaminated bam running with -contamination - // Created in GATK 3.8-1-1-gdde23f56a6 using the command: - // java -jar target/GenomeAnalysisTK.jar -T HaplotypeCaller -I ../hellbender/src/test/resources/large/contaminated_bams/CEUTrio.HiSeq.WGS.b37.NA12878.CONTAMINATED.WITH.HCC1143.NORMALS.AT.15PERCENT.bam -R ../hellbender/src/test/resources/large/human_g1k_v37.20.21.fasta -L 20:10100000-10150000 -contamination 0.15 -o ../hellbender/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.CEUTrio.HiSeq.WGS.b37.NA12878.CONTAMINATED.WITH.HCC1143.NORMALS.15PCT.20.10100000-10150000.gatk3.8-1-1-gdde23f56a6.g.vcf -ERC GVCF - final String expectedGATK3ContaminationCorrectedCallsGVCF = TEST_FILES_DIR + "expected.CEUTrio.HiSeq.WGS.b37.NA12878.CONTAMINATED.WITH.HCC1143.NORMALS.15PCT.20.10100000-10150000.gatk3.8-1-1-gdde23f56a6.g.vcf"; + // Expected calls from GATK ~4.0.8.1 with indel reference confidence fix + final String expectedGATK4ContaminationCorrectedCallsGVCF = TEST_FILES_DIR + "expected.CEUTrio.HiSeq.WGS.b37.NA12878.CONTAMINATED.WITH.HCC1143.NORMALS.15PCT.20.10100000-10150000.postIndelRefConfUpdate.g.vcf"; // Expected calls from GATK 4 on the uncontaminated bam (VCF mode) final String expectedGATK4UncontaminatedCallsVCF = TEST_FILES_DIR + "expected.CEUTrio.HiSeq.WGS.b37.NA12878.calls.20.10100000-10150000.vcf"; @@ -713,7 +711,7 @@ public Object[][] getContaminationCorrectionTestData() { b37_reference_20_21, true, // GVCF mode expectedGATK4UncontaminatedCallsGVCF, - expectedGATK3ContaminationCorrectedCallsGVCF + expectedGATK4ContaminationCorrectedCallsGVCF } }; } @@ -836,14 +834,14 @@ public void testContaminationCorrection( final String contaminatedBam, final String reference, final boolean gvcfMode, final String gatk4UncontaminatedCallsVCF, - final String gatk3ContaminationCorrectedCallsVCF ) throws Exception { + final String expectedContaminationCorrectedCallsVCF ) throws Exception { final File uncorrectedOutput = createTempFile("testContaminationCorrectionUncorrectedOutput", gvcfMode ? ".g.vcf" : ".vcf"); final File correctedOutput = createTempFile("testContaminationCorrectionCorrectedOutput", gvcfMode ? ".g.vcf" : ".vcf"); final File correctedOutputUsingContaminationFile = createTempFile("testContaminationCorrectionCorrectedOutputUsingContaminationFile", gvcfMode ? ".g.vcf" : ".vcf"); // Generate raw uncorrected calls on the contaminated bam, for comparison purposes // Note that there are a huge number of MNPs in this bam, and that in {@code gatk4UncontaminatedCallsVCF} and - // {@code gatk3ContaminationCorrectedCallsVCF} these are represented as independent consecutive SNPs + // {@code expectedContaminationCorrectedCallsVCF} these are represented as independent consecutive SNPs // Thus if we ever turn on MNPs by default, this will fail final String[] noContaminationCorrectionArgs = { "-I", contaminatedBam, @@ -887,14 +885,14 @@ public void testContaminationCorrection( final String contaminatedBam, // Calculate concordance vs. the contamination-corrected calls from GATK3. Here we count // all records in the output, including reference blocks. - final double correctedCallsVSGATK3CorrectedCallsConcordance = calculateConcordance(correctedOutput, new File(gatk3ContaminationCorrectedCallsVCF)); - final double correctedCallsFromFileVSGATK3CorrectedCallsConcordance = calculateConcordance(correctedOutputUsingContaminationFile, new File(gatk3ContaminationCorrectedCallsVCF)); + final double correctedCallsVSExpectedCorrectedCallsConcordance = calculateConcordance(correctedOutput, new File(expectedContaminationCorrectedCallsVCF)); + final double correctedCallsFromFileVSExpectedCorrectedCallsConcordance = calculateConcordance(correctedOutputUsingContaminationFile, new File(expectedContaminationCorrectedCallsVCF)); // Sanity checks: the concordance when running with -contamination should be the same as the // concordance when running with -contamination-file assertEqualsDoubleSmart(correctedCallsVSUncontaminatedCallsConcordance, correctedCallsFromFileVSUncontaminatedCallsConcordance, 0.001, "concordance running with -contamination and -contamination-file should be identical, but wasn't"); - assertEqualsDoubleSmart(correctedCallsVSGATK3CorrectedCallsConcordance, correctedCallsFromFileVSGATK3CorrectedCallsConcordance, 0.001, + assertEqualsDoubleSmart(correctedCallsVSExpectedCorrectedCallsConcordance, correctedCallsFromFileVSExpectedCorrectedCallsConcordance, 0.001, "concordance running with -contamination and -contamination-file should be identical, but wasn't"); // With -contamination correction on, concordance vs. the calls on the uncontaminated bam @@ -911,12 +909,12 @@ public void testContaminationCorrection( final String contaminatedBam, // -contamination corrected output in GATK4 should have >= 99% concordance // vs. -contamination corrected output in GATK3 - Assert.assertTrue(correctedCallsVSGATK3CorrectedCallsConcordance >= 0.99, + Assert.assertTrue(correctedCallsVSExpectedCorrectedCallsConcordance >= 0.99, "output with -contamination correction should have >= 99% concordance with contamination-corrected calls from GATK3, but it didn't"); // -contamination-file corrected output in GATK4 should have >= 99% concordance // vs. -contamination corrected output in GATK3 - Assert.assertTrue(correctedCallsFromFileVSGATK3CorrectedCallsConcordance >= 0.99, + Assert.assertTrue(correctedCallsFromFileVSExpectedCorrectedCallsConcordance >= 0.99, "output with -contamination-file correction should have >= 99% concordance with contamination-corrected calls from GATK3, but it didn't"); } diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java index eb762408c2b..7afeaa6f94b 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java @@ -1,6 +1,7 @@ package org.broadinstitute.hellbender.tools.walkers.haplotypecaller; import com.google.common.base.Strings; +import htsjdk.samtools.Cigar; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMReadGroupRecord; import htsjdk.variant.variantcontext.*; @@ -18,6 +19,7 @@ import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods; import org.broadinstitute.hellbender.utils.genotyper.SampleList; import org.broadinstitute.hellbender.utils.haplotype.Haplotype; +import org.broadinstitute.hellbender.utils.pileup.PileupElement; import org.broadinstitute.hellbender.utils.pileup.ReadPileup; import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; @@ -65,56 +67,74 @@ public Object[][] makeMyDataProvider() { { // very basic testing final String ref = "ACGT"; final String read = "ACGT"; - tests.add(new Object[]{read, ref, 1, Arrays.asList(1, 1, 1, 0)}); - tests.add(new Object[]{read, ref, 2, Arrays.asList(1, 1, 0, 0)}); - tests.add(new Object[]{read, ref, 3, Arrays.asList(1, 0, 0, 0)}); - tests.add(new Object[]{read, ref, 4, Arrays.asList(0, 0, 0, 0)}); + final String cigar = read.length() + "M"; + tests.add(new Object[]{read, cigar, ref, 1, Arrays.asList(1, 1, 1, 0)}); + tests.add(new Object[]{read, cigar, ref, 2, Arrays.asList(1, 1, 0, 0)}); + tests.add(new Object[]{read, cigar, ref, 3, Arrays.asList(1, 0, 0, 0)}); + tests.add(new Object[]{read, cigar, ref, 4, Arrays.asList(0, 0, 0, 0)}); } { // actually interesting case where some sites aren't informative - final String ref = "NNAAAANN"; - final String read1 = "NNA"; - final String read2 = "NNAA"; - final String read3 = "NNAAA"; - final String read4 = "NNAAAA"; - final String read5 = "NNAAAAN"; - tests.add(new Object[]{read1, ref, 1, Arrays.asList(1, 1, 0, 0, 0, 0, 0, 0)}); - tests.add(new Object[]{read2, ref, 1, Arrays.asList(1, 1, 0, 0, 0, 0, 0, 0)}); - tests.add(new Object[]{read3, ref, 1, Arrays.asList(1, 1, 0, 0, 0, 0, 0, 0)}); - tests.add(new Object[]{read4, ref, 1, Arrays.asList(1, 1, 0, 0, 0, 0, 0, 0)}); - tests.add(new Object[]{read5, ref, 1, Arrays.asList(1, 1, 1, 1, 1, 1, 0, 0)}); + final String ref = "TTAAAATT"; + final String read1 = "TTA"; + final String read2 = "TTAA"; + final String read3 = "TTAAA"; + final String read4 = "TTAAAA"; + final String read5 = "TTAAAAT"; + final String cigar1 = read1.length() + "M"; + final String cigar2 = read2.length() + "M"; + final String cigar3 = read3.length() + "M"; + final String cigar4 = read4.length() + "M"; + final String cigar5 = read5.length() + "M"; + + tests.add(new Object[]{read1, cigar1, ref, 1, Arrays.asList(1, 1, 0, 0, 0, 0, 0, 0)}); + tests.add(new Object[]{read2, cigar2, ref, 1, Arrays.asList(1, 1, 0, 0, 0, 0, 0, 0)}); + tests.add(new Object[]{read3, cigar3, ref, 1, Arrays.asList(1, 1, 0, 0, 0, 0, 0, 0)}); + tests.add(new Object[]{read4, cigar4, ref, 1, Arrays.asList(1, 1, 0, 0, 0, 0, 0, 0)}); + tests.add(new Object[]{read5, cigar5, ref, 1, Arrays.asList(1, 1, 1, 1, 1, 1, 0, 0)}); } - for ( final String repeatUnit : Arrays.asList("A", "CA", "TAG", "TAGC", "TCAGA")) { - final String anchor = Strings.repeat("N", repeatUnit.length()); + for ( final String repeatUnit : Arrays.asList("A", "CA", "TAC", "TAGC", "TCAGA")) { + final String anchor = Strings.repeat("G", repeatUnit.length()); for ( int nUnits = 1; nUnits < 10; nUnits++ ) { final String repeat = Strings.repeat(repeatUnit, nUnits); final String ref = anchor + repeat + anchor; + final String refCigar = ref.length() + "M"; for ( int readLen = repeatUnit.length(); readLen < repeat.length(); readLen++ ) { final String read = anchor + repeat.substring(0, readLen); + final String readCigar = read.length() + "M"; final List expected = new LinkedList<>(); for ( int i = 0; i < anchor.length(); i++ ) expected.add(1); for ( int i = 0; i < repeat.length(); i++ ) expected.add(readLen == repeat.length() ? 1 : 0); for ( int i = 0; i < anchor.length(); i++ ) expected.add(0); - tests.add(new Object[]{read, ref, repeatUnit.length(), expected}); + tests.add(new Object[]{read, readCigar, ref, repeatUnit.length(), expected}); final List result = new ArrayList<>(Collections.nCopies(ref.length() - anchor.length(), 1)); result.addAll(Collections.nCopies(anchor.length(), 0)); - tests.add(new Object[]{ref, ref, repeatUnit.length(), result}); + tests.add(new Object[]{ref, refCigar, ref, repeatUnit.length(), result}); } } } + {//regression tests for an issue from late Aug 2018 + final String ref = "AATATCATCTTTGGTGTTT"; + final String read = "AATATCATTGGTG"; + final String cigar1 = read.length() + "M"; + final String cigar2 = "7M3D6M"; + //real issue is the informativeness for offset zero, but might as well run the rest of the offsets + tests.add(new Object[]{read, cigar1, ref, 3, Arrays.asList(0,0,0,0,0,0,0,0,0,0,0,0,0)}); + tests.add(new Object[]{read, cigar2, ref, 3, Arrays.asList(1,1,1,1,1,1,0,0,0,0,0,0,0)}); + } return tests.toArray(new Object[][]{}); } @Test(dataProvider = "CalcNIndelInformativeReadsData") - public void testCalcNIndelInformativeReads(final String readBases, final String ref, final int maxIndelSize, final List expected ) { + public void testCalcNIndelInformativeReads(final String readBases, final String cigar, final String ref, final int maxIndelSize, final List expected ) { final byte qual = (byte)30; final byte[] quals = Utils.dupBytes(qual, readBases.length()); for ( int i = 0; i < readBases.getBytes().length; i++ ) { - final GATKRead read = ArtificialReadUtils.createArtificialRead(readBases.getBytes(), quals, readBases.length() + "M"); + final GATKRead read = ArtificialReadUtils.createArtificialRead(readBases.getBytes(), quals, cigar); final SimpleInterval loc = new SimpleInterval("20", i + 1, i + 1); final ReadPileup pileup = new ReadPileup(loc, Collections.singletonList(read), i); final int actual = model.calcNIndelInformativeReads(pileup, i, ref.getBytes(), maxIndelSize); @@ -183,6 +203,38 @@ public void testOverlappingVariantContext() { checkOverlapping(20, calls, null); } + @DataProvider(name = "OffsetTestData") + public Object[][] getOffsetTestData() { + List tests = new ArrayList<>(); + + final String read1 = "AATATCATTGGTG"; + final String cigar1 = "13M"; + final String cigar2 = "7M3D6M"; + final String cigar3 = "7M3I3M"; + final String cigar4 = "7M3D3I3M"; + //offset inside soft clip is not allowed + tests.add(new Object[]{read1, cigar1, 5, 5}); + tests.add(new Object[]{read1, cigar2, 5, 5}); + tests.add(new Object[]{read1, cigar2, 11, 14}); + tests.add(new Object[]{read1, cigar3, 5, 5}); + tests.add(new Object[]{read1, cigar3, 11, 8}); + tests.add(new Object[]{read1, cigar4, 5, 5}); + tests.add(new Object[]{read1, cigar4, 11, 11}); + + return tests.toArray(new Object[][]{}); + } + + @Test(dataProvider = "OffsetTestData") + public void testCigarModifiedOffset(final String readBases, final String cigar, final int pileupOffset, final int expectedNewOffset) { + final byte qual = (byte)30; + final byte[] quals = Utils.dupBytes(qual, readBases.length()); + + final GATKRead read = ArtificialReadUtils.createArtificialRead(readBases.getBytes(), quals, cigar); + final PileupElement pe = PileupElement.createPileupForReadAndOffset(read, pileupOffset); + final int newOffset = model.getCigarModifiedOffset(pe); + Assert.assertEquals(newOffset, expectedNewOffset); + } + private void checkOverlapping(final int pos, Collection calls, final VariantContext expected) { final GenomeLoc loc = parser.createGenomeLoc(parser.getSequenceDictionary().getSequences().get(0).getSequenceName(), pos, pos); final VariantContext actual = model.getOverlappingVariantContext(loc, calls); diff --git a/src/test/java/org/broadinstitute/hellbender/utils/read/CigarUtilsUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/read/CigarUtilsUnitTest.java index abf6aa7ae1e..31fcc28b74c 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/read/CigarUtilsUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/read/CigarUtilsUnitTest.java @@ -184,31 +184,31 @@ public Iterator testData_countRefBasesBasedOnCigar(final Method testMe @Test(dataProvider = "testData_countRefBasesBasedOnCigar") public void testCountRefBasesBasedOnCigar(final String cigarStrIn, final int start, final int end, final int expected){ final GATKRead read = ReadClipperTestUtils.makeReadFromCigar(cigarStrIn); - final int actual = CigarUtils.countRefBasesBasedOnCigar(read, start, end); + final int actual = CigarUtils.countRefBasesBasedOnUnclippedAlignment(read, start, end); Assert.assertEquals(actual, expected, cigarStrIn); } @Test(expectedExceptions = IllegalArgumentException.class) public void testCountRefBasesBasedOnCigarNull(){ - CigarUtils.countRefBasesBasedOnCigar(null, 1, 2); + CigarUtils.countRefBasesBasedOnUnclippedAlignment(null, 1, 2); } @Test(expectedExceptions = IllegalArgumentException.class) public void testCountRefBasesBasedOnCigarStart1(){ final String cigarStrIn = "1M1=1X"; final GATKRead read = ReadClipperTestUtils.makeReadFromCigar(cigarStrIn); - CigarUtils.countRefBasesBasedOnCigar(read, -1, 1); + CigarUtils.countRefBasesBasedOnUnclippedAlignment(read, -1, 1); } @Test(expectedExceptions = IllegalArgumentException.class) public void testCountRefBasesBasedOnCigarStart2(){ final String cigarStrIn = "1M1=1X"; final GATKRead read = ReadClipperTestUtils.makeReadFromCigar(cigarStrIn); - CigarUtils.countRefBasesBasedOnCigar(read, 2, 1); + CigarUtils.countRefBasesBasedOnUnclippedAlignment(read, 2, 1); } @Test(expectedExceptions = IllegalArgumentException.class) public void testCountRefBasesBasedOnCigarEnd2(){ final String cigarStrIn = "1M1=1X"; final GATKRead read = ReadClipperTestUtils.makeReadFromCigar(cigarStrIn); - CigarUtils.countRefBasesBasedOnCigar(read, 1, 6); + CigarUtils.countRefBasesBasedOnUnclippedAlignment(read, 1, 6); } diff --git a/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg38 b/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg38 index 14a3aca17e5..7f269223e50 120000 --- a/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg38 +++ b/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg38 @@ -1 +1,3 @@ -hg19/ \ No newline at end of file +version https://git-lfs.github.com/spec/v1 +oid sha256:bbcbe22ea1705114507a241904cbed049bf66f13da522adab3113579acc360d7 +size 24 diff --git a/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg38 b/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg38 index 14a3aca17e5..7f269223e50 120000 --- a/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg38 +++ b/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg38 @@ -1 +1,3 @@ -hg19/ \ No newline at end of file +version https://git-lfs.github.com/spec/v1 +oid sha256:bbcbe22ea1705114507a241904cbed049bf66f13da522adab3113579acc360d7 +size 24 diff --git a/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg38 b/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg38 index 14a3aca17e5..7f269223e50 120000 --- a/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg38 +++ b/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg38 @@ -1 +1,3 @@ -hg19/ \ No newline at end of file +version https://git-lfs.github.com/spec/v1 +oid sha256:bbcbe22ea1705114507a241904cbed049bf66f13da522adab3113579acc360d7 +size 24 diff --git a/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg38 b/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg38 index 14a3aca17e5..7f269223e50 120000 --- a/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg38 +++ b/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg38 @@ -1 +1,3 @@ -hg19/ \ No newline at end of file +version https://git-lfs.github.com/spec/v1 +oid sha256:bbcbe22ea1705114507a241904cbed049bf66f13da522adab3113579acc360d7 +size 24 diff --git a/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg38 b/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg38 index 14a3aca17e5..7f269223e50 120000 --- a/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg38 +++ b/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg38 @@ -1 +1,3 @@ -hg19/ \ No newline at end of file +version https://git-lfs.github.com/spec/v1 +oid sha256:bbcbe22ea1705114507a241904cbed049bf66f13da522adab3113579acc360d7 +size 24 diff --git a/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg38 b/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg38 index 14a3aca17e5..7f269223e50 120000 --- a/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg38 +++ b/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg38 @@ -1 +1,3 @@ -hg19/ \ No newline at end of file +version https://git-lfs.github.com/spec/v1 +oid sha256:bbcbe22ea1705114507a241904cbed049bf66f13da522adab3113579acc360d7 +size 24 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/GenomicsDBImport/expected.testGenomicsDBImportWithNonDiploidData.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/GenomicsDBImport/expected.testGenomicsDBImportWithNonDiploidData.vcf index f39639f76a8..9f2edcf2d5c 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/GenomicsDBImport/expected.testGenomicsDBImportWithNonDiploidData.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/GenomicsDBImport/expected.testGenomicsDBImportWithNonDiploidData.vcf @@ -1,6 +1,7 @@ ##fileformat=VCFv4.2 ##ALT= ##FILTER= +##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= 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GT:DP:GQ:MIN_DP:PL ./.:70:0:70:0,0,450 ./. -20 10004225 . A . . END=10004240 GT:DP:GQ:MIN_DP:PL ./.:70:99:65:0,114,1710 ./. +20 10004224 . A . . . GT:DP:GQ:MIN_DP:PL ./.:66:0:66:0,0,1403 ./. +20 10004225 . A . . END=10004240 GT:DP:GQ:MIN_DP:PL ./.:70:99:65:0,117,1755 ./. 20 10004241 . G . . . GT:DP:GQ:MIN_DP:PL ./.:66:0:66:0,0,1965 ./. 20 10004242 . A . . END=10004350 GT:DP:GQ:MIN_DP:PL ./.:73:99:58:0,120,1800 ./. 20 10004351 . C G, . . DP=70;ExcessHet=3.01;RAW_MQ=243987.00 GT:AD:DP:GQ:PL:SB ./.:0,70,0:70:99:2784,211,0,2784,211,2784:0,0,38,32 ./. @@ -321,7 +225,7 @@ 20 10004610 . A C, . . DP=89;ExcessHet=3.01;RAW_MQ=306605.00 GT:AD:DP:GQ:PL:SB ./.:0,89,0:89:99:3654,267,0,3654,267,3654:0,0,46,43 ./. 20 10004611 . C . . END=10004724 GT:DP:GQ:MIN_DP:PL ./.:75:99:64:0,120,1800 ./. 20 10004725 . A G, . . 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DP=79 GT:AD:DP:GQ:PL:SB ./.:37,27,0:64:99:1019,0,1471,1130,1554,2684:14,23,7,20 ./. 20 10004779 . C *, . . DP=79 GT:AD:DP:GQ:PL:SB ./.:37,27,0:64:99:1019,0,1471,1130,1554,2684:14,23,7,20 ./. -20 10004780 . A . . . GT:DP:GQ:MIN_DP:PL ./.:70:0:70:0,0,795 ./. -20 10004781 . A . . END=10004873 GT:DP:GQ:MIN_DP:PL ./.:77:99:69:0,120,1800 ./. +20 10004780 . A . . END=10004873 GT:DP:GQ:MIN_DP:PL ./.:77:99:69:0,120,1800 ./. 20 10004874 . A C, . . DP=87;ExcessHet=3.01;RAW_MQ=306223.00 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:0,87,0:87:99:0|1:10004874_A_C:3631,261,0,3631,261,3631:0,0,54,33 ./. 20 10004875 . T . . END=10004886 GT:DP:GQ:MIN_DP:PL ./.:86:99:85:0,120,1800 ./. 20 10004887 . A G, . . BaseQRankSum=0.356;DP=85;ExcessHet=3.01;MQRankSum=-6.700e-02;RAW_MQ=300482.00;ReadPosRankSum=-1.114e+00 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:45,40,0:85:99:0|1:10004874_A_C:1352,0,1542,1487,1662,3149:24,21,24,16 ./. @@ -342,7 +245,7 @@ 20 10005010 . C T, . . DP=72;ExcessHet=3.01;RAW_MQ=256441.00 GT:AD:DP:GQ:PL:SB ./.:0,72,0:72:99:2963,217,0,2963,217,2963:0,0,44,28 ./. 20 10005011 . G . . END=10005426 GT:DP:GQ:MIN_DP:PL ./.:72:99:51:0,120,1800 ./. 20 10005427 . C T, . . DP=55;ExcessHet=3.01;RAW_MQ=195241.00 GT:AD:DP:GQ:PL:SB ./.:0,55,0:55:99:2243,165,0,2243,165,2243:0,0,27,28 ./. -20 10005428 . A . . END=10005498 GT:DP:GQ:MIN_DP:PL ./.:71:99:58:0,120,1800 ./. +20 10005428 . A . . END=10005498 GT:DP:GQ:MIN_DP:PL ./.:71:99:57:0,120,1800 ./. 20 10005499 . A G, . . DP=76;ExcessHet=3.01;RAW_MQ=273600.00 GT:AD:DP:GQ:PL:SB ./.:0,76,0:76:99:3082,229,0,3082,229,3082:0,0,45,31 ./. 20 10005500 . T . . END=10005586 GT:DP:GQ:MIN_DP:PL ./.:71:99:66:0,120,1800 ./. 20 10005587 . A G, . . BaseQRankSum=-8.340e-01;DP=72;ExcessHet=3.01;MQRankSum=-9.720e-01;RAW_MQ=256969.00;ReadPosRankSum=0.248 GT:AD:DP:GQ:PL:SB ./.:36,36,0:72:99:1258,0,1236,1366,1345,2710:19,17,16,20 ./. @@ -354,21 +257,13 @@ 20 10006404 . A C, . . DP=77;ExcessHet=3.01;RAW_MQ=269451.00 GT:AD:DP:GQ:PL:SB ./.:0,76,0:76:99:2957,228,0,2957,228,2957:0,0,27,49 ./. 20 10006405 . C . . END=10006681 GT:DP:GQ:MIN_DP:PL ./.:78:99:65:0,120,1800 ./. 20 10006682 . T A, . . DP=73;ExcessHet=3.01;RAW_MQ=257810.00 GT:AD:DP:GQ:PL:SB ./.:0,73,0:73:99:2903,219,0,2903,219,2903:0,0,44,29 ./. -20 10006683 . A . . END=10006807 GT:DP:GQ:MIN_DP:PL ./.:65:99:61:0,99,1485 ./. -20 10006808 . C . . . GT:DP:GQ:MIN_DP:PL ./.:75:78:75:0,78,1170 ./. -20 10006809 . C . . END=10006813 GT:DP:GQ:MIN_DP:PL ./.:76:60:75:0,60,900 ./. -20 10006814 . T . . . GT:DP:GQ:MIN_DP:PL ./.:79:57:79:0,57,855 ./. -20 10006815 . C . . . GT:DP:GQ:MIN_DP:PL ./.:80:51:80:0,51,765 ./. -20 10006816 . T . . . GT:DP:GQ:MIN_DP:PL ./.:80:45:80:0,45,675 ./. -20 10006817 . A . . . GT:DP:GQ:MIN_DP:PL ./.:80:33:80:0,33,495 ./. -20 10006818 . A . . . GT:DP:GQ:MIN_DP:PL ./.:77:30:77:0,30,450 ./. +20 10006683 . A . . END=10006818 GT:DP:GQ:MIN_DP:PL ./.:65:99:61:0,120,1800 ./. 20 10006819 . AAAAC A, . . DP=76;ExcessHet=3.01;RAW_MQ=284000.00 GT:AD:DP:GQ:PL:SB ./.:0,58,0:58:99:2569,176,0,2569,176,2569:0,0,30,28 ./. 20 10006820 . A *, . . DP=76 GT:AD:DP:GQ:PL:SB ./.:0,58,0:58:99:2569,176,0,2569,176,2569:0,0,30,28 ./. 20 10006821 . A *, . . DP=76 GT:AD:DP:GQ:PL:SB ./.:0,58,0:58:99:2569,176,0,2569,176,2569:0,0,30,28 ./. 20 10006822 . A *, . . DP=76 GT:AD:DP:GQ:PL:SB ./.:0,58,0:58:99:2569,176,0,2569,176,2569:0,0,30,28 ./. 20 10006823 . C *, . . DP=76 GT:AD:DP:GQ:PL:SB ./.:0,58,0:58:99:2569,176,0,2569,176,2569:0,0,30,28 ./. -20 10006824 . A . . . GT:DP:GQ:MIN_DP:PL ./.:75:0:75:0,0,0 ./. -20 10006825 . A . . END=10007149 GT:DP:GQ:MIN_DP:PL ./.:77:99:59:0,120,1800 ./. +20 10006824 . A . . END=10007149 GT:DP:GQ:MIN_DP:PL ./.:77:99:59:0,120,1800 ./. 20 10007150 . G C, . . BaseQRankSum=-4.476e+00;DP=63;ExcessHet=3.01;MQRankSum=0.00;RAW_MQ=226800.00;ReadPosRankSum=-7.700e-02 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:38,25,0:63:99:0|1:10007150_G_C:698,0,1479,813,1554,2366:16,22,14,11 ./. 20 10007151 . G . . END=10007174 GT:DP:GQ:MIN_DP:PL ./.:57:99:56:0,120,1800 ./. 20 10007175 . C T, . . BaseQRankSum=2.25;DP=61;ExcessHet=3.01;MQRankSum=1.32;RAW_MQ=216841.00;ReadPosRankSum=-1.213e+00 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:23,38,0:61:99:1|0:10007150_G_C:1379,0,780,1448,894,2343:9,14,18,20 ./. @@ -378,71 +273,34 @@ 20 10007531 . A G, . . DP=72;ExcessHet=3.01;RAW_MQ=256969.00 GT:AD:DP:GQ:PL:SB ./.:0,72,0:72:99:2949,217,0,2949,217,2949:0,0,48,24 ./. 20 10007532 . G . . END=10007979 GT:DP:GQ:MIN_DP:PL ./.:80:99:65:0,120,1800 ./. 20 10007980 . A C, . . DP=90;ExcessHet=3.01;RAW_MQ=331800.00 GT:AD:DP:GQ:PL:SB ./.:0,90,0:90:99:3553,270,0,3553,270,3553:0,0,39,51 ./. -20 10007981 . A . . END=10008013 GT:DP:GQ:MIN_DP:PL ./.:85:99:81:0,99,1485 ./. -20 10008014 . C . . . GT:DP:GQ:MIN_DP:PL ./.:85:90:85:0,90,1350 ./. -20 10008015 . C . . . GT:DP:GQ:MIN_DP:PL ./.:88:87:88:0,87,1305 ./. -20 10008016 . A . . END=10008020 GT:DP:GQ:MIN_DP:PL ./.:90:72:89:0,72,1080 ./. -20 10008021 . G . . . GT:DP:GQ:MIN_DP:PL ./.:86:54:86:0,54,810 ./. -20 10008022 . A . . END=10008023 GT:DP:GQ:MIN_DP:PL ./.:85:33:85:0,33,495 ./. -20 10008024 . A . . END=10008028 GT:DP:GQ:MIN_DP:PL ./.:87:9:86:0,9,135 ./. +20 10007981 . A . . END=10008028 GT:DP:GQ:MIN_DP:PL ./.:86:99:80:0,120,1800 ./. 20 10008029 . T TA, . . BaseQRankSum=0.409;DP=88;ExcessHet=3.01;MQRankSum=0.576;RAW_MQ=327251.00;ReadPosRankSum=-1.326e+00 GT:AD:DP:GQ:PL:SB ./.:3,72,0:75:99:2024,145,0,2033,222,2110:1,2,27,45 ./. -20 10008030 . A . . . GT:DP:GQ:MIN_DP:PL ./.:91:0:91:0,0,0 ./. -20 10008031 . A . . END=10008127 GT:DP:GQ:MIN_DP:PL ./.:82:99:77:0,105,1575 ./. -20 10008128 . T . . END=10008129 GT:DP:GQ:MIN_DP:PL ./.:79:93:78:0,93,1395 ./. -20 10008130 . T . . END=10008131 GT:DP:GQ:MIN_DP:PL ./.:78:78:77:0,78,1170 ./. -20 10008132 . C . . END=10008133 GT:DP:GQ:MIN_DP:PL ./.:77:60:76:0,60,900 ./. -20 10008134 . A . . . GT:DP:GQ:MIN_DP:PL ./.:79:54:79:0,54,810 ./. -20 10008135 . G . . . GT:DP:GQ:MIN_DP:PL ./.:79:48:79:0,48,720 ./. -20 10008136 . A . . . GT:DP:GQ:MIN_DP:PL ./.:78:24:78:0,24,360 ./. -20 10008137 . T . . END=10008139 GT:DP:GQ:MIN_DP:PL ./.:77:21:76:0,21,315 ./. -20 10008140 . T . . . GT:DP:GQ:MIN_DP:PL ./.:78:18:78:0,18,270 ./. -20 10008141 . C . . . GT:DP:GQ:MIN_DP:PL ./.:79:9:79:0,9,135 ./. -20 10008142 . T . . . GT:DP:GQ:MIN_DP:PL ./.:77:6:77:0,6,90 ./. -20 10008143 . C . . END=10008145 GT:DP:GQ:MIN_DP:PL ./.:77:3:76:0,3,45 ./. +20 10008030 . A . . END=10008145 GT:DP:GQ:MIN_DP:PL ./.:82:99:76:0,120,1800 ./. 20 10008146 . TA T, . . DP=73;ExcessHet=3.01;RAW_MQ=268000.00 GT:AD:DP:GQ:PL:SB ./.:0,70,0:70:99:2179,211,0,2179,211,2179:0,0,38,32 ./. 20 10008147 . A *, . . 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GT:DP:GQ:MIN_DP:PL ./.:47:94:47:0,94,1689 ./. +20 10008734 . G . . END=10008741 GT:DP:GQ:MIN_DP:PL ./.:48:99:47:0,120,1800 ./. 20 10008742 . G T, . . BaseQRankSum=3.89;DP=49;ExcessHet=3.01;MQRankSum=-1.502e+00;RAW_MQ=67874.00;ReadPosRankSum=0.190 GT:AD:DP:GQ:PL:SB ./.:23,26,0:49:99:744,0,580,813,658,1471:10,13,11,15 ./. -20 10008743 . T . . END=10008744 GT:DP:GQ:MIN_DP:PL ./.:52:72:52:0,72,1080 ./. -20 10008745 . T . . END=10008746 GT:DP:GQ:MIN_DP:PL ./.:52:63:52:0,63,945 ./. -20 10008747 . T . . END=10008749 GT:DP:GQ:MIN_DP:PL ./.:49:57:48:0,57,855 ./. -20 10008750 . T . . . GT:DP:GQ:MIN_DP:PL ./.:47:51:47:0,51,765 ./. -20 10008751 . A . . . GT:DP:GQ:MIN_DP:PL ./.:49:30:49:0,30,450 ./. -20 10008752 . A . . END=10008754 GT:DP:GQ:MIN_DP:PL ./.:51:33:51:0,33,495 ./. -20 10008755 . A . . . GT:DP:GQ:MIN_DP:PL ./.:51:36:51:0,36,540 ./. -20 10008756 . T . . . GT:DP:GQ:MIN_DP:PL ./.:45:33:45:0,33,495 ./. -20 10008757 . A . . . GT:DP:GQ:MIN_DP:PL ./.:48:24:48:0,24,360 ./. +20 10008743 . T . . END=10008757 GT:DP:GQ:MIN_DP:PL ./.:46:99:42:0,99,1485 ./. 20 10008758 . C CA, . . BaseQRankSum=0.130;DP=44;ExcessHet=3.01;MQRankSum=-1.168e+00;RAW_MQ=54656.00;ReadPosRankSum=-5.200e-02 GT:AD:DP:GQ:PL:SB ./.:4,31,0:35:10:721,10,0,733,102,825:3,1,16,15 ./. -20 10008759 . A . . . GT:DP:GQ:MIN_DP:PL ./.:55:0:55:0,0,0 ./. -20 10008760 . A . . END=10008772 GT:DP:GQ:MIN_DP:PL ./.:55:99:53:0,120,1800 ./. +20 10008759 . A . . END=10008772 GT:DP:GQ:MIN_DP:PL ./.:55:99:53:0,120,1800 ./. 20 10008773 . T . . . GT:DP:GQ:MIN_DP:PL ./.:54:0:54:0,0,1660 ./. 20 10008774 . T . . . GT:DP:GQ:MIN_DP:PL ./.:55:99:55:0,117,1755 ./. 20 10008775 . A . . . GT:DP:GQ:MIN_DP:PL ./.:55:60:55:0,60,1923 ./. -20 10008776 . G . . END=10008910 GT:DP:GQ:MIN_DP:PL ./.:55:99:45:0,100,1530 ./. -20 10008911 . G . . . GT:DP:GQ:MIN_DP:PL ./.:45:93:45:0,93,1395 ./. -20 10008912 . A . . END=10008916 GT:DP:GQ:MIN_DP:PL ./.:46:84:45:0,84,1260 ./. -20 10008917 . G . . . GT:DP:GQ:MIN_DP:PL ./.:46:78:46:0,78,1170 ./. -20 10008918 . T . . END=10008920 GT:DP:GQ:MIN_DP:PL ./.:50:66:48:0,66,990 ./. +20 10008776 . G . . END=10008920 GT:DP:GQ:MIN_DP:PL ./.:54:99:45:0,99,1480 ./. 20 10008921 . C CA, . . BaseQRankSum=0.610;DP=49;ExcessHet=3.01;MQRankSum=-1.906e+00;RAW_MQ=155512.00;ReadPosRankSum=0.173 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:18,16,0:34:99:0|1:10008921_C_CA:291,0,366,345,415,761:10,8,8,8 ./. -20 10008922 . A . . . GT:DP:GQ:MIN_DP:PL ./.:51:0:51:0,0,714 ./. -20 10008923 . A . . END=10008934 GT:DP:GQ:MIN_DP:PL ./.:58:99:55:0,117,1755 ./. -20 10008935 . T . . END=10008936 GT:DP:GQ:MIN_DP:PL ./.:54:73:52:0,73,1586 ./. -20 10008937 . A . . END=10008938 GT:DP:GQ:MIN_DP:PL ./.:55:99:54:0,111,1665 ./. -20 10008939 . T . . END=10008940 GT:DP:GQ:MIN_DP:PL ./.:52:93:51:0,93,1395 ./. -20 10008941 . A . . END=10008942 GT:DP:GQ:MIN_DP:PL ./.:50:84:49:0,84,1260 ./. -20 10008943 . A . . END=10008946 GT:DP:GQ:MIN_DP:PL ./.:49:72:49:0,72,1080 ./. -20 10008947 . T . . . GT:DP:GQ:MIN_DP:PL ./.:48:66:48:0,66,990 ./. +20 10008922 . A . . END=10008942 GT:DP:GQ:MIN_DP:PL ./.:53:99:47:0,114,1710 ./. +20 10008943 . A . . END=10008944 GT:DP:GQ:MIN_DP:PL ./.:47:78:47:0,78,1170 ./. +20 10008945 . A . . END=10008947 GT:DP:GQ:MIN_DP:PL ./.:47:81:46:0,81,1215 ./. 20 10008948 . TA T, . . BaseQRankSum=0.994;DP=52;ExcessHet=3.01;MQRankSum=2.05;RAW_MQ=138622.00;ReadPosRankSum=0.884 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:1,50,0:51:99:0|1:10008921_C_CA:2095,107,0,2098,159,2150:1,0,35,15 ./. 20 10008949 . A *, . . DP=52 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:1,50,0:51:99:0|1:10008921_C_CA:2095,107,0,2098,159,2150:1,0,35,15 ./. -20 10008950 . A . . END=10008951 GT:DP:GQ:MIN_DP:PL ./.:48:0:48:0,0,0 ./. +20 10008950 . A . . . GT:DP:GQ:MIN_DP:PL ./.:52:99:52:0,99,1485 ./. +20 10008951 . A . . . GT:DP:GQ:MIN_DP:PL ./.:51:93:51:0,93,1395 ./. 20 10008952 . CACACACACACACA C,CCA,CCACACACACA,CCACACACACACA, . . BaseQRankSum=0.941;DP=59;ExcessHet=3.01;MQRankSum=1.84;RAW_MQ=154068.00;ReadPosRankSum=0.716 GT:AD:DP:GQ:PL:SB ./.:1,3,14,5,11,0:34:99:1704,876,1258,525,811,845,726,514,173,703,582,342,0,443,530,1135,1092,744,779,607,1321:1,0,25,8 ./. 20 10008953 . A *, . . DP=59 GT:AD:DP:GQ:PL:SB ./.:1,11,0:34:99:1704,582,530,1135,607,1321:1,0,25,8 ./. 20 10008954 . C *, . . DP=59 GT:AD:DP:GQ:PL:SB ./.:1,11,0:34:99:1704,582,530,1135,607,1321:1,0,25,8 ./. @@ -457,8 +315,7 @@ 20 10008963 . A *, . . DP=59 GT:AD:DP:GQ:PL:SB ./.:1,11,0:34:99:1704,582,530,1135,607,1321:1,0,25,8 ./. 20 10008964 . C *, . . DP=59 GT:AD:DP:GQ:PL:SB ./.:1,11,0:34:99:1704,582,530,1135,607,1321:1,0,25,8 ./. 20 10008965 . A *, . . DP=59 GT:AD:DP:GQ:PL:SB ./.:1,11,0:34:99:1704,582,530,1135,607,1321:1,0,25,8 ./. -20 10008966 . C . . . GT:DP:GQ:MIN_DP:PL ./.:56:95:56:0,95,1995 ./. -20 10008967 . A . . END=10008986 GT:DP:GQ:MIN_DP:PL ./.:58:99:56:0,120,1800 ./. +20 10008966 . C . . END=10008986 GT:DP:GQ:MIN_DP:PL ./.:58:99:56:0,120,1800 ./. 20 10008987 . A . . END=10008989 GT:DP:GQ:MIN_DP:PL ./.:59:94:59:0,94,2181 ./. 20 10008990 . C . . END=10009226 GT:DP:GQ:MIN_DP:PL ./.:61:99:38:0,102,1530 ./. 20 10009227 . A G, . . BaseQRankSum=-2.220e+00;DP=62;ExcessHet=3.01;MQRankSum=1.43;RAW_MQ=202588.00;ReadPosRankSum=-1.159e+00 GT:AD:DP:GQ:PL:SB ./.:23,39,0:62:99:1398,0,740,1468,857,2325:16,7,19,20 ./. @@ -472,42 +329,30 @@ 20 10009719 . A G, . . DP=59;ExcessHet=3.01;RAW_MQ=207410.00 GT:AD:DP:GQ:PL:SB ./.:0,59,0:59:99:1924,175,0,1924,175,1924:0,0,26,33 ./. 20 10009720 . T . . END=10009794 GT:DP:GQ:MIN_DP:PL ./.:54:99:47:0,120,1800 ./. 20 10009795 . A G, . . DP=47;ExcessHet=3.01;RAW_MQ=166969.00 GT:AD:DP:GQ:PL:SB ./.:0,47,0:47:99:1909,141,0,1909,141,1909:0,0,16,31 ./. -20 10009796 . C . . END=10009828 GT:DP:GQ:MIN_DP:PL ./.:48:99:44:0,120,1800 ./. -20 10009829 . A . . . GT:DP:GQ:MIN_DP:PL ./.:54:69:54:0,69,1035 ./. -20 10009830 . G . . . GT:DP:GQ:MIN_DP:PL ./.:54:72:54:0,72,1080 ./. -20 10009831 . A . . END=10009832 GT:DP:GQ:MIN_DP:PL ./.:54:63:53:0,63,945 ./. -20 10009833 . A . . . GT:DP:GQ:MIN_DP:PL ./.:53:27:53:0,27,405 ./. -20 10009834 . G . . . GT:DP:GQ:MIN_DP:PL ./.:53:30:53:0,30,450 ./. -20 10009835 . A . . END=10009838 GT:DP:GQ:MIN_DP:PL ./.:55:33:54:0,33,495 ./. -20 10009839 . A . . . GT:DP:GQ:MIN_DP:PL ./.:54:30:54:0,30,450 ./. -20 10009840 . A . . . GT:DP:GQ:MIN_DP:PL ./.:54:33:54:0,33,495 ./. -20 10009841 . A . . . GT:DP:GQ:MIN_DP:PL ./.:55:27:55:0,27,405 ./. +20 10009796 . C . . END=10009832 GT:DP:GQ:MIN_DP:PL ./.:49:99:44:0,99,1485 ./. +20 10009833 . A . . END=10009840 GT:DP:GQ:MIN_DP:PL ./.:53:66:51:0,66,990 ./. +20 10009841 . A . . . GT:DP:GQ:MIN_DP:PL ./.:51:39:51:0,39,585 ./. 20 10009842 . G GAA, . . BaseQRankSum=0.872;DP=51;ExcessHet=3.01;MQRankSum=-6.030e-01;RAW_MQ=150092.00;ReadPosRankSum=1.72 GT:AD:DP:GQ:PL:SB ./.:19,15,0:34:99:570,0,690,629,738,1367:9,10,8,7 ./. -20 10009843 . A . . . GT:DP:GQ:MIN_DP:PL ./.:56:27:56:0,27,405 ./. +20 10009843 . A . . . GT:DP:GQ:MIN_DP:PL ./.:51:36:51:0,36,540 ./. 20 10009844 . G A, . . BaseQRankSum=1.05;DP=51;ExcessHet=3.01;MQRankSum=0.975;RAW_MQ=147168.00;ReadPosRankSum=-1.555e+00 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:16,19,0:35:99:0|1:10009844_G_A:690,0,586,739,644,1382:8,8,9,10 ./. -20 10009845 . A . . END=10009847 GT:DP:GQ:MIN_DP:PL ./.:55:30:55:0,30,450 ./. -20 10009848 . G . . . GT:DP:GQ:MIN_DP:PL ./.:58:39:58:0,39,585 ./. -20 10009849 . A . . END=10009850 GT:DP:GQ:MIN_DP:PL ./.:59:45:58:0,45,675 ./. -20 10009851 . A . . . GT:DP:GQ:MIN_DP:PL ./.:60:51:60:0,51,765 ./. -20 10009852 . G . . . GT:DP:GQ:MIN_DP:PL ./.:60:54:60:0,54,810 ./. -20 10009853 . A . . . GT:DP:GQ:MIN_DP:PL ./.:61:57:61:0,57,855 ./. -20 10009854 . G . . END=10009860 GT:DP:GQ:MIN_DP:PL ./.:61:60:60:0,60,900 ./. -20 10009861 . A . . END=10009867 GT:DP:GQ:MIN_DP:PL ./.:58:72:56:0,72,1080 ./. -20 10009868 . G . . END=10009870 GT:DP:GQ:MIN_DP:PL ./.:57:81:56:0,81,1215 ./. +20 10009845 . A . . END=10009847 GT:DP:GQ:MIN_DP:PL ./.:51:42:51:0,42,630 ./. +20 10009848 . G . . . GT:DP:GQ:MIN_DP:PL ./.:54:51:54:0,51,765 ./. +20 10009849 . A . . END=10009850 GT:DP:GQ:MIN_DP:PL ./.:55:57:54:0,57,855 ./. +20 10009851 . A . . END=10009853 GT:DP:GQ:MIN_DP:PL ./.:56:63:56:0,63,945 ./. +20 10009854 . G . . END=10009860 GT:DP:GQ:MIN_DP:PL ./.:57:72:56:0,72,1080 ./. +20 10009861 . A . . END=10009864 GT:DP:GQ:MIN_DP:PL ./.:58:84:56:0,84,1260 ./. +20 10009865 . A . . END=10009869 GT:DP:GQ:MIN_DP:PL ./.:57:90:56:0,90,1350 ./. +20 10009870 . G . . . GT:DP:GQ:MIN_DP:PL ./.:57:99:57:0,99,1485 ./. 20 10009871 . A G, . . BaseQRankSum=-8.030e-01;DP=60;ExcessHet=3.01;MQRankSum=1.50;RAW_MQ=154737.00;ReadPosRankSum=1.54 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:17,19,0:36:99:0|1:10009844_G_A:687,0,594,739,652,1391:10,7,9,10 ./. -20 10009872 . G . . END=10009873 GT:DP:GQ:MIN_DP:PL ./.:57:96:55:0,96,1440 ./. -20 10009874 . G . . . GT:DP:GQ:MIN_DP:PL ./.:58:99:58:0,102,1530 ./. +20 10009872 . G . . END=10009874 GT:DP:GQ:MIN_DP:PL ./.:57:99:55:0,108,1620 ./. 20 10009875 . A G,AGGGAGG, . . BaseQRankSum=0.378;DP=57;ExcessHet=3.01;MQRankSum=1.36;RAW_MQ=143937.00;ReadPosRankSum=1.04 GT:AD:DP:GQ:PL:SB ./.:2,15,13,0:30:99:2407,645,533,697,0,574,1881,655,700,1805:2,0,12,16 ./. -20 10009876 . G . . . GT:DP:GQ:MIN_DP:PL ./.:57:99:57:0,108,2100 ./. -20 10009877 . A . . . GT:DP:GQ:MIN_DP:PL ./.:55:85:55:0,85,1858 ./. -20 10009878 . G . . . GT:DP:GQ:MIN_DP:PL ./.:55:99:55:0,108,1620 ./. +20 10009876 . G . . END=10009878 GT:DP:GQ:MIN_DP:PL ./.:52:99:51:0,114,1710 ./. 20 10009879 . A G, . . BaseQRankSum=1.53;DP=49;ExcessHet=3.01;MQRankSum=1.57;RAW_MQ=120661.00;ReadPosRankSum=1.11 GT:AD:DP:GQ:PL:SB ./.:2,47,0:49:99:2273,150,0,2276,154,2279:2,0,15,32 ./. -20 10009880 . G . . . GT:DP:GQ:MIN_DP:PL ./.:52:80:52:0,80,1858 ./. -20 10009881 . A . . END=10009882 GT:DP:GQ:MIN_DP:PL ./.:51:99:50:0,108,1755 ./. +20 10009880 . G . . END=10009882 GT:DP:GQ:MIN_DP:PL ./.:49:99:48:0,120,1800 ./. 20 10009883 . A G, . . DP=49;ExcessHet=3.01;RAW_MQ=129338.00 GT:AD:DP:GQ:PL:SB ./.:0,47,0:47:99:2180,147,0,2180,147,2181:0,0,15,32 ./. 20 10009884 . G . . . GT:DP:GQ:MIN_DP:PL ./.:53:99:53:0,120,1800 ./. -20 10009885 . A . . . GT:DP:GQ:MIN_DP:PL ./.:52:58:52:0,58,1739 ./. -20 10009886 . A . . . GT:DP:GQ:MIN_DP:PL ./.:53:0:53:0,0,1490 ./. +20 10009885 . A . . . GT:DP:GQ:MIN_DP:PL ./.:52:96:52:0,96,1815 ./. +20 10009886 . A . . . GT:DP:GQ:MIN_DP:PL ./.:53:0:53:0,0,1567 ./. 20 10009887 . G . . . GT:DP:GQ:MIN_DP:PL ./.:50:99:50:0,109,1906 ./. 20 10009888 . A . . . GT:DP:GQ:MIN_DP:PL ./.:51:0:51:0,0,1610 ./. 20 10009889 . A . . END=10009891 GT:DP:GQ:MIN_DP:PL ./.:49:99:49:0,106,1800 ./. @@ -516,20 +361,9 @@ 20 10009894 . G . . . GT:DP:GQ:MIN_DP:PL ./.:53:48:53:0,48,1842 ./. 20 10009895 . G . . END=10010392 GT:DP:GQ:MIN_DP:PL ./.:70:99:45:0,111,1665 ./. 20 10010393 . T G, . . BaseQRankSum=-3.351e+00;DP=79;ExcessHet=3.01;MQRankSum=-1.284e+00;RAW_MQ=278882.00;ReadPosRankSum=-1.738e+00 GT:AD:DP:GQ:PL:SB ./.:36,43,0:79:99:1493,0,1230,1601,1359,2961:24,12,19,24 ./. -20 10010394 . T . . END=10010518 GT:DP:GQ:MIN_DP:PL ./.:82:99:67:0,102,1530 ./. -20 10010519 . T . . END=10010522 GT:DP:GQ:MIN_DP:PL ./.:90:81:89:0,81,1215 ./. -20 10010523 . G . . END=10010526 GT:DP:GQ:MIN_DP:PL ./.:92:63:90:0,63,945 ./. -20 10010527 . A . . . GT:DP:GQ:MIN_DP:PL ./.:88:54:88:0,54,810 ./. -20 10010528 . T . . . GT:DP:GQ:MIN_DP:PL ./.:88:51:88:0,51,765 ./. -20 10010529 . T . . . GT:DP:GQ:MIN_DP:PL ./.:88:48:88:0,48,720 ./. -20 10010530 . T . . END=10010531 GT:DP:GQ:MIN_DP:PL ./.:87:45:86:0,45,675 ./. -20 10010532 . A . . . GT:DP:GQ:MIN_DP:PL ./.:84:39:84:0,39,585 ./. -20 10010533 . G . . . GT:DP:GQ:MIN_DP:PL ./.:83:33:83:0,33,495 ./. -20 10010534 . A . . . GT:DP:GQ:MIN_DP:PL ./.:84:24:84:0,24,360 ./. -20 10010535 . A . . . GT:DP:GQ:MIN_DP:PL ./.:85:12:85:0,12,180 ./. +20 10010394 . T . . END=10010535 GT:DP:GQ:MIN_DP:PL ./.:83:99:67:0,120,1800 ./. 20 10010536 . G GA, . . DP=85;ExcessHet=3.01;RAW_MQ=322900.00 GT:AD:DP:GQ:PL:SB ./.:0,79,0:79:99:2500,243,0,2500,244,2500:0,0,36,43 ./. -20 10010537 . A . . . GT:DP:GQ:MIN_DP:PL ./.:88:0:88:0,0,0 ./. -20 10010538 . A . . END=10010765 GT:DP:GQ:MIN_DP:PL ./.:79:99:68:0,120,1800 ./. +20 10010537 . A . . END=10010765 GT:DP:GQ:MIN_DP:PL ./.:79:99:68:0,120,1800 ./. 20 10010766 . T G, . . DP=67;ExcessHet=3.01;RAW_MQ=241200.00 GT:AD:DP:GQ:PL:SB ./.:0,66,0:66:99:2440,199,0,2440,199,2440:0,0,35,31 ./. 20 10010767 . G . . END=10010831 GT:DP:GQ:MIN_DP:PL ./.:74:99:61:0,120,1800 ./. 20 10010832 . T C, . . DP=75;ExcessHet=3.01;RAW_MQ=265538.00 GT:AD:DP:GQ:PL:SB ./.:0,75,0:75:99:2980,226,0,2980,226,2980:0,0,31,44 ./. @@ -545,46 +379,26 @@ 20 10011666 . C T, . . DP=73;ExcessHet=3.01;RAW_MQ=254523.00 GT:AD:DP:GQ:PL:SB ./.:0,73,0:73:99:2990,220,0,2990,220,2990:0,0,43,30 ./. 20 10011667 . A . . END=10011938 GT:DP:GQ:MIN_DP:PL ./.:87:99:64:0,111,1665 ./. 20 10011939 . C T, . . DP=61;ExcessHet=3.01;RAW_MQ=193043.00 GT:AD:DP:GQ:PL:SB ./.:0,61,0:61:99:2498,184,0,2498,184,2498:0,0,23,38 ./. -20 10011940 . G . . END=10011944 GT:DP:GQ:MIN_DP:PL ./.:62:99:54:0,114,1710 ./. -20 10011945 . G . . . GT:DP:GQ:MIN_DP:PL ./.:50:84:50:0,84,1730 ./. -20 10011946 . T . . END=10011992 GT:DP:GQ:MIN_DP:PL ./.:53:99:44:0,102,1530 ./. -20 10011993 . C . . END=10011996 GT:DP:GQ:MIN_DP:PL ./.:59:90:57:0,90,1350 ./. -20 10011997 . A . . END=10011998 GT:DP:GQ:MIN_DP:PL ./.:59:75:59:0,75,1125 ./. -20 10011999 . T . . END=10012000 GT:DP:GQ:MIN_DP:PL ./.:60:63:59:0,63,945 ./. -20 10012001 . A . . . GT:DP:GQ:MIN_DP:PL ./.:60:57:60:0,57,855 ./. -20 10012002 . C . . . GT:DP:GQ:MIN_DP:PL ./.:61:51:61:0,51,765 ./. -20 10012003 . T . . END=10012005 GT:DP:GQ:MIN_DP:PL ./.:61:48:61:0,48,720 ./. -20 10012006 . T . . . GT:DP:GQ:MIN_DP:PL ./.:63:39:63:0,39,585 ./. -20 10012007 . A . . . GT:DP:GQ:MIN_DP:PL ./.:64:36:64:0,36,540 ./. -20 10012008 . G . . END=10012010 GT:DP:GQ:MIN_DP:PL ./.:64:33:63:0,33,495 ./. -20 10012011 . T . . . GT:DP:GQ:MIN_DP:PL ./.:65:24:65:0,24,360 ./. -20 10012012 . C . . . GT:DP:GQ:MIN_DP:PL ./.:65:21:65:0,21,315 ./. -20 10012013 . C . . . GT:DP:GQ:MIN_DP:PL ./.:66:18:66:0,18,270 ./. -20 10012014 . A . . END=10012015 GT:DP:GQ:MIN_DP:PL ./.:66:9:66:0,9,135 ./. -20 10012016 . T . . . GT:DP:GQ:MIN_DP:PL ./.:68:3:68:0,3,45 ./. -20 10012017 . A . . END=10012020 GT:DP:GQ:MIN_DP:PL ./.:68:0:68:0,0,0 ./. +20 10011940 . G . . END=10012020 GT:DP:GQ:MIN_DP:PL ./.:56:99:42:0,101,1575 ./. 20 10012021 . CA C, . . DP=70;ExcessHet=3.01;RAW_MQ=228076.00 GT:AD:DP:GQ:PL:SB ./.:0,66,0:66:99:2013,198,0,2013,198,2013:0,0,26,40 ./. 20 10012022 . A *, . . DP=70 GT:AD:DP:GQ:PL:SB ./.:0,66,0:66:99:2013,198,0,2013,198,2013:0,0,26,40 ./. -20 10012023 . A . . . GT:DP:GQ:MIN_DP:PL ./.:69:0:69:0,0,0 ./. -20 10012024 . A . . END=10012147 GT:DP:GQ:MIN_DP:PL ./.:70:99:38:0,99,1485 ./. +20 10012023 . A . . END=10012147 GT:DP:GQ:MIN_DP:PL ./.:70:99:38:0,99,1485 ./. 20 10012148 . G . . END=10012157 GT:DP:GQ:MIN_DP:PL ./.:38:90:37:0,90,1350 ./. 20 10012158 . A . . END=10012159 GT:DP:GQ:MIN_DP:PL ./.:35:84:34:0,84,1260 ./. 20 10012160 . C . . END=10012162 GT:DP:GQ:MIN_DP:PL ./.:34:78:34:0,78,1170 ./. 20 10012163 . G . . END=10012167 GT:DP:GQ:MIN_DP:PL ./.:34:81:33:0,81,1215 ./. 20 10012168 . C . . END=10012170 GT:DP:GQ:MIN_DP:PL ./.:31:78:29:0,78,1170 ./. -20 10012171 . T . . END=10012174 GT:DP:GQ:MIN_DP:PL ./.:29:61:29:0,61,1035 ./. -20 10012175 . C . . . GT:DP:GQ:MIN_DP:PL ./.:30:72:30:0,72,1080 ./. -20 10012176 . A . . . GT:DP:GQ:MIN_DP:PL ./.:29:69:29:0,69,1035 ./. -20 10012177 . C . . END=10012179 GT:DP:GQ:MIN_DP:PL ./.:31:72:30:0,72,1080 ./. -20 10012180 . C . . END=10012181 GT:DP:GQ:MIN_DP:PL ./.:30:81:29:0,81,1215 ./. -20 10012182 . C . . END=10012183 GT:DP:GQ:MIN_DP:PL ./.:30:78:29:0,78,1170 ./. -20 10012184 . C . . END=10012196 GT:DP:GQ:MIN_DP:PL ./.:32:81:30:0,81,1215 ./. -20 10012197 . C . . . GT:DP:GQ:MIN_DP:PL ./.:32:90:32:0,90,1350 ./. -20 10012198 . G . . END=10012200 GT:DP:GQ:MIN_DP:PL ./.:33:84:32:0,84,1260 ./. -20 10012201 . T . . . GT:DP:GQ:MIN_DP:PL ./.:30:53:30:0,53,1087 ./. +20 10012171 . T . . . GT:DP:GQ:MIN_DP:PL ./.:29:61:29:0,61,1086 ./. +20 10012172 . C . . END=10012178 GT:DP:GQ:MIN_DP:PL ./.:29:72:29:0,72,1080 ./. +20 10012179 . G . . END=10012188 GT:DP:GQ:MIN_DP:PL ./.:31:81:29:0,81,1157 ./. +20 10012189 . G . . . GT:DP:GQ:MIN_DP:PL ./.:33:90:33:0,90,1350 ./. +20 10012190 . C . . END=10012196 GT:DP:GQ:MIN_DP:PL ./.:32:87:30:0,87,1305 ./. +20 10012197 . C . . . GT:DP:GQ:MIN_DP:PL ./.:32:93:32:0,93,1395 ./. +20 10012198 . G . . . GT:DP:GQ:MIN_DP:PL ./.:32:87:32:0,87,1305 ./. +20 10012199 . C . . END=10012200 GT:DP:GQ:MIN_DP:PL ./.:33:90:33:0,90,1350 ./. +20 10012201 . T . . . GT:DP:GQ:MIN_DP:PL ./.:30:87:30:0,87,1305 ./. 20 10012202 . C . . . GT:DP:GQ:MIN_DP:PL ./.:32:62:32:0,62,1157 ./. -20 10012203 . C . . . GT:DP:GQ:MIN_DP:PL ./.:32:53:32:0,53,1153 ./. -20 10012204 . T . . END=10012211 GT:DP:GQ:MIN_DP:PL ./.:32:90:31:0,90,1350 ./. +20 10012203 . C . . END=10012211 GT:DP:GQ:MIN_DP:PL ./.:32:90:31:0,90,1350 ./. 20 10012212 . G . . END=10012215 GT:DP:GQ:MIN_DP:PL ./.:31:84:30:0,84,1260 ./. 20 10012216 . C . . END=10012221 GT:DP:GQ:MIN_DP:PL ./.:33:72:32:0,72,1080 ./. 20 10012222 . T . . END=10012224 GT:DP:GQ:MIN_DP:PL ./.:32:69:32:0,69,1035 ./. @@ -636,10 +450,7 @@ 20 10012399 . G . . END=10012402 GT:DP:GQ:MIN_DP:PL ./.:16:45:15:0,45,561 ./. 20 10012403 . T . . . GT:DP:GQ:MIN_DP:PL ./.:15:17:15:0,17,521 ./. 20 10012404 . G . . . GT:DP:GQ:MIN_DP:PL ./.:14:42:14:0,42,564 ./. -20 10012405 . G . . . GT:DP:GQ:MIN_DP:PL ./.:15:39:15:0,39,585 ./. -20 10012406 . C . . . GT:DP:GQ:MIN_DP:PL ./.:15:3:15:0,3,396 ./. -20 10012407 . G . . . GT:DP:GQ:MIN_DP:PL ./.:15:2:15:0,2,481 ./. -20 10012408 . G . . END=10012409 GT:DP:GQ:MIN_DP:PL ./.:15:39:15:0,39,585 ./. +20 10012405 . G . . END=10012409 GT:DP:GQ:MIN_DP:PL ./.:15:39:15:0,39,585 ./. 20 10012410 . C . . . GT:DP:GQ:MIN_DP:PL ./.:15:33:15:0,33,495 ./. 20 10012411 . C . . END=10012412 GT:DP:GQ:MIN_DP:PL ./.:15:30:14:0,30,450 ./. 20 10012413 . C . . END=10012416 GT:DP:GQ:MIN_DP:PL ./.:16:33:14:0,33,495 ./. @@ -674,64 +485,57 @@ 20 10012475 . C . . END=10012476 GT:DP:GQ:MIN_DP:PL ./.:20:36:19:0,36,540 ./. 20 10012477 . G . . END=10012478 GT:DP:GQ:MIN_DP:PL ./.:18:33:17:0,33,495 ./. 20 10012479 . A G, . . DP=17;ExcessHet=3.01;RAW_MQ=45990.00 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:0,17,0:17:50:0|1:10012479_A_G:621,50,0,621,50,621:0,0,9,8 ./. -20 10012480 . G . . END=10012482 GT:DP:GQ:MIN_DP:PL ./.:17:24:16:0,24,360 ./. +20 10012480 . G . . END=10012482 GT:DP:GQ:MIN_DP:PL ./.:16:24:15:0,24,360 ./. 20 10012483 . G . . 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GT:DP:GQ:MIN_DP:PL ./.:12:27:12:0,27,405 ./. -20 10012516 . G . . END=10012517 GT:DP:GQ:MIN_DP:PL ./.:12:24:11:0,24,360 ./. +20 10012499 . G . . END=10012501 GT:DP:GQ:MIN_DP:PL ./.:11:27:9:0,27,334 ./. +20 10012502 . C . . END=10012503 GT:DP:GQ:MIN_DP:PL ./.:11:24:11:0,24,360 ./. +20 10012504 . C . . END=10012508 GT:DP:GQ:MIN_DP:PL ./.:10:21:10:0,21,315 ./. +20 10012509 . A . . END=10012513 GT:DP:GQ:MIN_DP:PL ./.:11:27:10:0,27,405 ./. +20 10012514 . C . . END=10012515 GT:DP:GQ:MIN_DP:PL ./.:10:21:10:0,21,315 ./. +20 10012516 . G . . END=10012517 GT:DP:GQ:MIN_DP:PL ./.:10:18:9:0,18,270 ./. 20 10012518 . T C, . . DP=9;ExcessHet=3.01;RAW_MQ=15102.00 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:0,9,0:9:30:0|1:10012479_A_G:435,30,0,435,30,435:0,0,4,5 ./. -20 10012519 . C . . . GT:DP:GQ:MIN_DP:PL ./.:12:27:12:0,27,405 ./. -20 10012520 . A . . . GT:DP:GQ:MIN_DP:PL ./.:12:24:12:0,24,400 ./. +20 10012519 . C . . END=10012520 GT:DP:GQ:MIN_DP:PL ./.:10:21:10:0,21,315 ./. 20 10012521 . C T, . . BaseQRankSum=2.36;DP=11;ExcessHet=3.01;MQRankSum=-3.800e-02;RAW_MQ=19192.00;ReadPosRankSum=1.97 GT:AD:DP:GQ:PL:SB ./.:8,3,0:11:75:75,0,224,99,233,332:4,4,2,1 ./. -20 10012522 . A . . END=10012525 GT:DP:GQ:MIN_DP:PL ./.:12:30:11:0,30,450 ./. -20 10012526 . G . . . GT:DP:GQ:MIN_DP:PL ./.:10:27:10:0,27,405 ./. -20 10012527 . C . . . GT:DP:GQ:MIN_DP:PL ./.:10:24:10:0,24,360 ./. -20 10012528 . T . . END=10012536 GT:DP:GQ:MIN_DP:PL ./.:10:21:9:0,21,315 ./. -20 10012537 . T . . END=10012541 GT:DP:GQ:MIN_DP:PL ./.:8:18:8:0,18,270 ./. -20 10012542 . C . . END=10012544 GT:DP:GQ:MIN_DP:PL ./.:8:15:8:0,15,225 ./. -20 10012545 . C . . END=10012546 GT:DP:GQ:MIN_DP:PL ./.:7:12:6:0,12,180 ./. -20 10012547 . G . . . GT:DP:GQ:MIN_DP:PL ./.:8:7:8:0,7,219 ./. -20 10012548 . G . . . GT:DP:GQ:MIN_DP:PL ./.:8:12:8:0,12,180 ./. -20 10012549 . C . . . GT:DP:GQ:MIN_DP:PL ./.:8:7:8:0,7,255 ./. -20 10012550 . C . . END=10012552 GT:DP:GQ:MIN_DP:PL ./.:10:12:10:0,12,180 ./. -20 10012553 . A . . END=10012555 GT:DP:GQ:MIN_DP:PL ./.:10:9:10:0,9,135 ./. -20 10012556 . T . . END=10012557 GT:DP:GQ:MIN_DP:PL ./.:9:6:9:0,6,90 ./. -20 10012558 . C . . . GT:DP:GQ:MIN_DP:PL ./.:9:3:9:0,3,45 ./. -20 10012559 . C . . END=10012569 GT:DP:GQ:MIN_DP:PL ./.:9:0:8:0,0,0 ./. +20 10012522 . A . . END=10012525 GT:DP:GQ:MIN_DP:PL ./.:11:24:9:0,24,360 ./. +20 10012526 . G . . . GT:DP:GQ:MIN_DP:PL ./.:8:21:8:0,21,315 ./. +20 10012527 . C . . END=10012545 GT:DP:GQ:MIN_DP:PL ./.:7:18:6:0,18,188 ./. +20 10012546 . G . . . GT:DP:GQ:MIN_DP:PL ./.:5:15:5:0,15,174 ./. +20 10012547 . G . . END=10012548 GT:DP:GQ:MIN_DP:PL ./.:6:18:6:0,18,207 ./. +20 10012549 . C . . . GT:DP:GQ:MIN_DP:PL ./.:6:1:6:0,1,186 ./. +20 10012550 . C . . END=10012562 GT:DP:GQ:MIN_DP:PL ./.:8:24:8:0,24,296 ./. +20 10012563 . G . . END=10012564 GT:DP:GQ:MIN_DP:PL ./.:8:21:8:0,21,315 ./. +20 10012565 . G . . END=10012567 GT:DP:GQ:MIN_DP:PL ./.:9:24:8:0,24,261 ./. +20 10012568 . G . . END=10012569 GT:DP:GQ:MIN_DP:PL ./.:9:21:8:0,21,315 ./. 20 10012570 . G GCA, . . DP=9;ExcessHet=3.01;RAW_MQ=12736.00 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:0,9,0:9:33:0|1:10012570_G_GCA:495,33,0,495,33,495:0,0,8,1 ./. -20 10012571 . G . . . GT:DP:GQ:MIN_DP:PL ./.:11:0:11:0,0,0 ./. +20 10012571 . G . . . GT:DP:GQ:MIN_DP:PL ./.:11:27:11:0,27,405 ./. 20 10012572 . GT G, . . DP=11;ExcessHet=3.01;RAW_MQ=17177.00 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:0,11,0:11:33:0|1:10012570_G_GCA:495,33,0,495,33,495:0,0,10,1 ./. 20 10012573 . T *, . . DP=11 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:0,11,0:11:33:0|1:10012570_G_GCA:495,33,0,495,33,495:0,0,10,1 ./. -20 10012574 . G . . END=10012575 GT:DP:GQ:MIN_DP:PL ./.:12:0:12:0,0,0 ./. -20 10012576 . T . . . GT:DP:GQ:MIN_DP:PL ./.:12:4:12:0,4,413 ./. -20 10012577 . C . . . GT:DP:GQ:MIN_DP:PL ./.:12:9:12:0,9,419 ./. -20 10012578 . G . . . GT:DP:GQ:MIN_DP:PL ./.:12:2:12:0,2,328 ./. +20 10012574 . G . . END=10012575 GT:DP:GQ:MIN_DP:PL ./.:12:30:11:0,30,450 ./. +20 10012576 . T . . 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GT:DP:GQ:MIN_DP:PL ./.:30:81:30:0,81,1215 ./. 20 10012753 . T . . . GT:DP:GQ:MIN_DP:PL ./.:29:74:29:0,74,1014 ./. @@ -807,8 +613,7 @@ 20 10014590 . A . . . GT:DP:GQ:MIN_DP:PL ./.:44:93:44:0,93,1625 ./. 20 10014591 . T . . END=10014989 GT:DP:GQ:MIN_DP:PL ./.:72:99:42:0,116,1732 ./. 20 10014990 . C CAT, . . BaseQRankSum=1.93;DP=87;ExcessHet=3.01;MQRankSum=3.11;RAW_MQ=321369.00;ReadPosRankSum=-4.370e-01 GT:AD:DP:GQ:PL:SB ./.:38,38,0:76:99:1275,0,1248,1389,1365,2755:28,10,25,13 ./. -20 10014991 . A . . . GT:DP:GQ:MIN_DP:PL ./.:88:0:88:0,0,402 ./. -20 10014992 . T . . END=10015385 GT:DP:GQ:MIN_DP:PL ./.:73:99:41:0,102,1530 ./. +20 10014991 . A . . END=10015385 GT:DP:GQ:MIN_DP:PL ./.:73:99:41:0,102,1530 ./. 20 10015386 . G . . END=10015388 GT:DP:GQ:MIN_DP:PL ./.:39:90:39:0,90,1350 ./. 20 10015389 . A . . END=10015390 GT:DP:GQ:MIN_DP:PL ./.:38:81:38:0,81,1215 ./. 20 10015391 . G . . END=10015392 GT:DP:GQ:MIN_DP:PL ./.:37:78:36:0,78,1170 ./. @@ -871,17 +676,11 @@ 20 10015662 . G . . 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END=10015701 GT:DP:GQ:MIN_DP:PL ./.:12:27:11:0,27,405 ./. -20 10015702 . C . . END=10015707 GT:DP:GQ:MIN_DP:PL ./.:12:30:11:0,30,450 ./. +20 10015680 . G . . END=10015683 GT:DP:GQ:MIN_DP:PL ./.:10:24:10:0,24,360 ./. +20 10015684 . C . . END=10015687 GT:DP:GQ:MIN_DP:PL ./.:11:27:10:0,27,405 ./. +20 10015688 . C . . END=10015690 GT:DP:GQ:MIN_DP:PL ./.:10:30:10:0,30,292 ./. +20 10015691 . C . . END=10015701 GT:DP:GQ:MIN_DP:PL ./.:11:27:10:0,27,405 ./. +20 10015702 . C . . END=10015707 GT:DP:GQ:MIN_DP:PL ./.:11:30:11:0,30,450 ./. 20 10015708 . G . . . GT:DP:GQ:MIN_DP:PL ./.:12:33:12:0,33,495 ./. 20 10015709 . C . . END=10015714 GT:DP:GQ:MIN_DP:PL ./.:13:36:13:0,36,540 ./. 20 10015715 . C . . END=10015716 GT:DP:GQ:MIN_DP:PL ./.:13:33:13:0,33,495 ./. @@ -899,7 +698,7 @@ 20 10015743 . C . . END=10015747 GT:DP:GQ:MIN_DP:PL ./.:19:54:19:0,54,810 ./. 20 10015748 . G . . END=10015752 GT:DP:GQ:MIN_DP:PL ./.:19:57:19:0,57,608 ./. 20 10015753 . T . . END=10015760 GT:DP:GQ:MIN_DP:PL ./.:21:60:20:0,60,757 ./. -20 10015761 . T C, . . BaseQRankSum=-1.982e+00;DP=22;ExcessHet=3.01;MQRankSum=1.29;RAW_MQ=76441.00;ReadPosRankSum=1.81 GT:AD:DP:GQ:PL:SB ./.:9,13,0:22:99:373,0,284,400,323,723:9,0,12,1 ./. +20 10015761 . T C, . . BaseQRankSum=-1.982e+00;DP=22;ExcessHet=3.01;MQRankSum=1.29;RAW_MQ=76441.00;ReadPosRankSum=1.80 GT:AD:DP:GQ:PL:SB ./.:9,13,0:22:99:373,0,284,400,323,723:9,0,12,1 ./. 20 10015762 . A . . END=10015766 GT:DP:GQ:MIN_DP:PL ./.:23:66:22:0,66,839 ./. 20 10015767 . C . . END=10015769 GT:DP:GQ:MIN_DP:PL ./.:24:72:24:0,72,906 ./. 20 10015770 . C . . . GT:DP:GQ:MIN_DP:PL ./.:24:69:24:0,69,1035 ./. @@ -950,9 +749,7 @@ 20 10020890 . A . . END=10020896 GT:DP:GQ:MIN_DP:PL ./.:42:93:40:0,93,1395 ./. 20 10020897 . C . . END=10020918 GT:DP:GQ:MIN_DP:PL ./.:41:99:37:0,102,1530 ./. 20 10020919 . T . . . GT:DP:GQ:MIN_DP:PL ./.:45:95:45:0,95,1765 ./. -20 10020920 . T . . END=10021606 GT:DP:GQ:MIN_DP:PL ./.:79:99:46:0,105,1721 ./. -20 10021607 . C . . . GT:DP:GQ:MIN_DP:PL ./.:98:98:98:0,98,3341 ./. -20 10021608 . T . . END=10023688 GT:DP:GQ:MIN_DP:PL ./.:80:99:54:0,110,1800 ./. +20 10020920 . T . . END=10023688 GT:DP:GQ:MIN_DP:PL ./.:80:99:46:0,105,1721 ./. 20 10023689 . G A, . . BaseQRankSum=2.14;DP=80;ExcessHet=3.01;MQRankSum=1.35;RAW_MQ=285769.00;ReadPosRankSum=1.16 GT:AD:DP:GQ:PL:SB ./.:29,51,0:80:99:1881,0,946,1968,1099,3067:16,13,26,25 ./. 20 10023690 . G . . END=10023768 GT:DP:GQ:MIN_DP:PL ./.:70:99:57:0,120,1800 ./. 20 10023769 . G . . END=10023971 GT:DP:GQ:MIN_DP:PL ./.:70:99:57:0,120,1800 ./././././././././.:378:18:156:0,18,39,62,89,120,159,209,280,400,1800 @@ -964,22 +761,20 @@ 20 10024288 . C . . . GT:DP:GQ:MIN_DP:PL ./.:71:0:71:0,0,1411 ./. 20 10024289 . T . . END=10024293 GT:DP:GQ:MIN_DP:PL ./.:72:99:70:0,120,1800 ./. 20 10024294 . C . . . GT:DP:GQ:MIN_DP:PL ./.:69:0:69:0,0,1358 ./. -20 10024295 . T . . . GT:DP:GQ:MIN_DP:PL ./.:69:99:69:0,120,1800 ./. -20 10024296 . T . . . GT:DP:GQ:MIN_DP:PL ./.:67:82:67:0,82,2254 ./. +20 10024295 . T . . END=10024296 GT:DP:GQ:MIN_DP:PL ./.:68:99:67:0,120,1800 ./. 20 10024297 . T . . . GT:DP:GQ:MIN_DP:PL ./.:68:65:68:0,65,2188 ./. -20 10024298 . T . . . GT:DP:GQ:MIN_DP:PL ./.:66:37:66:0,37,2037 ./. -20 10024299 . C . . . GT:DP:GQ:MIN_DP:PL ./.:62:0:62:0,0,1430 ./. +20 10024298 . T . . . GT:DP:GQ:MIN_DP:PL ./.:66:59:66:0,59,2080 ./. +20 10024299 . C . . . GT:DP:GQ:MIN_DP:PL ./.:62:0:62:0,0,1480 ./. 20 10024300 . CTT C,CT,CTTTT, . . BaseQRankSum=2.45;DP=50;ExcessHet=3.01;MQRankSum=-6.000e-01;RAW_MQ=134695.00;ReadPosRankSum=-1.073e+00 GT:AD:DP:GQ:PL:SB ./.:3,4,3,8,0:18:1:122,67,400,91,215,231,19,0,1,156,161,279,257,107,347:1,2,11,4 ./. 20 10024301 . T *, . . DP=50 GT:AD:DP:GQ:PL:SB ./.:3,3,0:18:1:122,91,231,161,257,347:1,2,11,4 ./. 20 10024302 . T *, . . DP=50 GT:AD:DP:GQ:PL:SB ./.:3,3,0:18:1:122,91,231,161,257,347:1,2,11,4 ./. 20 10024303 . T . . . GT:DP:GQ:MIN_DP:PL ./.:67:57:67:0,57,855 ./. 20 10024304 . T . . END=10024307 GT:DP:GQ:MIN_DP:PL ./.:69:63:68:0,63,945 ./. 20 10024308 . T . . END=10024310 GT:DP:GQ:MIN_DP:PL ./.:70:78:70:0,78,1170 ./. -20 10024311 . T . . END=10024315 GT:DP:GQ:MIN_DP:PL ./.:66:81:66:0,81,1215 ./. -20 10024316 . T . . . GT:DP:GQ:MIN_DP:PL ./.:66:69:66:0,69,1035 ./. -20 10024317 . T . . . GT:DP:GQ:MIN_DP:PL ./.:64:72:64:0,72,1080 ./. -20 10024318 . T . . . GT:DP:GQ:MIN_DP:PL ./.:62:63:62:0,63,945 ./. -20 10024319 . T . . END=10024320 GT:DP:GQ:MIN_DP:PL ./.:63:75:62:0,75,1125 ./. +20 10024311 . T . . END=10024314 GT:DP:GQ:MIN_DP:PL ./.:66:81:66:0,81,1215 ./. +20 10024315 . T . . . GT:DP:GQ:MIN_DP:PL ./.:66:72:66:0,72,1080 ./. +20 10024316 . T . . END=10024318 GT:DP:GQ:MIN_DP:PL ./.:64:60:62:0,60,900 ./. +20 10024319 . T . . END=10024320 GT:DP:GQ:MIN_DP:PL ./.:63:72:62:0,72,1080 ./. 20 10024321 . T . . . GT:DP:GQ:MIN_DP:PL ./.:62:90:62:0,90,1350 ./. 20 10024322 . T . . . GT:DP:GQ:MIN_DP:PL ./.:60:69:60:0,69,2100 ./. 20 10024323 . T . . . GT:DP:GQ:MIN_DP:PL ./.:56:27:56:0,27,1860 ./. @@ -994,38 +789,31 @@ 20 10026357 . T C, . . BaseQRankSum=-1.700e+00;DP=63;ExcessHet=3.01;MQRankSum=-1.480e-01;RAW_MQ=215117.00;ReadPosRankSum=-7.600e-02 GT:AD:DP:GQ:PL:SB ./.:28,35,0:63:99:1195,0,932,1279,1037,2316:10,18,20,15 ./. 20 10026358 . A . . END=10026793 GT:DP:GQ:MIN_DP:PL ./.:72:99:41:0,102,1530 ./. 20 10026794 . C T, . . BaseQRankSum=2.83;DP=52;ExcessHet=3.01;MQRankSum=-7.190e-01;RAW_MQ=184441.00;ReadPosRankSum=-5.330e-01 GT:AD:DP:GQ:PL:SB ./.:19,33,0:52:99:1113,0,529,1170,627,1798:7,12,15,18 ./. -20 10026795 . G . . END=10027227 GT:DP:GQ:MIN_DP:PL ./.:71:99:52:0,105,1575 ./. -20 10027228 . G . . . GT:DP:GQ:MIN_DP:PL ./.:66:96:66:0,96,1440 ./. -20 10027229 . A . . . GT:DP:GQ:MIN_DP:PL ./.:67:99:67:0,99,1485 ./. -20 10027230 . A . . . GT:DP:GQ:MIN_DP:PL ./.:66:96:66:0,96,1440 ./. -20 10027231 . A . . END=10027233 GT:DP:GQ:MIN_DP:PL ./.:70:99:68:0,102,1530 ./. +20 10026795 . G . . END=10027233 GT:DP:GQ:MIN_DP:PL ./.:70:99:52:0,115,1800 ./. 20 10027234 . A ATTAG, . . BaseQRankSum=-4.060e-01;DP=72;ExcessHet=3.01;MQRankSum=-8.450e-01;RAW_MQ=236651.00;ReadPosRankSum=-9.790e-01 GT:AD:DP:GQ:PL:SB ./.:34,35,0:69:99:1358,0,1964,1461,2069,3531:18,16,15,20 ./. -20 10027235 . T . . . GT:DP:GQ:MIN_DP:PL ./.:72:0:72:0,0,334 ./. -20 10027236 . T . . END=10027867 GT:DP:GQ:MIN_DP:PL ./.:78:99:56:0,120,1800 ./. +20 10027235 . T . . END=10027867 GT:DP:GQ:MIN_DP:PL ./.:78:99:56:0,120,1800 ./. 20 10027868 . A G, . . BaseQRankSum=-5.793e+00;DP=89;ExcessHet=3.01;MQRankSum=0.032;RAW_MQ=314882.00;ReadPosRankSum=1.87 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:44,45,0:89:99:0|1:10027868_A_G:1768,0,3201,1901,3340,5240:19,25,26,19 ./. 20 10027869 . A . . END=10027871 GT:DP:GQ:MIN_DP:PL ./.:86:99:85:0,120,1800 ./. 20 10027872 . A G, . . BaseQRankSum=-5.491e+00;DP=85;ExcessHet=3.01;MQRankSum=0.101;RAW_MQ=300482.00;ReadPosRankSum=1.05 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:40,45,0:85:99:0|1:10027868_A_G:1753,0,3136,1879,3272,5151:16,24,26,19 ./. 20 10027873 . G . . END=10028866 GT:DP:GQ:MIN_DP:PL ./.:80:99:55:0,120,1800 ./. 20 10028867 . A ATG, . . BaseQRankSum=-8.740e-01;DP=92;ExcessHet=3.01;MQRankSum=2.71;RAW_MQ=338841.00;ReadPosRankSum=0.364 GT:AD:DP:GQ:PL:SB ./.:32,39,0:71:99:1144,0,916,1242,1033,2275:11,21,18,21 ./. -20 10028868 . T . . . GT:DP:GQ:MIN_DP:PL ./.:92:0:92:0,0,401 ./. -20 10028869 . G . . END=10030036 GT:DP:GQ:MIN_DP:PL ./.:80:99:60:0,120,1800 ./. +20 10028868 . T . . END=10030036 GT:DP:GQ:MIN_DP:PL ./.:80:99:60:0,120,1800 ./. 20 10030037 . G . . END=10030187 GT:DP:GQ:MIN_DP:PL ./.:80:99:60:0,120,1800 ./././././././././.:198:18:57:0,18,39,62,89,120,159,209,280,400,1800 20 10030188 . T A, . . BaseQRankSum=0.711;ClippingRankSum=0.00;DP=419;ExcessHet=3.01;MQRankSum=0.00;RAW_MQ=1505641.00;ReadPosRankSum=1.23 GT:AD:DP:GQ:PL:SB ./.:42,39,0:81:99:1401,0,1524,1527,1641,3168:24,18,15,24 ./././././././././.:294,41,0:335:28:798,0,28,126,272,464,716,1054,1545,2400,9304,932,150,198,323,504,748,1081,1569,2421,9323,1082,320,394,555,788,1114,1596,2445,9344,1252,517,627,839,1153,1628,2472,9367,1449,749,911,1204,1668,2505,9395,1681,1033,1276,1719,2544,9427,1965,1398,1791,2595,9467,2330,1913,2667,9518,2845,2789,9589,3721,9712,10644:130,164,23,18 20 10030189 . G . . END=10030451 GT:DP:GQ:MIN_DP:PL ./.:71:99:41:0,103,1575 ./././././././././.:217:18:152:0,18,39,62,89,120,159,209,280,400,1800 20 10030452 . G A, . . BaseQRankSum=-2.464e+00;ClippingRankSum=0.00;DP=254;MQRankSum=0.00;RAW_MQ=766800.00;ReadPosRankSum=-6.050e-01 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:.:71:99:41:0,103,1575,103,1575,1575 ./././././././././.:181,29,0:210:6:.:640,0,6,60,144,259,412,618,919,1446,6012,722,93,110,181,288,435,637,936,1461,6025,815,197,232,324,463,660,955,1477,6040,920,318,375,499,688,978,1497,6056,1041,461,550,724,1006,1520,6076,1184,637,775,1042,1548,6099,1359,862,1093,1584,6127,1585,1180,1635,6163,1902,1722,6214,2444,6301,7023:106,75,17,12 20 10030453 . A . . END=10030566 GT:DP:GQ:MIN_DP:PL ./.:71:99:41:0,103,1575 ./././././././././.:230:18:51:0,18,38,60,87,117,155,204,273,390,1755 20 10030567 . G . . . GT:DP:GQ:MIN_DP:PL ./.:41:90:41:0,90,1511 ./././././././././.:230:18:51:0,18,38,60,87,117,155,204,273,390,1755 -20 10030568 . C . . END=10030849 GT:DP:GQ:MIN_DP:PL ./.:70:99:42:0,99,1485 ./././././././././.:230:18:51:0,18,38,60,87,117,155,204,273,390,1755 -20 10030850 . C . . END=10030851 GT:DP:GQ:MIN_DP:PL ./.:70:99:42:0,99,1485 ./././././././././.:49:17:48:0,17,36,57,82,111,147,193,259,370,1665 -20 10030852 . T . . END=10030855 GT:DP:GQ:MIN_DP:PL ./.:70:99:42:0,99,1485 ./././././././././.:47:16:45:0,16,33,53,75,102,135,178,238,340,1530 -20 10030856 . A . . END=10030857 GT:DP:GQ:MIN_DP:PL ./.:70:99:42:0,99,1485 ./././././././././.:43:15:41:0,15,31,50,71,96,127,167,224,320,1440 -20 10030858 . A . . . GT:DP:GQ:MIN_DP:PL ./.:70:99:42:0,99,1485 ./././././././././.:40:14:40:0,14,29,46,67,90,119,157,210,300,1350 -20 10030859 . G . . END=10030861 GT:DP:GQ:MIN_DP:PL ./.:70:99:42:0,99,1485 ./././././././././.:39:13:38:0,13,27,43,62,84,111,146,196,280,1260 -20 10030862 . T . . . GT:DP:GQ:MIN_DP:PL ./.:70:99:42:0,99,1485 ./././././././././.:39:12:39:0,12,26,42,60,81,107,141,189,270,1215 -20 10030863 . A . . END=10031253 GT:DP:GQ:MIN_DP:PL ./.:70:99:42:0,99,1485 ./. +20 10030568 . C . . END=10030849 GT:DP:GQ:MIN_DP:PL ./.:70:99:42:0,114,1710 ./././././././././.:230:18:51:0,18,38,60,87,117,155,204,273,390,1755 +20 10030850 . C . . END=10030851 GT:DP:GQ:MIN_DP:PL ./.:70:99:42:0,114,1710 ./././././././././.:49:17:48:0,17,36,57,82,111,147,193,259,370,1665 +20 10030852 . T . . END=10030855 GT:DP:GQ:MIN_DP:PL ./.:70:99:42:0,114,1710 ./././././././././.:47:16:45:0,16,33,53,75,102,135,178,238,340,1530 +20 10030856 . A . . END=10030857 GT:DP:GQ:MIN_DP:PL ./.:70:99:42:0,114,1710 ./././././././././.:43:15:41:0,15,31,50,71,96,127,167,224,320,1440 +20 10030858 . A . . . GT:DP:GQ:MIN_DP:PL ./.:70:99:42:0,114,1710 ./././././././././.:40:14:40:0,14,29,46,67,90,119,157,210,300,1350 +20 10030859 . G . . END=10030861 GT:DP:GQ:MIN_DP:PL ./.:70:99:42:0,114,1710 ./././././././././.:39:13:38:0,13,27,43,62,84,111,146,196,280,1260 +20 10030862 . T . . . GT:DP:GQ:MIN_DP:PL ./.:70:99:42:0,114,1710 ./././././././././.:39:12:39:0,12,26,42,60,81,107,141,189,270,1215 +20 10030863 . A . . END=10031253 GT:DP:GQ:MIN_DP:PL ./.:70:99:42:0,114,1710 ./. 20 10031254 . A AT, . . BaseQRankSum=-9.100e-02;DP=87;ExcessHet=3.01;MQRankSum=0.017;RAW_MQ=309510.00;ReadPosRankSum=0.495 GT:AD:DP:GQ:PL:SB ./.:38,47,0:85:99:1501,0,1159,1616,1300,2916:27,11,25,22 ./. -20 10031255 . T . . . GT:DP:GQ:MIN_DP:PL ./.:88:0:88:0,0,0 ./. -20 10031256 . G . . END=10031341 GT:DP:GQ:MIN_DP:PL ./.:96:99:87:0,120,1800 ./. +20 10031255 . T . . END=10031341 GT:DP:GQ:MIN_DP:PL ./.:95:99:86:0,120,1800 ./. 20 10031342 . G A, . . BaseQRankSum=1.83;DP=93;ExcessHet=3.01;MQRankSum=-8.660e-01;RAW_MQ=332041.00;ReadPosRankSum=-1.200e-02 GT:AD:DP:GQ:PL:SB ./.:41,52,0:93:99:1863,0,1375,1986,1531,3517:22,19,31,21 ./. 20 10031343 . A . . END=10031797 GT:DP:GQ:MIN_DP:PL ./.:91:99:66:0,120,1800 ./. 20 10031798 . G A, . . DP=104;ExcessHet=3.01;RAW_MQ=369410.00 GT:AD:DP:GQ:PL:SB ./.:0,104,0:104:99:4325,313,0,4325,313,4325:0,0,57,47 ./. @@ -1039,11 +827,9 @@ 20 10032414 . T . . END=10032539 GT:DP:GQ:MIN_DP:PL ./.:70:99:55:0,120,1800 ./././././././././.:252:18:102:0,18,39,62,89,120,159,209,280,400,1800 20 10032540 . A . . END=10032881 GT:DP:GQ:MIN_DP:PL ./.:70:99:55:0,120,1800 ./. 20 10032882 . A T, . . BaseQRankSum=-3.697e+00;DP=75;ExcessHet=3.01;MQRankSum=-1.014e+00;RAW_MQ=267241.00;ReadPosRankSum=0.626 GT:AD:DP:GQ:PL:SB ./.:39,36,0:75:99:1231,0,1406,1348,1514,2862:28,11,22,14 ./. -20 10032883 . A . . END=10032966 GT:DP:GQ:MIN_DP:PL ./.:67:99:61:0,99,1485 ./. -20 10032967 . T . . END=10032971 GT:DP:GQ:MIN_DP:PL ./.:68:90:67:0,90,1350 ./. +20 10032883 . A . . END=10032971 GT:DP:GQ:MIN_DP:PL ./.:67:99:61:0,120,1800 ./. 20 10032972 . C CAT, . . BaseQRankSum=-3.540e-01;DP=65;ExcessHet=3.01;MQRankSum=-1.017e+00;RAW_MQ=231241.00;ReadPosRankSum=-1.232e+00 GT:AD:DP:GQ:PL:SB ./.:33,30,0:63:99:1160,0,1477,1260,1568,2827:17,16,11,19 ./. -20 10032973 . T . . . GT:DP:GQ:MIN_DP:PL ./.:65:0:65:0,0,104 ./. -20 10032974 . G . . END=10033636 GT:DP:GQ:MIN_DP:PL ./.:78:99:50:0,120,1800 ./. +20 10032973 . T . . END=10033636 GT:DP:GQ:MIN_DP:PL ./.:78:99:50:0,120,1800 ./. 20 10033637 . C . . . GT:DP:GQ:MIN_DP:PL ./.:58:97:58:0,97,2210 ./. 20 10033638 . C . . END=10033758 GT:DP:GQ:MIN_DP:PL ./.:85:99:53:0,120,1800 ./. 20 10033759 . G . . END=10033919 GT:DP:GQ:MIN_DP:PL ./.:85:99:53:0,120,1800 ./././././././././.:122:18:49:0,18,39,62,89,120,159,209,280,400,1800 @@ -1088,8 +874,7 @@ 20 10036948 . A *, . . DP=93 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 ./. 20 10036949 . T *, . . DP=93 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 ./. 20 10036950 . A *, . . DP=93 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 ./. -20 10036951 . G . . . GT:DP:GQ:MIN_DP:PL ./.:77:0:77:0,0,1197 ./. -20 10036952 . A . . END=10036956 GT:DP:GQ:MIN_DP:PL ./.:74:99:70:0,120,1800 ./. +20 10036951 . G . . 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GT:DP:GQ:MIN_DP:PL ./.:90:72:90:0,72,1080 ./. -20 10037103 . A . . . GT:DP:GQ:MIN_DP:PL ./.:90:66:90:0,66,990 ./. -20 10037104 . T . . . GT:DP:GQ:MIN_DP:PL ./.:89:0:89:0,0,2830 ./. -20 10037105 . A . . END=10037107 GT:DP:GQ:MIN_DP:PL ./.:89:54:88:0,54,810 ./. -20 10037108 . G . . . GT:DP:GQ:MIN_DP:PL ./.:85:21:85:0,21,315 ./. -20 10037109 . A . . . GT:DP:GQ:MIN_DP:PL ./.:84:18:84:0,18,270 ./. +20 10037038 . G . . END=10037109 GT:DP:GQ:MIN_DP:PL ./.:88:99:75:0,120,1800 ./. 20 10037110 . T TGATA, . . DP=74;ExcessHet=3.01;RAW_MQ=240219.00 GT:AD:DP:GQ:PL:SB ./.:0,61,0:61:99:2818,189,0,2819,190,2820:0,0,35,26 ./. -20 10037111 . G . . . GT:DP:GQ:MIN_DP:PL ./.:84:0:84:0,0,0 ./. -20 10037112 . A . . END=10037121 GT:DP:GQ:MIN_DP:PL ./.:83:99:81:0,120,1800 ./. -20 10037122 . A . . END=10037126 GT:DP:GQ:MIN_DP:PL ./.:80:0:79:0,0,1989 ./. -20 10037127 . A . . . GT:DP:GQ:MIN_DP:PL ./.:79:85:79:0,85,2945 ./. -20 10037128 . T . . END=10037131 GT:DP:GQ:MIN_DP:PL ./.:77:99:74:0,114,1710 ./. -20 10037132 . T . . END=10037134 GT:DP:GQ:MIN_DP:PL ./.:73:0:72:0,0,1990 ./. -20 10037135 . A . . END=10037137 GT:DP:GQ:MIN_DP:PL ./.:70:99:70:0,111,1665 ./. -20 10037138 . G . . END=10037140 GT:DP:GQ:MIN_DP:PL ./.:70:93:68:0,93,1395 ./. -20 10037141 . A . . END=10037143 GT:DP:GQ:MIN_DP:PL ./.:70:0:68:0,0,1786 ./. +20 10037111 . G . . END=10037143 GT:DP:GQ:MIN_DP:PL ./.:77:99:68:0,120,1800 ./. 20 10037144 . T TGATAGATA, . . DP=70;ExcessHet=3.01;RAW_MQ=187352.00 GT:AD:DP:GQ:PL:SB ./.:0,36,0:36:99:1861,127,0,1864,129,1866:0,0,15,21 ./. -20 10037145 . G . . . GT:DP:GQ:MIN_DP:PL ./.:75:0:75:0,0,8 ./. -20 10037146 . A . . END=10037186 GT:DP:GQ:MIN_DP:PL ./.:70:99:65:0,117,1755 ./. +20 10037145 . G . . END=10037186 GT:DP:GQ:MIN_DP:PL ./.:70:99:65:0,111,1665 ./. 20 10037187 . G . . . GT:DP:GQ:MIN_DP:PL ./.:68:0:68:0,0,2259 ./. 20 10037188 . A . . . GT:DP:GQ:MIN_DP:PL ./.:66:99:66:0,120,1800 ./. 20 10037189 . T . . . GT:DP:GQ:MIN_DP:PL ./.:67:50:67:0,50,2476 ./. @@ -1141,58 +908,25 @@ 20 10038583 . C . . . GT:DP:GQ:MIN_DP:PL ./.:55:91:55:0,91,1806 ./. 20 10038584 . A . . END=10039370 GT:DP:GQ:MIN_DP:PL ./.:76:99:54:0,120,1800 ./. 20 10039371 . T G, . . BaseQRankSum=-3.260e+00;DP=74;ExcessHet=3.01;MQRankSum=0.00;RAW_MQ=266400.00;ReadPosRankSum=0.391 GT:AD:DP:GQ:PL:SB ./.:34,40,0:74:99:1353,0,1194,1455,1315,2770:15,19,24,16 ./. -20 10039372 . T . . END=10040748 GT:DP:GQ:MIN_DP:PL ./.:76:99:56:0,105,1575 ./. -20 10040749 . T . . END=10040752 GT:DP:GQ:MIN_DP:PL ./.:87:87:84:0,87,1305 ./. -20 10040753 . C . . . GT:DP:GQ:MIN_DP:PL ./.:88:90:88:0,90,1350 ./. -20 10040754 . T . . . GT:DP:GQ:MIN_DP:PL ./.:91:81:91:0,81,1215 ./. -20 10040755 . G . . . GT:DP:GQ:MIN_DP:PL ./.:89:69:89:0,69,1035 ./. -20 10040756 . T . . END=10040758 GT:DP:GQ:MIN_DP:PL ./.:89:45:89:0,45,675 ./. -20 10040759 . T . . . GT:DP:GQ:MIN_DP:PL ./.:89:48:89:0,48,720 ./. -20 10040760 . T . . . GT:DP:GQ:MIN_DP:PL ./.:89:51:89:0,51,765 ./. -20 10040761 . C . . . GT:DP:GQ:MIN_DP:PL ./.:88:48:88:0,48,720 ./. -20 10040762 . T . . . GT:DP:GQ:MIN_DP:PL ./.:87:42:87:0,42,630 ./. -20 10040763 . T . . . GT:DP:GQ:MIN_DP:PL ./.:87:30:87:0,30,450 ./. -20 10040764 . T . . END=10040766 GT:DP:GQ:MIN_DP:PL ./.:85:39:84:0,39,585 ./. -20 10040767 . C . . . GT:DP:GQ:MIN_DP:PL ./.:83:36:83:0,36,540 ./. -20 10040768 . T . . END=10040771 GT:DP:GQ:MIN_DP:PL ./.:83:15:81:0,15,225 ./. +20 10039372 . T . . END=10040770 GT:DP:GQ:MIN_DP:PL ./.:76:99:56:0,120,1800 ./. +20 10040771 . T . . . GT:DP:GQ:MIN_DP:PL ./.:81:60:81:0,60,2763 ./. 20 10040772 . C CT, . . DP=79;ExcessHet=3.01;RAW_MQ=211048.00 GT:AD:DP:GQ:PL:SB ./.:0,70,0:70:99:2033,210,0,2034,210,2034:0,0,37,33 ./. -20 10040773 . T . . . GT:DP:GQ:MIN_DP:PL ./.:81:0:81:0,0,0 ./. -20 10040774 . T . . END=10040795 GT:DP:GQ:MIN_DP:PL ./.:80:99:77:0,99,1485 ./. -20 10040796 . T . . END=10040797 GT:DP:GQ:MIN_DP:PL ./.:78:93:77:0,93,1395 ./. -20 10040798 . C . . . GT:DP:GQ:MIN_DP:PL ./.:78:84:78:0,84,1260 ./. -20 10040799 . T . . END=10040801 GT:DP:GQ:MIN_DP:PL ./.:79:72:78:0,72,1080 ./. -20 10040802 . G . . END=10040803 GT:DP:GQ:MIN_DP:PL ./.:79:63:78:0,63,945 ./. -20 10040804 . A . . END=10040805 GT:DP:GQ:MIN_DP:PL ./.:78:57:77:0,57,855 ./. -20 10040806 . T . . END=10040807 GT:DP:GQ:MIN_DP:PL ./.:79:48:78:0,48,720 ./. -20 10040808 . A . . END=10040809 GT:DP:GQ:MIN_DP:PL ./.:80:42:79:0,42,630 ./. -20 10040810 . C . . . GT:DP:GQ:MIN_DP:PL ./.:81:15:81:0,15,225 ./. -20 10040811 . A . . . GT:DP:GQ:MIN_DP:PL ./.:80:3:80:0,3,45 ./. +20 10040773 . T . . END=10040811 GT:DP:GQ:MIN_DP:PL ./.:77:99:75:0,120,1800 ./. 20 10040812 . AT A, . . DP=79;ExcessHet=3.01;RAW_MQ=203299.00 GT:AD:DP:GQ:PL:SB ./.:0,71,0:71:99:2645,214,0,2645,214,2645:0,0,36,35 ./. 20 10040813 . T *, . . DP=79 GT:AD:DP:GQ:PL:SB ./.:0,71,0:71:99:2645,214,0,2645,214,2645:0,0,36,35 ./. -20 10040814 . T . . . GT:DP:GQ:MIN_DP:PL ./.:82:0:82:0,0,0 ./. -20 10040815 . T . . END=10040819 GT:DP:GQ:MIN_DP:PL ./.:79:99:78:0,109,1800 ./. -20 10040820 . T . . . GT:DP:GQ:MIN_DP:PL ./.:77:75:77:0,75,2723 ./. +20 10040814 . T . . END=10040820 GT:DP:GQ:MIN_DP:PL ./.:78:99:77:0,120,1800 ./. 20 10040821 . T A, . . BaseQRankSum=-2.100e-02;DP=78;ExcessHet=3.01;MQRankSum=-9.700e-02;RAW_MQ=199699.00;ReadPosRankSum=-1.385e+00 GT:AD:DP:GQ:PL:SB ./.:38,40,0:78:99:1200,0,1099,1314,1219,2533:20,18,21,19 ./. 20 10040822 . A . . END=10041303 GT:DP:GQ:MIN_DP:PL ./.:71:99:54:0,119,1800 ./. 20 10041304 . C T, . . DP=68;ExcessHet=3.01;RAW_MQ=239810.00 GT:AD:DP:GQ:PL:SB ./.:0,68,0:68:99:2794,204,0,2794,204,2794:0,0,34,34 ./. -20 10041305 . G . . END=10041688 GT:DP:GQ:MIN_DP:PL ./.:61:99:48:0,105,1575 ./. -20 10041689 . T . . . GT:DP:GQ:MIN_DP:PL ./.:72:93:72:0,93,1395 ./. -20 10041690 . C . . . GT:DP:GQ:MIN_DP:PL ./.:72:87:72:0,87,1305 ./. -20 10041691 . A . . END=10041692 GT:DP:GQ:MIN_DP:PL ./.:73:69:73:0,69,1035 ./. -20 10041693 . T . . END=10041694 GT:DP:GQ:MIN_DP:PL ./.:76:51:75:0,51,765 ./. -20 10041695 . A . . . GT:DP:GQ:MIN_DP:PL ./.:75:48:75:0,48,720 ./. -20 10041696 . A . . . GT:DP:GQ:MIN_DP:PL ./.:75:45:75:0,45,675 ./. -20 10041697 . A . . . GT:DP:GQ:MIN_DP:PL ./.:75:12:75:0,12,180 ./. +20 10041305 . G . . END=10041697 GT:DP:GQ:MIN_DP:PL ./.:62:99:48:0,120,1800 ./. 20 10041698 . C CAT, . . BaseQRankSum=1.89;DP=74;ExcessHet=3.01;MQRankSum=0.844;RAW_MQ=265497.00;ReadPosRankSum=0.579 GT:AD:DP:GQ:PL:SB ./.:48,6,0:54:17:17,0,1425,166,1446,1612:21,27,2,4 ./. -20 10041699 . A . . . GT:DP:GQ:MIN_DP:PL ./.:77:5:77:0,5,2671 ./. -20 10041700 . T . . . GT:DP:GQ:MIN_DP:PL ./.:77:27:77:0,27,405 ./. +20 10041699 . A . . END=10041700 GT:DP:GQ:MIN_DP:PL ./.:79:99:78:0,120,1800 ./. 20 10041701 . A ATG,ATATG, . . BaseQRankSum=0.848;DP=78;ExcessHet=3.01;MQRankSum=0.340;RAW_MQ=270590.00;ReadPosRankSum=-2.230e-01 GT:AD:DP:GQ:PL:SB ./.:8,0,48,0:56:58:1441,1582,2726,0,261,58,1575,2317,264,2201:2,6,21,27 ./. -20 10041702 . T . . . GT:DP:GQ:MIN_DP:PL ./.:75:0:75:0,0,0 ./. -20 10041703 . G . . END=10042318 GT:DP:GQ:MIN_DP:PL ./.:64:99:49:0,117,1800 ./. +20 10041702 . T . . END=10042318 GT:DP:GQ:MIN_DP:PL ./.:64:99:49:0,117,1800 ./. 20 10042319 . C T, . . DP=66;ExcessHet=3.01;RAW_MQ=229851.00 GT:AD:DP:GQ:PL:SB ./.:0,66,0:66:99:2687,199,0,2687,199,2687:0,0,38,28 ./. 20 10042320 . C . . END=10042760 GT:DP:GQ:MIN_DP:PL ./.:74:99:60:0,120,1800 ./. 20 10042761 . A G, . . DP=91;ExcessHet=3.01;RAW_MQ=327600.00 GT:AD:DP:GQ:PL:SB ./.:0,91,0:91:99:3582,272,0,3582,272,3582:0,0,58,33 ./. -20 10042762 . G . . END=10042828 GT:DP:GQ:MIN_DP:PL ./.:91:99:79:0,120,1800 ./. +20 10042762 . G . . END=10042828 GT:DP:GQ:MIN_DP:PL ./.:90:99:78:0,120,1800 ./. 20 10042829 . A G, . . DP=78;ExcessHet=3.01;RAW_MQ=278569.00 GT:AD:DP:GQ:PL:SB ./.:0,78,0:78:99:3084,235,0,3084,235,3084:0,0,42,36 ./. 20 10042830 . C . . END=10043001 GT:DP:GQ:MIN_DP:PL ./.:65:99:56:0,120,1800 ./. 20 10043002 . A T, . . 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END=10046170 GT:DP:GQ:MIN_DP:PL ./.:61:51:59:0,51,765 ./. -20 10046171 . A . . END=10046172 GT:DP:GQ:MIN_DP:PL ./.:64:39:63:0,39,585 ./. -20 10046173 . A . . END=10046176 GT:DP:GQ:MIN_DP:PL ./.:63:21:62:0,21,315 ./. -20 10046177 . A . . . GT:DP:GQ:MIN_DP:PL ./.:60:15:60:0,15,225 ./. +20 10045643 . A . . END=10046177 GT:DP:GQ:MIN_DP:PL ./.:79:99:58:0,120,1800 ./. 20 10046178 . AAGAAAGAAAG A, . . DP=61;ExcessHet=3.01;RAW_MQ=140545.00 GT:AD:DP:GQ:PL:SB ./.:0,50,0:50:99:2197,152,0,2197,152,2197:0,0,23,27 ./. 20 10046179 . A *, . . DP=61 GT:AD:DP:GQ:PL:SB ./.:0,50,0:50:99:2197,152,0,2197,152,2197:0,0,23,27 ./. 20 10046180 . G *, . . DP=61 GT:AD:DP:GQ:PL:SB ./.:0,50,0:50:99:2197,152,0,2197,152,2197:0,0,23,27 ./. @@ -1222,8 +948,7 @@ 20 10046186 . A *, . . DP=61 GT:AD:DP:GQ:PL:SB ./.:0,50,0:50:99:2197,152,0,2197,152,2197:0,0,23,27 ./. 20 10046187 . A *, . . DP=61 GT:AD:DP:GQ:PL:SB ./.:0,50,0:50:99:2197,152,0,2197,152,2197:0,0,23,27 ./. 20 10046188 . G *, . . 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DP=69 GT:AD:DP:GQ:PL:SB ./.:2,9,0:22:99:651,135,106,443,170,627:1,1,12,8 ./. @@ -1294,16 +1012,9 @@ 20 10067056 . A *, . . DP=69 GT:AD:DP:GQ:PL:SB ./.:2,9,0:22:99:651,135,106,443,170,627:1,1,12,8 ./. 20 10067057 . A *, . . DP=69 GT:AD:DP:GQ:PL:SB ./.:2,9,0:22:99:651,135,106,443,170,627:1,1,12,8 ./. 20 10067058 . A *, . . DP=69 GT:AD:DP:GQ:PL:SB ./.:2,9,0:22:99:651,135,106,443,170,627:1,1,12,8 ./. -20 10067059 . A . . END=10067060 GT:DP:GQ:MIN_DP:PL ./.:57:87:56:0,87,1305 ./. -20 10067061 . A . . . GT:DP:GQ:MIN_DP:PL ./.:59:90:59:0,90,1350 ./. -20 10067062 . A . . END=10067066 GT:DP:GQ:MIN_DP:PL ./.:61:99:56:0,99,1485 ./. -20 10067067 . A . . . GT:DP:GQ:MIN_DP:PL ./.:52:19:52:0,19,1692 ./. -20 10067068 . A . . . GT:DP:GQ:MIN_DP:PL ./.:47:0:47:0,0,1430 ./. -20 10067069 . A . . . GT:DP:GQ:MIN_DP:PL ./.:42:26:42:0,26,1402 ./. -20 10067070 . A . . . GT:DP:GQ:MIN_DP:PL ./.:40:84:40:0,84,1498 ./. -20 10067071 . A . . END=10067075 GT:DP:GQ:MIN_DP:PL ./.:41:99:39:0,105,1471 ./. -20 10067076 . A . . . GT:DP:GQ:MIN_DP:PL ./.:44:97:44:0,97,1535 ./. -20 10067077 . G . . END=10067089 GT:DP:GQ:MIN_DP:PL ./.:48:99:45:0,110,1645 ./. +20 10067059 . A . . END=10067067 GT:DP:GQ:MIN_DP:PL ./.:57:99:50:0,99,1485 ./. +20 10067068 . A . . END=10067070 GT:DP:GQ:MIN_DP:PL ./.:44:96:44:0,96,1440 ./. +20 10067071 . A . . END=10067089 GT:DP:GQ:MIN_DP:PL ./.:48:99:46:0,102,1530 ./. 20 10067090 . C A, . . DP=55;ExcessHet=3.01;RAW_MQ=165948.00 GT:AD:DP:GQ:PL:SB ./.:0,55,0:55:99:2033,164,0,2033,164,2033:0,0,27,28 ./. 20 10067091 . T . . END=10067263 GT:DP:GQ:MIN_DP:PL ./.:76:99:50:0,120,1800 ./. 20 10067264 . G A, . . DP=73;ExcessHet=3.01;RAW_MQ=257282.00 GT:AD:DP:GQ:PL:SB ./.:0,73,0:73:99:2951,219,0,2951,219,2951:0,0,38,35 ./. @@ -1320,13 +1031,12 @@ 20 10068034 . G . . END=10068040 GT:DP:GQ:MIN_DP:PL ./.:30:81:30:0,81,1215 ./. 20 10068041 . T . . END=10068043 GT:DP:GQ:MIN_DP:PL ./.:32:90:31:0,90,1350 ./. 20 10068044 . T . . 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GT:DP:GQ:MIN_DP:PL ./.:20:18:20:0,18,270 ./. 20 10068176 . A . . END=10068180 GT:DP:GQ:MIN_DP:PL ./.:19:24:17:0,24,360 ./. 20 10068181 . T . . END=10068185 GT:DP:GQ:MIN_DP:PL ./.:16:27:16:0,27,405 ./. 20 10068186 . A . . . GT:DP:GQ:MIN_DP:PL ./.:16:9:16:0,9,570 ./. @@ -1358,16 +1068,14 @@ 20 10068200 . A . . . GT:DP:GQ:MIN_DP:PL ./.:16:45:16:0,45,675 ./. 20 10068201 . T . . . GT:DP:GQ:MIN_DP:PL ./.:18:51:18:0,51,765 ./. 20 10068202 . A . . END=10068203 GT:DP:GQ:MIN_DP:PL ./.:19:54:19:0,54,810 ./. -20 10068204 . A . . END=10068206 GT:DP:GQ:MIN_DP:PL ./.:21:57:20:0,57,855 ./. -20 10068207 . C . . END=10068209 GT:DP:GQ:MIN_DP:PL ./.:22:60:21:0,60,900 ./. -20 10068210 . T . . END=10068215 GT:DP:GQ:MIN_DP:PL ./.:26:75:26:0,75,960 ./. -20 10068216 . C . . . GT:DP:GQ:MIN_DP:PL ./.:27:81:27:0,81,1065 ./. -20 10068217 . C . . . GT:DP:GQ:MIN_DP:PL ./.:27:78:27:0,78,1170 ./. -20 10068218 . A . . END=10068223 GT:DP:GQ:MIN_DP:PL ./.:29:81:28:0,81,1215 ./. -20 10068224 . G . . 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END=10075492 GT:DP:GQ:MIN_DP:PL ./.:71:75:70:0,75,1125 ./. -20 10075493 . G . . END=10075495 GT:DP:GQ:MIN_DP:PL ./.:72:63:71:0,63,945 ./. -20 10075496 . G . . END=10075497 GT:DP:GQ:MIN_DP:PL ./.:73:54:73:0,54,810 ./. -20 10075498 . T . . . GT:DP:GQ:MIN_DP:PL ./.:72:42:72:0,42,630 ./. -20 10075499 . G . . . GT:DP:GQ:MIN_DP:PL ./.:73:33:73:0,33,495 ./. -20 10075500 . A . . . GT:DP:GQ:MIN_DP:PL ./.:73:27:73:0,27,405 ./. -20 10075501 . T . . END=10075502 GT:DP:GQ:MIN_DP:PL ./.:72:21:71:0,21,315 ./. -20 10075503 . A . . END=10075506 GT:DP:GQ:MIN_DP:PL ./.:75:3:72:0,3,45 ./. -20 10075507 . A . . . GT:DP:GQ:MIN_DP:PL ./.:80:6:80:0,6,90 ./. +20 10075169 . G . . END=10075507 GT:DP:GQ:MIN_DP:PL ./.:68:99:49:0,119,1800 ./. 20 10075508 . GA G, . . DP=77;ExcessHet=3.01;RAW_MQ=288121.00 GT:AD:DP:GQ:PL:SB ./.:0,70,0:70:99:1966,210,0,1966,210,1966:0,0,29,41 ./. 20 10075509 . A *, . . DP=77 GT:AD:DP:GQ:PL:SB ./.:0,70,0:70:99:1966,210,0,1966,210,1966:0,0,29,41 ./. -20 10075510 . A . . . GT:DP:GQ:MIN_DP:PL ./.:80:0:80:0,0,0 ./. -20 10075511 . A . . END=10076249 GT:DP:GQ:MIN_DP:PL ./.:76:99:55:0,120,1800 ./. +20 10075510 . A . . END=10076249 GT:DP:GQ:MIN_DP:PL ./.:76:99:55:0,120,1800 ./. 20 10076250 . A G, . . BaseQRankSum=-3.386e+00;DP=79;ExcessHet=3.01;MQRankSum=-1.423e+00;RAW_MQ=278666.00;ReadPosRankSum=0.270 GT:AD:DP:GQ:PL:SB ./.:40,39,0:79:99:1136,0,1339,1257,1456,2712:14,26,20,19 ./. 20 10076251 . A . . END=10076338 GT:DP:GQ:MIN_DP:PL ./.:70:99:62:0,120,1800 ./. -20 10076339 . A G, . . BaseQRankSum=-6.900e-02;DP=72;ExcessHet=3.01;MQRankSum=-8.660e-01;RAW_MQ=256441.00;ReadPosRankSum=1.02 GT:AD:DP:GQ:PL:SB ./.:32,40,0:72:99:1338,0,1035,1435,1156,2590:12,20,18,22 ./. -20 10076340 . A . . END=10076398 GT:DP:GQ:MIN_DP:PL ./.:88:99:72:0,120,1800 ./. +20 10076339 . A G, . . BaseQRankSum=-6.900e-02;DP=72;ExcessHet=3.01;MQRankSum=-8.660e-01;RAW_MQ=256441.00;ReadPosRankSum=1.01 GT:AD:DP:GQ:PL:SB ./.:32,40,0:72:99:1338,0,1035,1435,1156,2590:12,20,18,22 ./. +20 10076340 . A . . END=10076398 GT:DP:GQ:MIN_DP:PL ./.:88:99:71:0,120,1800 ./. 20 10076399 . G A, . . BaseQRankSum=4.15;DP=94;ExcessHet=3.01;MQRankSum=0.00;RAW_MQ=338400.00;ReadPosRankSum=-1.058e+00 GT:AD:DP:GQ:PL:SB ./.:44,50,0:94:99:1836,0,1544,1969,1694,3663:22,22,22,28 ./. -20 10076400 . G . . END=10076988 GT:DP:GQ:MIN_DP:PL ./.:73:99:51:0,102,1530 ./. +20 10076400 . G . . END=10076988 GT:DP:GQ:MIN_DP:PL ./.:73:99:51:0,120,1800 ./. 20 10076989 . CAA C,CA,CAAA, . . BaseQRankSum=-6.250e-01;DP=75;ExcessHet=3.01;MQRankSum=-4.730e-01;RAW_MQ=253446.00;ReadPosRankSum=-9.180e-01 GT:AD:DP:GQ:PL:SB ./.:7,3,13,7,0:30:41:252,271,1146,41,448,376,147,276,0,361,322,712,423,318,705:4,3,12,11 ./. 20 10076990 . A *, . . DP=75 GT:AD:DP:GQ:PL:SB ./.:7,13,0:30:41:252,41,376,322,423,705:4,3,12,11 ./. 20 10076991 . A *, . . DP=75 GT:AD:DP:GQ:PL:SB ./.:7,13,0:30:41:252,41,376,322,423,705:4,3,12,11 ./. -20 10076992 . A . . END=10077007 GT:DP:GQ:MIN_DP:PL ./.:72:99:61:0,113,1800 ./. +20 10076992 . A . . END=10077007 GT:DP:GQ:MIN_DP:PL ./.:69:99:59:0,120,1800 ./. 20 10077008 . T A, . . BaseQRankSum=-1.806e+00;DP=51;ExcessHet=3.01;MQRankSum=-1.608e+00;RAW_MQ=175323.00;ReadPosRankSum=0.805 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:46,4,0:50:42:0|1:10077008_T_A:0,42,2066,148,2078,2184:18,28,4,0 ./. -20 10077009 . A . . . GT:DP:GQ:MIN_DP:PL ./.:54:99:54:0,120,1800 ./. +20 10077009 . A . . . GT:DP:GQ:MIN_DP:PL ./.:52:99:52:0,120,1800 ./. 20 10077010 . G A, . . BaseQRankSum=-1.841e+00;DP=53;ExcessHet=3.01;MQRankSum=-1.658e+00;RAW_MQ=182523.00;ReadPosRankSum=0.911 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:48,4,0:52:42:0|1:10077008_T_A:0,42,2066,148,2078,2184:18,30,4,0 ./. 20 10077011 . A . . END=10077751 GT:DP:GQ:MIN_DP:PL ./.:69:99:44:0,102,1654 ./. 20 10077752 . T C, . . BaseQRankSum=-6.503e+00;DP=79;ExcessHet=3.01;MQRankSum=0.00;RAW_MQ=284400.00;ReadPosRankSum=-3.520e-01 GT:AD:DP:GQ:PL:SB ./.:34,45,0:79:99:1374,0,1187,1477,1322,2799:16,18,16,29 ./. @@ -1492,7 +1182,7 @@ 20 10086284 . G . . END=10086618 GT:DP:GQ:MIN_DP:PL ./.:80:99:51:0,120,1800 ./. 20 10086619 . T A, . . BaseQRankSum=0.256;DP=70;ExcessHet=3.01;MQRankSum=-1.312e+00;RAW_MQ=249241.00;ReadPosRankSum=-7.600e-01 GT:AD:DP:GQ:PL:SB ./.:45,25,0:70:99:825,0,1603,961,1679,2639:18,27,9,16 ./. 20 10086620 . T . . END=10086852 GT:DP:GQ:MIN_DP:PL ./.:81:99:65:0,120,1800 ./. -20 10086853 . G A, . . BaseQRankSum=3.92;DP=73;ExcessHet=3.01;MQRankSum=-1.770e-01;RAW_MQ=257810.00;ReadPosRankSum=-1.000e-01 GT:AD:DP:GQ:PL:SB ./.:41,32,0:73:99:1031,0,1280,1154,1376,2530:21,20,17,15 ./. +20 10086853 . G A, . . BaseQRankSum=3.91;DP=73;ExcessHet=3.01;MQRankSum=-1.770e-01;RAW_MQ=257810.00;ReadPosRankSum=-1.000e-01 GT:AD:DP:GQ:PL:SB ./.:41,32,0:73:99:1031,0,1280,1154,1376,2530:21,20,17,15 ./. 20 10086854 . T . . END=10086953 GT:DP:GQ:MIN_DP:PL ./.:67:99:60:0,120,1800 ./. 20 10086954 . G A, . . BaseQRankSum=2.61;DP=68;ExcessHet=3.01;MQRankSum=0.00;RAW_MQ=244800.00;ReadPosRankSum=-5.340e-01 GT:AD:DP:GQ:PL:SB ./.:34,34,0:68:99:1124,0,1051,1226,1153,2380:16,18,21,13 ./. 20 10086955 . C . . END=10087229 GT:DP:GQ:MIN_DP:PL ./.:70:99:55:0,120,1800 ./. @@ -1501,27 +1191,29 @@ 20 10087394 . T G, . . BaseQRankSum=-2.340e+00;DP=84;ExcessHet=3.01;MQRankSum=1.21;RAW_MQ=299641.00;ReadPosRankSum=0.885 GT:AD:DP:GQ:PL:SB ./.:35,49,0:84:99:1717,0,1186,1823,1334,3156:21,14,24,25 ./. 20 10087395 . T . . END=10087753 GT:DP:GQ:MIN_DP:PL ./.:83:99:61:0,120,1800 ./. 20 10087754 . T G, . . BaseQRankSum=0.355;DP=79;ExcessHet=3.01;MQRankSum=2.19;RAW_MQ=288141.00;ReadPosRankSum=-5.510e-01 GT:AD:DP:GQ:PL:SB ./.:37,41,0:78:99:1376,0,1239,1488,1362,2849:23,14,24,17 ./. -20 10087755 . G . . END=10087803 GT:DP:GQ:MIN_DP:PL ./.:102:99:83:0,120,1800 ./. +20 10087755 . G . . END=10087803 GT:DP:GQ:MIN_DP:PL ./.:100:99:81:0,120,1800 ./. 20 10087804 . C T, . . BaseQRankSum=1.94;DP=100;ExcessHet=3.01;MQRankSum=2.62;RAW_MQ=369310.00;ReadPosRankSum=0.341 GT:AD:DP:GQ:PL:SB ./.:50,50,0:100:99:1648,0,1511,1797,1661,3458:33,17,28,22 ./. -20 10087805 . G . . END=10087819 GT:DP:GQ:MIN_DP:PL ./.:101:99:97:0,120,1800 ./. +20 10087805 . G . . END=10087819 GT:DP:GQ:MIN_DP:PL ./.:101:99:96:0,120,1800 ./. 20 10087820 . CAG C,CAGAG, . . BaseQRankSum=-1.974e+00;DP=99;ExcessHet=3.01;MQRankSum=0.422;RAW_MQ=362700.00;ReadPosRankSum=-3.570e-01 GT:AD:DP:GQ:PL:SB ./.:35,0,18,0:53:99:466,669,2577,0,1197,1168,661,2237,1238,2189:17,18,8,10 ./. 20 10087821 . A *, . . DP=99 GT:AD:DP:GQ:PL:SB ./.:35,0,0:53:99:466,669,2577,661,2237,2189:17,18,8,10 ./. 20 10087822 . G *, . . DP=99 GT:AD:DP:GQ:PL:SB ./.:35,0,0:53:99:466,669,2577,661,2237,2189:17,18,8,10 ./. -20 10087823 . A . . END=10087841 GT:DP:GQ:MIN_DP:PL ./.:87:99:83:0,120,1800 ./. -20 10087842 . A . . . GT:DP:GQ:MIN_DP:PL ./.:82:64:82:0,64,2763 ./. -20 10087843 . A . . END=10088062 GT:DP:GQ:MIN_DP:PL ./.:95:99:71:0,120,1800 ./. -20 10088063 . C T, . . BaseQRankSum=3.41;DP=93;ExcessHet=3.01;MQRankSum=0.515;RAW_MQ=327579.00;ReadPosRankSum=0.285 GT:AD:DP:GQ:PL:SB ./.:49,44,0:93:99:1446,0,1403,1592,1535,3128:24,25,18,26 ./. +20 10087823 . A . . END=10087841 GT:DP:GQ:MIN_DP:PL ./.:86:99:83:0,120,1800 ./. +20 10087842 . A . . . GT:DP:GQ:MIN_DP:PL ./.:82:0:82:0,0,2206 ./. +20 10087843 . A . . . GT:DP:GQ:MIN_DP:PL ./.:82:73:82:0,73,2973 ./. +20 10087844 . G . . . GT:DP:GQ:MIN_DP:PL ./.:80:0:80:0,0,2190 ./. +20 10087845 . A . . END=10088062 GT:DP:GQ:MIN_DP:PL ./.:95:99:71:0,120,1800 ./. +20 10088063 . C T, . . BaseQRankSum=3.40;DP=93;ExcessHet=3.01;MQRankSum=0.515;RAW_MQ=327579.00;ReadPosRankSum=0.285 GT:AD:DP:GQ:PL:SB ./.:49,44,0:93:99:1446,0,1403,1592,1535,3128:24,25,18,26 ./. 20 10088064 . G . . END=10088698 GT:DP:GQ:MIN_DP:PL ./.:87:99:60:0,120,1800 ./. 20 10088699 . C T, . . BaseQRankSum=3.80;DP=63;ExcessHet=3.01;MQRankSum=-3.140e+00;RAW_MQ=199738.00;ReadPosRankSum=-1.456e+00 GT:AD:DP:GQ:PL:SB ./.:36,26,0:62:99:805,0,1088,913,1166,2079:15,21,19,7 ./. -20 10088700 . G . . END=10088729 GT:DP:GQ:MIN_DP:PL ./.:54:99:52:0,120,1800 ./. +20 10088700 . G . . END=10088729 GT:DP:GQ:MIN_DP:PL ./.:53:99:51:0,120,1800 ./. 20 10088730 . G A, . . BaseQRankSum=0.224;DP=52;ExcessHet=3.01;MQRankSum=-4.839e+00;RAW_MQ=148358.00;ReadPosRankSum=0.581 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:29,23,0:52:99:0|1:10088730_G_A:1001,0,1152,1092,1231,2322:11,18,16,7 ./. -20 10088731 . G . . END=10088735 GT:DP:GQ:MIN_DP:PL ./.:56:99:56:0,120,1800 ./. +20 10088731 . G . . END=10088735 GT:DP:GQ:MIN_DP:PL ./.:55:99:55:0,120,1800 ./. 20 10088736 . A C, . . BaseQRankSum=0.282;DP=55;ExcessHet=3.01;MQRankSum=-5.169e+00;RAW_MQ=149682.00;ReadPosRankSum=0.573 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:28,27,0:55:99:0|1:10088730_G_A:1110,0,1194,1203,1281,2484:10,18,16,11 ./. -20 10088737 . C . . END=10088746 GT:DP:GQ:MIN_DP:PL ./.:57:99:53:0,120,1800 ./. +20 10088737 . C . . END=10088746 GT:DP:GQ:MIN_DP:PL ./.:56:99:53:0,120,1800 ./. 20 10088747 . A G, . . BaseQRankSum=-3.877e+00;DP=55;ExcessHet=3.01;MQRankSum=-4.907e+00;RAW_MQ=146239.00;ReadPosRankSum=9.000e-03 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:25,29,0:54:99:0|1:10088730_G_A:1140,0,995,1219,1085,2304:10,15,18,11 ./. -20 10088748 . G . . END=10088798 GT:DP:GQ:MIN_DP:PL ./.:50:99:46:0,109,1710 ./. +20 10088748 . G . . END=10088798 GT:DP:GQ:MIN_DP:PL ./.:49:99:46:0,114,1710 ./. 20 10088799 . G A, . . BaseQRankSum=5.50;DP=53;ExcessHet=3.01;MQRankSum=-2.498e+00;RAW_MQ=150040.00;ReadPosRankSum=1.08 GT:AD:DP:GQ:PL:SB ./.:22,31,0:53:99:1047,0,617,1114,711,1824:14,8,12,19 ./. -20 10088800 . T . . END=10088831 GT:DP:GQ:MIN_DP:PL ./.:54:99:50:0,108,1800 ./. +20 10088800 . T . . END=10088831 GT:DP:GQ:MIN_DP:PL ./.:54:99:50:0,113,1800 ./. 20 10088832 . G . . END=10088842 GT:DP:GQ:MIN_DP:PL ./.:53:63:36:0,63,945 ./. 20 10088843 . C . . . GT:DP:GQ:MIN_DP:PL ./.:25:16:25:0,16,759 ./. 20 10088844 . A . . . GT:DP:GQ:MIN_DP:PL ./.:25:37:25:0,37,718 ./. @@ -1540,17 +1232,11 @@ 20 10088867 . A . . END=10088870 GT:DP:GQ:MIN_DP:PL ./.:32:90:32:0,90,1350 ./. 20 10088871 . T . . END=10088894 GT:DP:GQ:MIN_DP:PL ./.:39:99:33:0,99,1294 ./. 20 10088895 . C T, . . BaseQRankSum=2.46;DP=41;ExcessHet=3.01;MQRankSum=0.577;RAW_MQ=134450.00;ReadPosRankSum=1.30 GT:AD:DP:GQ:PL:SB ./.:23,18,0:41:99:561,0,673,630,726,1356:10,13,8,10 ./. -20 10088896 . G . . END=10088963 GT:DP:GQ:MIN_DP:PL ./.:50:99:42:0,99,1485 ./. -20 10088964 . G . . . GT:DP:GQ:MIN_DP:PL ./.:68:61:68:0,61,1979 ./. -20 10088965 . T . . . GT:DP:GQ:MIN_DP:PL ./.:68:55:68:0,55,2178 ./. -20 10088966 . C . . END=10088967 GT:DP:GQ:MIN_DP:PL ./.:71:0:70:0,0,2081 ./. +20 10088896 . G . . END=10088967 GT:DP:GQ:MIN_DP:PL ./.:49:99:42:0,110,1709 ./. 20 10088968 . C CAAA, . . BaseQRankSum=0.552;DP=62;ExcessHet=3.01;MQRankSum=-4.750e+00;RAW_MQ=177808.00;ReadPosRankSum=2.42 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:30,23,0:53:99:0|1:10088968_C_CAAA:1213,0,1367,1310,1463,2773:16,14,14,9 ./. -20 10088969 . A . . . GT:DP:GQ:MIN_DP:PL ./.:72:0:72:0,0,1374 ./. -20 10088970 . A . . END=10088978 GT:DP:GQ:MIN_DP:PL ./.:76:99:75:0,120,1800 ./. -20 10088979 . A . . . GT:DP:GQ:MIN_DP:PL ./.:78:57:78:0,57,2694 ./. +20 10088969 . A . . END=10088979 GT:DP:GQ:MIN_DP:PL ./.:71:99:70:0,120,1800 ./. 20 10088980 . T C, . . BaseQRankSum=-1.585e+00;DP=68;ExcessHet=3.01;MQRankSum=-5.232e+00;RAW_MQ=176353.00;ReadPosRankSum=1.29 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:37,31,0:68:99:0|1:10088968_C_CAAA:1276,0,1627,1394,1729,3123:19,18,15,16 ./. -20 10088981 . A . . . GT:DP:GQ:MIN_DP:PL ./.:78:40:78:0,40,2558 ./. -20 10088982 . A . . END=10088984 GT:DP:GQ:MIN_DP:PL ./.:78:99:77:0,120,1800 ./. +20 10088981 . A . . END=10088984 GT:DP:GQ:MIN_DP:PL ./.:71:99:69:0,120,1800 ./. 20 10088985 . T C, . . BaseQRankSum=-1.920e-01;DP=74;ExcessHet=3.01;MQRankSum=-5.248e+00;RAW_MQ=191764.00;ReadPosRankSum=1.23 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:42,32,0:74:99:0|1:10088968_C_CAAA:1207,0,1729,1333,1826,3159:22,20,15,17 ./. 20 10088986 . A . . END=10088989 GT:DP:GQ:MIN_DP:PL ./.:82:99:81:0,120,1800 ./. 20 10088990 . A . . . GT:DP:GQ:MIN_DP:PL ./.:84:7:84:0,7,2771 ./. @@ -1566,17 +1252,13 @@ 20 10089043 . T . . . GT:DP:GQ:MIN_DP:PL ./.:76:79:76:0,79,2231 ./. 20 10089044 . G . . END=10089440 GT:DP:GQ:MIN_DP:PL ./.:82:99:74:0,120,1800 ./. 20 10089441 . A G, . . BaseQRankSum=-4.885e+00;DP=76;ExcessHet=3.01;MQRankSum=-9.480e-01;RAW_MQ=270841.00;ReadPosRankSum=-1.560e-01 GT:AD:DP:GQ:PL:SB ./.:37,39,0:76:99:1208,0,1313,1319,1430,2749:19,18,14,25 ./. -20 10089442 . G . . END=10089524 GT:DP:GQ:MIN_DP:PL ./.:82:99:74:0,120,1800 ./. +20 10089442 . G . . END=10089524 GT:DP:GQ:MIN_DP:PL ./.:81:99:74:0,120,1800 ./. 20 10089525 . C T, . . BaseQRankSum=5.86;DP=81;ExcessHet=3.01;MQRankSum=1.53;RAW_MQ=286610.00;ReadPosRankSum=0.862 GT:AD:DP:GQ:PL:SB ./.:38,43,0:81:99:1577,0,1088,1691,1217,2908:22,16,20,23 ./. -20 10089526 . G . . END=10090283 GT:DP:GQ:MIN_DP:PL ./.:73:99:55:0,108,1620 ./. -20 10090284 . A . . . GT:DP:GQ:MIN_DP:PL ./.:69:87:69:0,87,1305 ./. -20 10090285 . A . . END=10090287 GT:DP:GQ:MIN_DP:PL ./.:70:90:70:0,90,1350 ./. -20 10090288 . C . . . GT:DP:GQ:MIN_DP:PL ./.:70:78:70:0,78,1170 ./. +20 10089526 . G . . END=10090288 GT:DP:GQ:MIN_DP:PL ./.:72:99:55:0,111,1800 ./. 20 10090289 . CAA C,CA, . . BaseQRankSum=0.441;DP=80;ExcessHet=3.01;MQRankSum=1.39;RAW_MQ=287682.00;ReadPosRankSum=0.048 GT:AD:DP:GQ:PL:SB ./.:14,4,20,0:38:99:422,360,986,0,261,230,477,867,348,928:7,7,11,13 ./. 20 10090290 . A *, . . DP=80 GT:AD:DP:GQ:PL:SB ./.:14,20,0:38:99:422,0,230,477,348,928:7,7,11,13 ./. 20 10090291 . A *, . . DP=80 GT:AD:DP:GQ:PL:SB ./.:14,20,0:38:99:422,0,230,477,348,928:7,7,11,13 ./. -20 10090292 . A . . . GT:DP:GQ:MIN_DP:PL ./.:79:38:79:0,38,2756 ./. -20 10090293 . A . . END=10090763 GT:DP:GQ:MIN_DP:PL ./.:75:99:61:0,120,1800 ./. +20 10090292 . A . . END=10090763 GT:DP:GQ:MIN_DP:PL ./.:75:99:61:0,120,1800 ./. 20 10090764 . A G, . . BaseQRankSum=-2.659e+00;DP=63;ExcessHet=3.01;MQRankSum=0.00;RAW_MQ=226800.00;ReadPosRankSum=1.21 GT:AD:DP:GQ:PL:SB ./.:34,29,0:63:99:869,0,1207,972,1294,2265:12,22,14,15 ./. 20 10090765 . A . . END=10090969 GT:DP:GQ:MIN_DP:PL ./.:75:99:65:0,120,1800 ./. 20 10090970 . T C, . . BaseQRankSum=-4.840e-01;DP=69;ExcessHet=3.01;MQRankSum=1.51;RAW_MQ=243938.00;ReadPosRankSum=-7.200e-02 GT:AD:DP:GQ:PL:SB ./.:33,36,0:69:99:1286,0,1092,1384,1201,2585:20,13,20,16 ./. @@ -1586,15 +1268,11 @@ 20 10092415 . A G, . . BaseQRankSum=-6.731e+00;DP=101;ExcessHet=3.01;MQRankSum=0.00;RAW_MQ=363600.00;ReadPosRankSum=0.082 GT:AD:DP:GQ:PL:SB ./.:52,49,0:101:99:1664,0,1902,1820,2049,3870:27,25,24,25 ./. 20 10092416 . G . . END=10092926 GT:DP:GQ:MIN_DP:PL ./.:80:99:60:0,120,1800 ./. 20 10092927 . G T, . . BaseQRankSum=-2.507e+00;DP=73;ExcessHet=3.01;MQRankSum=-3.009e+00;RAW_MQ=257282.00;ReadPosRankSum=-2.200e-01 GT:AD:DP:GQ:PL:SB ./.:59,13,0:72:99:135,0,1864,310,1901,2211:43,16,0,13 ./. -20 10092928 . T . . END=10093558 GT:DP:GQ:MIN_DP:PL ./.:79:99:57:0,111,1665 ./. -20 10093559 . T . . END=10093562 GT:DP:GQ:MIN_DP:PL ./.:62:90:60:0,90,1350 ./. -20 10093563 . G . . END=10093566 GT:DP:GQ:MIN_DP:PL ./.:61:84:60:0,84,1260 ./. -20 10093567 . G . . . GT:DP:GQ:MIN_DP:PL ./.:59:75:59:0,75,1125 ./. +20 10092928 . T . . END=10093567 GT:DP:GQ:MIN_DP:PL ./.:79:99:57:0,120,1800 ./. 20 10093568 . GTT G,GT,GTTT, . . BaseQRankSum=0.426;DP=59;ExcessHet=3.01;MQRankSum=0.410;RAW_MQ=203561.00;ReadPosRankSum=1.26 GT:AD:DP:GQ:PL:SB ./.:17,4,17,4,0:42:99:364,329,1122,0,430,386,377,710,293,909,431,838,449,780,885:7,10,10,15 ./. 20 10093569 . T *, . . DP=59 GT:AD:DP:GQ:PL:SB ./.:17,17,0:42:99:364,0,386,431,449,885:7,10,10,15 ./. 20 10093570 . T *, . . DP=59 GT:AD:DP:GQ:PL:SB ./.:17,17,0:42:99:364,0,386,431,449,885:7,10,10,15 ./. -20 10093571 . T . . . GT:DP:GQ:MIN_DP:PL ./.:57:59:57:0,59,2043 ./. -20 10093572 . T . . END=10093922 GT:DP:GQ:MIN_DP:PL ./.:62:99:51:0,99,1485 ./. +20 10093571 . T . . END=10093922 GT:DP:GQ:MIN_DP:PL ./.:62:99:51:0,99,1485 ./. 20 10093923 . T A, . . BaseQRankSum=-6.670e-01;DP=67;ExcessHet=3.01;MQRankSum=0.358;RAW_MQ=234704.00;ReadPosRankSum=-1.583e+00 GT:AD:DP:GQ:PL:SB ./.:35,32,0:67:99:1104,0,1257,1209,1353,2563:18,17,15,17 ./. 20 10093924 . G . . END=10094250 GT:DP:GQ:MIN_DP:PL ./.:66:99:53:0,120,1800 ./. 20 10094251 . T A, . . BaseQRankSum=0.251;DP=62;ExcessHet=3.01;MQRankSum=0.00;RAW_MQ=223200.00;ReadPosRankSum=1.81 GT:AD:DP:GQ:PL:SB ./.:26,36,0:62:99:1299,0,781,1376,889,2265:10,16,23,13 ./. @@ -1603,7 +1281,7 @@ 20 10094583 . T . . END=10094773 GT:DP:GQ:MIN_DP:PL ./.:78:99:67:0,120,1800 ./. 20 10094774 . C T, . . BaseQRankSum=-7.840e-01;DP=75;ExcessHet=3.01;MQRankSum=0.962;RAW_MQ=267241.00;ReadPosRankSum=0.197 GT:AD:DP:GQ:PL:SB ./.:40,35,0:75:99:1065,0,1282,1185,1385,2570:24,16,21,14 ./. 20 10094775 . A . . END=10095431 GT:DP:GQ:MIN_DP:PL ./.:77:99:63:0,120,1800 ./. -20 10095432 . GTGATGATGA G, . . BaseQRankSum=1.27;DP=77;ExcessHet=3.01;MQRankSum=-4.431e+00;RAW_MQ=227748.00;ReadPosRankSum=0.396 GT:AD:DP:GQ:PL:SB ./.:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11 ./. +20 10095432 . GTGATGATGA G, . . BaseQRankSum=1.26;DP=77;ExcessHet=3.01;MQRankSum=-4.431e+00;RAW_MQ=227748.00;ReadPosRankSum=0.396 GT:AD:DP:GQ:PL:SB ./.:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11 ./. 20 10095433 . T *, . . DP=77 GT:AD:DP:GQ:PL:SB ./.:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11 ./. 20 10095434 . G *, . . DP=77 GT:AD:DP:GQ:PL:SB ./.:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11 ./. 20 10095435 . A *, . . DP=77 GT:AD:DP:GQ:PL:SB ./.:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11 ./. @@ -1613,8 +1291,7 @@ 20 10095439 . T *, . . DP=77 GT:AD:DP:GQ:PL:SB ./.:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11 ./. 20 10095440 . G *, . . DP=77 GT:AD:DP:GQ:PL:SB ./.:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11 ./. 20 10095441 . A *, . . DP=77 GT:AD:DP:GQ:PL:SB ./.:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11 ./. -20 10095442 . T . . . GT:DP:GQ:MIN_DP:PL ./.:71:0:71:0,0,1080 ./. -20 10095443 . G . . END=10095740 GT:DP:GQ:MIN_DP:PL ./.:81:99:64:0,120,1800 ./. +20 10095442 . T . . END=10095740 GT:DP:GQ:MIN_DP:PL ./.:80:99:64:0,120,1800 ./. 20 10095741 . A G, . . BaseQRankSum=-5.340e-01;DP=71;ExcessHet=3.01;MQRankSum=-2.313e+00;RAW_MQ=233528.00;ReadPosRankSum=-5.000e-01 GT:AD:DP:GQ:PL:SB ./.:36,34,0:70:99:1104,0,1233,1213,1335,2547:14,22,18,16 ./. 20 10095742 . G . . END=10096292 GT:DP:GQ:MIN_DP:PL ./.:73:99:63:0,120,1800 ./. 20 10096293 . C T, . . BaseQRankSum=4.66;DP=75;ExcessHet=3.01;MQRankSum=1.40;RAW_MQ=257261.00;ReadPosRankSum=-1.135e+00 GT:AD:DP:GQ:PL:SB ./.:37,38,0:75:99:1384,0,1258,1495,1372,2867:21,16,21,17 ./. @@ -1622,40 +1299,30 @@ 20 10096596 . C T, . . BaseQRankSum=2.73;DP=87;ExcessHet=3.01;MQRankSum=0.612;RAW_MQ=300461.00;ReadPosRankSum=-1.700e-01 GT:AD:DP:GQ:PL:SB ./.:40,47,0:87:99:1591,0,1273,1711,1414,3125:19,21,23,24 ./. 20 10096597 . T . . END=10096767 GT:DP:GQ:MIN_DP:PL ./.:90:99:75:0,120,1800 ./. 20 10096768 . A C, . . BaseQRankSum=-2.764e+00;DP=91;ExcessHet=3.01;MQRankSum=-1.609e+00;RAW_MQ=319323.00;ReadPosRankSum=0.613 GT:AD:DP:GQ:PL:SB ./.:42,49,0:91:99:1711,0,1452,1838,1600,3437:25,17,24,25 ./. -20 10096769 . A . . END=10096898 GT:DP:GQ:MIN_DP:PL ./.:78:99:65:0,99,1485 ./. +20 10096769 . A . . END=10096898 GT:DP:GQ:MIN_DP:PL ./.:78:99:65:0,120,1800 ./. 20 10096899 . G T, . . BaseQRankSum=2.76;DP=79;ExcessHet=3.01;MQRankSum=-1.387e+00;RAW_MQ=279938.00;ReadPosRankSum=0.422 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:39,40,0:79:99:0|1:10096899_G_T:1643,0,1520,1764,1649,3413:19,20,12,28 ./. -20 10096900 . G . . END=10096904 GT:DP:GQ:MIN_DP:PL ./.:83:99:79:0,108,1620 ./. +20 10096900 . G . . END=10096904 GT:DP:GQ:MIN_DP:PL ./.:82:99:78:0,120,1800 ./. 20 10096905 . TA T, . . BaseQRankSum=-7.550e-01;DP=83;ExcessHet=3.01;MQRankSum=-1.677e+00;RAW_MQ=291579.00;ReadPosRankSum=0.461 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:40,43,0:83:99:0|1:10096899_G_T:1638,0,1623,1768,1752,3520:20,20,13,30 ./. 20 10096906 . A *, . . DP=83 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:40,43,0:83:99:0|1:10096899_G_T:1638,0,1623,1768,1752,3520:20,20,13,30 ./. -20 10096907 . A . . . GT:DP:GQ:MIN_DP:PL ./.:83:0:83:0,0,0 ./. -20 10096908 . T . . END=10096932 GT:DP:GQ:MIN_DP:PL ./.:85:99:83:0,120,1800 ./. +20 10096907 . A . . END=10096932 GT:DP:GQ:MIN_DP:PL ./.:84:99:82:0,120,1800 ./. 20 10096933 . G C, . . BaseQRankSum=-1.914e+00;DP=85;ExcessHet=3.01;MQRankSum=-1.802e+00;RAW_MQ=298779.00;ReadPosRankSum=0.334 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:44,41,0:85:99:0|1:10096933_G_C:1540,0,1770,1684,1896,3580:28,16,13,28 ./. -20 10096934 . T . . END=10096957 GT:DP:GQ:MIN_DP:PL ./.:91:99:87:0,120,1800 ./. +20 10096934 . T . . END=10096957 GT:DP:GQ:MIN_DP:PL ./.:90:99:86:0,120,1800 ./. 20 10096958 . G A, . . BaseQRankSum=2.84;DP=92;ExcessHet=3.01;MQRankSum=-1.701e+00;RAW_MQ=323979.00;ReadPosRankSum=-1.833e+00 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:45,47,0:92:99:0|1:10096933_G_C:1795,0,1629,1929,1773,3702:27,18,16,31 ./. 20 10096959 . G . . END=10097074 GT:DP:GQ:MIN_DP:PL ./.:92:99:84:0,120,1800 ./. 20 10097075 . T G, . . BaseQRankSum=-2.533e+00;DP=92;ExcessHet=3.01;MQRankSum=-1.389e+00;RAW_MQ=315628.00;ReadPosRankSum=0.082 GT:AD:DP:GQ:PL:SB ./.:44,48,0:92:99:1474,0,1482,1606,1626,3232:18,26,26,22 ./. -20 10097076 . A . . END=10097100 GT:DP:GQ:MIN_DP:PL ./.:92:99:79:0,99,1485 ./. +20 10097076 . A . . END=10097100 GT:DP:GQ:MIN_DP:PL ./.:91:99:77:0,120,1800 ./. 20 10097101 . C CTTT,CTTTT, . . BaseQRankSum=-1.134e+00;DP=76;ExcessHet=3.01;MQRankSum=-2.428e+00;RAW_MQ=252294.00;ReadPosRankSum=2.09 GT:AD:DP:GQ:PL:SB ./.:34,26,4,0:64:99:1129,0,1306,558,1324,2012,982,1430,2052,2377:22,12,15,15 ./. -20 10097102 . T . . . GT:DP:GQ:MIN_DP:PL ./.:77:0:77:0,0,200 ./. -20 10097103 . T . . END=10097435 GT:DP:GQ:MIN_DP:PL ./.:70:99:60:0,99,1485 ./. +20 10097102 . T . . END=10097435 GT:DP:GQ:MIN_DP:PL ./.:70:99:60:0,120,1800 ./. 20 10097436 . CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT C, . . BaseQRankSum=1.82;DP=89;ExcessHet=3.01;MQRankSum=-6.464e+00;RAW_MQ=262143.00;ReadPosRankSum=-3.097e+00 GT:AD:DP:GQ:PL:SB ./.:57,32,0:89:99:1092,0,2241,1263,2338,3601:23,34,11,21 ./. 20 10097437 . TTTTC *,T, . . DP=76;ExcessHet=3.01;RAW_MQ=217330.00 GT:AD:DP:GQ:PL:SB ./.:0,32,23,0:55:99:2127,940,1799,1195,0,1125,2201,1453,1262,2642:0,0,16,39 ./. 20 10097438 . T *, . . DP=76 GT:AD:DP:GQ:PL:SB ./.:0,23,0:55:99:2127,1195,1125,2201,1262,2642:0,0,16,39 ./. 20 10097439 . T *, . . DP=76 GT:AD:DP:GQ:PL:SB ./.:0,23,0:55:99:2127,1195,1125,2201,1262,2642:0,0,16,39 ./. 20 10097440 . T *, . . DP=76 GT:AD:DP:GQ:PL:SB ./.:0,23,0:55:99:2127,1195,1125,2201,1262,2642:0,0,16,39 ./. 20 10097441 . C *, . . DP=76 GT:AD:DP:GQ:PL:SB ./.:0,23,0:55:99:2127,1195,1125,2201,1262,2642:0,0,16,39 ./. -20 10097442 . T . . . GT:DP:GQ:MIN_DP:PL ./.:63:0:63:0,0,698 ./. -20 10097443 . T . . END=10097445 GT:DP:GQ:MIN_DP:PL ./.:63:75:63:0,75,1125 ./. -20 10097446 . T . . END=10097450 GT:DP:GQ:MIN_DP:PL ./.:64:81:63:0,81,1215 ./. -20 10097451 . T . . END=10097452 GT:DP:GQ:MIN_DP:PL ./.:63:90:61:0,90,1350 ./. -20 10097453 . C . . END=10097455 GT:DP:GQ:MIN_DP:PL ./.:63:71:62:0,71,2168 ./. -20 10097456 . T . . END=10097458 GT:DP:GQ:MIN_DP:PL ./.:64:0:61:0,0,1556 ./. -20 10097459 . T . . . GT:DP:GQ:MIN_DP:PL ./.:60:21:60:0,21,2116 ./. -20 10097460 . T . . . GT:DP:GQ:MIN_DP:PL ./.:61:24:61:0,24,2071 ./. -20 10097461 . C . . END=10097475 GT:DP:GQ:MIN_DP:PL ./.:61:0:58:0,0,1102 ./. +20 10097442 . T . . END=10097475 GT:DP:GQ:MIN_DP:PL ./.:78:0:63:0,0,557 ./. 20 10097476 . T . . . GT:DP:GQ:MIN_DP:PL ./.:66:11:66:0,11,2255 ./. 20 10097477 . C . . END=10097625 GT:DP:GQ:MIN_DP:PL ./.:69:99:45:0,109,1710 ./. -20 10097626 . C A, . . BaseQRankSum=1.09;DP=48;ExcessHet=3.01;MQRankSum=-1.331e+00;RAW_MQ=162820.00;ReadPosRankSum=1.02 GT:AD:DP:GQ:PL:SB ./.:28,20,0:48:99:655,0,957,739,1017,1757:8,20,8,12 ./. +20 10097626 . C A, . . BaseQRankSum=1.09;DP=48;ExcessHet=3.01;MQRankSum=-1.331e+00;RAW_MQ=162820.00;ReadPosRankSum=1.01 GT:AD:DP:GQ:PL:SB ./.:28,20,0:48:99:655,0,957,739,1017,1757:8,20,8,12 ./. 20 10097627 . T . . END=10097788 GT:DP:GQ:MIN_DP:PL ./.:60:99:49:0,120,1800 ./. 20 10097789 . T C, . . BaseQRankSum=-1.157e+00;DP=57;ExcessHet=3.01;MQRankSum=-2.805e+00;RAW_MQ=191405.00;ReadPosRankSum=0.220 GT:AD:DP:GQ:PL:SB ./.:34,23,0:57:99:717,0,1190,820,1260,2079:14,20,13,10 ./. 20 10097790 . C . . END=10097915 GT:DP:GQ:MIN_DP:PL ./.:69:99:42:0,108,1620 ./. @@ -1705,16 +1372,10 @@ 20 10098149 . T . . END=10098150 GT:DP:GQ:MIN_DP:PL ./.:34:90:33:0,90,1350 ./. 20 10098151 . A . . END=10098160 GT:DP:GQ:MIN_DP:PL ./.:33:83:31:0,83,1260 ./. 20 10098161 . A . . END=10098176 GT:DP:GQ:MIN_DP:PL ./.:33:90:31:0,90,1350 ./. -20 10098177 . C . . END=10098185 GT:DP:GQ:MIN_DP:PL ./.:31:81:31:0,81,1215 ./. -20 10098186 . A . . END=10098199 GT:DP:GQ:MIN_DP:PL ./.:29:72:27:0,72,1080 ./. -20 10098200 . C . . END=10098203 GT:DP:GQ:MIN_DP:PL ./.:28:60:28:0,60,900 ./. -20 10098204 . G . . . GT:DP:GQ:MIN_DP:PL ./.:28:48:28:0,48,720 ./. -20 10098205 . T . . END=10098206 GT:DP:GQ:MIN_DP:PL ./.:28:45:28:0,45,675 ./. -20 10098207 . T . . END=10098208 GT:DP:GQ:MIN_DP:PL ./.:28:42:27:0,42,630 ./. -20 10098209 . T . . END=10098214 GT:DP:GQ:MIN_DP:PL ./.:24:36:24:0,36,540 ./. -20 10098215 . T . . END=10098216 GT:DP:GQ:MIN_DP:PL ./.:22:33:21:0,33,495 ./. -20 10098217 . T . . . GT:DP:GQ:MIN_DP:PL ./.:21:27:21:0,27,405 ./. -20 10098218 . G . . . GT:DP:GQ:MIN_DP:PL ./.:21:22:21:0,22,768 ./. +20 10098177 . C . . END=10098197 GT:DP:GQ:MIN_DP:PL ./.:30:81:27:0,81,1116 ./. +20 10098198 . A . . END=10098203 GT:DP:GQ:MIN_DP:PL ./.:28:72:27:0,72,1080 ./. +20 10098204 . G . . END=10098216 GT:DP:GQ:MIN_DP:PL ./.:24:60:21:0,60,900 ./. +20 10098217 . T . . END=10098218 GT:DP:GQ:MIN_DP:PL ./.:21:54:21:0,54,810 ./. 20 10098219 . TATATATA T, . . BaseQRankSum=3.15;DP=21;ExcessHet=3.01;MQRankSum=-2.050e-01;RAW_MQ=65705.00;ReadPosRankSum=0.427 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:12,9,0:21:99:0|1:10098219_TATATATA_T:333,0,461,369,488,858:0,12,0,9 ./. 20 10098220 . A *, . . DP=21 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:12,9,0:21:99:0|1:10098219_TATATATA_T:333,0,461,369,488,858:0,12,0,9 ./. 20 10098221 . T *, . . DP=21 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:12,9,0:21:99:0|1:10098219_TATATATA_T:333,0,461,369,488,858:0,12,0,9 ./. @@ -1723,23 +1384,19 @@ 20 10098224 . A *, . . DP=21 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:12,9,0:21:99:0|1:10098219_TATATATA_T:333,0,461,369,488,858:0,12,0,9 ./. 20 10098225 . T *, . . DP=21 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:12,9,0:21:99:0|1:10098219_TATATATA_T:333,0,461,369,488,858:0,12,0,9 ./. 20 10098226 . A *, . . DP=21 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:12,9,0:21:99:0|1:10098219_TATATATA_T:333,0,461,369,488,858:0,12,0,9 ./. -20 10098227 . T . . . GT:DP:GQ:MIN_DP:PL ./.:18:0:18:0,0,86 ./. -20 10098228 . T . . . GT:DP:GQ:MIN_DP:PL ./.:18:14:18:0,14,662 ./. -20 10098229 . A . . . GT:DP:GQ:MIN_DP:PL ./.:18:21:18:0,21,315 ./. -20 10098230 . T . . . GT:DP:GQ:MIN_DP:PL ./.:18:16:18:0,16,657 ./. -20 10098231 . A . . . GT:DP:GQ:MIN_DP:PL ./.:18:19:18:0,19,656 ./. -20 10098232 . T . . . GT:DP:GQ:MIN_DP:PL ./.:17:11:17:0,11,615 ./. -20 10098233 . A . . END=10098236 GT:DP:GQ:MIN_DP:PL ./.:15:21:12:0,21,315 ./. +20 10098227 . T . . END=10098228 GT:DP:GQ:MIN_DP:PL ./.:18:30:18:0,30,450 ./. +20 10098229 . A . . END=10098236 GT:DP:GQ:MIN_DP:PL ./.:17:21:13:0,21,315 ./. 20 10098237 . A T, . . BaseQRankSum=6.000e-03;DP=13;ExcessHet=3.01;MQRankSum=-1.742e+00;RAW_MQ=37064.00;ReadPosRankSum=0.277 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:6,7,0:13:99:0|1:10098219_TATATATA_T:273,0,273,294,294,588:0,6,0,7 ./. -20 10098238 . A . . END=10098244 GT:DP:GQ:MIN_DP:PL ./.:10:21:8:0,21,315 ./. -20 10098245 . T . . END=10098248 GT:DP:GQ:MIN_DP:PL ./.:9:24:9:0,24,360 ./. -20 10098249 . A . . END=10098255 GT:DP:GQ:MIN_DP:PL ./.:8:18:8:0,18,270 ./. +20 10098238 . A . . END=10098244 GT:DP:GQ:MIN_DP:PL ./.:10:21:9:0,21,315 ./. +20 10098245 . T . . END=10098248 GT:DP:GQ:MIN_DP:PL ./.:10:24:10:0,24,360 ./. +20 10098249 . A . . END=10098250 GT:DP:GQ:MIN_DP:PL ./.:10:18:9:0,18,270 ./. +20 10098251 . A . . END=10098255 GT:DP:GQ:MIN_DP:PL ./.:8:15:8:0,15,225 ./. 20 10098256 . T . . END=10098264 GT:DP:GQ:MIN_DP:PL ./.:8:9:6:0,9,135 ./. 20 10098265 . T C, . . BaseQRankSum=1.83;DP=6;ExcessHet=3.01;MQRankSum=-1.834e+00;RAW_MQ=10564.00;ReadPosRankSum=0.00 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:2,4,0:6:59:0|1:10098219_TATATATA_T:162,0,59,168,71,239:0,2,0,4 ./. -20 10098266 . A . . END=10098276 GT:DP:GQ:MIN_DP:PL ./.:4:9:3:0,9,121 ./. -20 10098277 . T . . END=10098279 GT:DP:GQ:MIN_DP:PL ./.:3:6:3:0,6,90 ./. -20 10098280 . A . . END=10098296 GT:DP:GQ:MIN_DP:PL ./.:4:9:3:0,9,114 ./. -20 10098297 . A . . END=10098307 GT:DP:GQ:MIN_DP:PL ./.:3:6:2:0,6,86 ./. +20 10098266 . A . . END=10098272 GT:DP:GQ:MIN_DP:PL ./.:4:9:4:0,9,135 ./. +20 10098273 . A . . END=10098279 GT:DP:GQ:MIN_DP:PL ./.:3:6:3:0,6,90 ./. +20 10098280 . A . . END=10098290 GT:DP:GQ:MIN_DP:PL ./.:4:9:3:0,9,126 ./. +20 10098291 . A . . END=10098307 GT:DP:GQ:MIN_DP:PL ./.:3:6:2:0,6,86 ./. 20 10098308 . AAT A, . . DP=2;ExcessHet=3.01;RAW_MQ=7200.00 GT:AD:DP:GQ:PL:SB ./.:2,0,0:2:6:0,6,81,6,81,81:0,2,0,0 ./. 20 10098309 . A *, . . DP=2 GT:AD:DP:GQ:PL:SB ./.:2,0,0:2:6:0,6,81,6,81,81:0,2,0,0 ./. 20 10098310 . T *, . . DP=2 GT:AD:DP:GQ:PL:SB ./.:2,0,0:2:6:0,6,81,6,81,81:0,2,0,0 ./. @@ -1749,9 +1406,8 @@ 20 10098330 . A . . END=10098343 GT:DP:GQ:MIN_DP:PL ./.:4:9:4:0,9,135 ./. 20 10098344 . A . . . GT:DP:GQ:MIN_DP:PL ./.:4:0:4:0,0,1 ./. 20 10098345 . T . . END=10098350 GT:DP:GQ:MIN_DP:PL ./.:3:9:3:0,9,125 ./. -20 10098351 . T . . END=10098357 GT:DP:GQ:MIN_DP:PL ./.:3:6:3:0,6,90 ./. -20 10098358 . T . . END=10098359 GT:DP:GQ:MIN_DP:PL ./.:3:3:3:0,3,45 ./. -20 10098360 . A . . END=10098380 GT:DP:GQ:MIN_DP:PL ./.:1:0:1:0,0,0 ./. +20 10098351 . T . . END=10098360 GT:DP:GQ:MIN_DP:PL ./.:3:3:3:0,3,45 ./. +20 10098361 . T . . END=10098380 GT:DP:GQ:MIN_DP:PL ./.:1:0:1:0,0,0 ./. 20 10098381 . T . . END=10098454 GT:DP:GQ:MIN_DP:PL ./.:1:3:1:0,3,37 ./. 20 10098455 . A . . END=10098551 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./. 20 10098552 . T . . END=10098637 GT:DP:GQ:MIN_DP:PL ./.:1:3:1:0,3,40 ./. @@ -1800,24 +1456,21 @@ 20 10098821 . T . . END=10098823 GT:DP:GQ:MIN_DP:PL ./.:17:51:17:0,51,677 ./. 20 10098824 . A . . END=10098826 GT:DP:GQ:MIN_DP:PL ./.:18:54:18:0,54,705 ./. 20 10098827 . T . . . GT:DP:GQ:MIN_DP:PL ./.:19:57:19:0,57,752 ./. -20 10098828 . T . . END=10098857 GT:DP:GQ:MIN_DP:PL ./.:25:60:20:0,60,799 ./. -20 10098858 . G . . . GT:DP:GQ:MIN_DP:PL ./.:24:57:24:0,57,855 ./. +20 10098828 . T . . END=10098835 GT:DP:GQ:MIN_DP:PL ./.:21:60:20:0,60,799 ./. +20 10098836 . G . . END=10098841 GT:DP:GQ:MIN_DP:PL ./.:24:72:24:0,72,906 ./. +20 10098842 . C . . . GT:DP:GQ:MIN_DP:PL ./.:24:69:24:0,69,1035 ./. +20 10098843 . A . . END=10098858 GT:DP:GQ:MIN_DP:PL ./.:26:72:24:0,72,990 ./. 20 10098859 . G . . . GT:DP:GQ:MIN_DP:PL ./.:24:29:24:0,29,851 ./. -20 10098860 . T . . END=10098861 GT:DP:GQ:MIN_DP:PL ./.:24:57:23:0,57,855 ./. -20 10098862 . T . . . GT:DP:GQ:MIN_DP:PL ./.:25:60:25:0,60,900 ./. -20 10098863 . G . . END=10098867 GT:DP:GQ:MIN_DP:PL ./.:25:57:25:0,57,855 ./. -20 10098868 . C . . . GT:DP:GQ:MIN_DP:PL ./.:25:54:25:0,54,810 ./. -20 10098869 . G . . END=10098870 GT:DP:GQ:MIN_DP:PL ./.:27:60:27:0,60,900 ./. -20 10098871 . C . . END=10098873 GT:DP:GQ:MIN_DP:PL ./.:29:57:28:0,57,855 ./. -20 10098874 . A . . . GT:DP:GQ:MIN_DP:PL ./.:30:54:30:0,54,810 ./. -20 10098875 . C . . END=10098876 GT:DP:GQ:MIN_DP:PL ./.:30:48:30:0,48,720 ./. -20 10098877 . G . . END=10098880 GT:DP:GQ:MIN_DP:PL ./.:31:45:30:0,45,675 ./. -20 10098881 . C . . . GT:DP:GQ:MIN_DP:PL ./.:31:48:31:0,48,720 ./. -20 10098882 . C . . END=10098883 GT:DP:GQ:MIN_DP:PL ./.:32:51:32:0,51,765 ./. -20 10098884 . C . . . GT:DP:GQ:MIN_DP:PL ./.:32:48:32:0,48,720 ./. +20 10098860 . T . . . GT:DP:GQ:MIN_DP:PL ./.:23:69:23:0,69,881 ./. +20 10098861 . G . . END=10098868 GT:DP:GQ:MIN_DP:PL ./.:25:72:24:0,72,960 ./. +20 10098869 . G . . END=10098877 GT:DP:GQ:MIN_DP:PL ./.:29:81:27:0,81,902 ./. +20 10098878 . C . . . GT:DP:GQ:MIN_DP:PL ./.:30:78:30:0,78,1170 ./. +20 10098879 . A . . END=10098881 GT:DP:GQ:MIN_DP:PL ./.:31:81:31:0,81,1215 ./. +20 10098882 . C . . . GT:DP:GQ:MIN_DP:PL ./.:32:60:32:0,60,1207 ./. +20 10098883 . T . . . GT:DP:GQ:MIN_DP:PL ./.:32:56:32:0,56,1237 ./. +20 10098884 . C . . . GT:DP:GQ:MIN_DP:PL ./.:32:84:32:0,84,1260 ./. 20 10098885 . C CA, . . BaseQRankSum=0.165;DP=31;ExcessHet=3.01;MQRankSum=-4.449e+00;RAW_MQ=77157.00;ReadPosRankSum=-1.073e+00 GT:AD:DP:GQ:PL:SB ./.:17,14,0:31:99:471,0,572,523,614,1137:16,1,13,1 ./. -20 10098886 . C . . . GT:DP:GQ:MIN_DP:PL ./.:31:0:31:0,0,240 ./. -20 10098887 . C . . END=10098890 GT:DP:GQ:MIN_DP:PL ./.:31:84:29:0,84,1260 ./. +20 10098886 . C . . END=10098890 GT:DP:GQ:MIN_DP:PL ./.:31:84:29:0,84,1260 ./. 20 10098891 . C . . . GT:DP:GQ:MIN_DP:PL ./.:32:90:32:0,90,1350 ./. 20 10098892 . G . . END=10098900 GT:DP:GQ:MIN_DP:PL ./.:31:81:30:0,81,1215 ./. 20 10098901 . T . . END=10098907 GT:DP:GQ:MIN_DP:PL ./.:29:72:28:0,72,1080 ./. @@ -1860,28 +1513,28 @@ 20 10099044 . A C, . . BaseQRankSum=-1.148e+00;DP=24;ExcessHet=3.01;MQRankSum=-4.418e+00;RAW_MQ=59851.00;ReadPosRankSum=-2.207e+00 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:15,9,0:24:99:0|1:10099029_T_C:363,0,768,420,798,1218:12,3,7,2 ./. 20 10099045 . C . . . GT:DP:GQ:MIN_DP:PL ./.:24:60:24:0,60,900 ./. 20 10099046 . T C, . . BaseQRankSum=-2.165e+00;DP=24;ExcessHet=3.01;MQRankSum=-4.418e+00;RAW_MQ=59851.00;ReadPosRankSum=-2.297e+00 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:15,9,0:24:99:0|1:10099029_T_C:333,0,603,378,630,1008:12,3,7,2 ./. -20 10099047 . G . . END=10099054 GT:DP:GQ:MIN_DP:PL ./.:26:63:25:0,63,945 ./. +20 10099047 . G . . END=10099052 GT:DP:GQ:MIN_DP:PL ./.:24:57:23:0,57,855 ./. +20 10099053 . G . . END=10099054 GT:DP:GQ:MIN_DP:PL ./.:23:54:23:0,54,810 ./. 20 10099055 . T C, . . BaseQRankSum=-1.554e+00;DP=23;ExcessHet=3.01;MQRankSum=-4.316e+00;RAW_MQ=58555.00;ReadPosRankSum=-1.970e+00 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:15,8,0:23:99:0|1:10099029_T_C:285,0,673,336,697,1033:11,4,6,2 ./. -20 10099056 . T . . END=10099059 GT:DP:GQ:MIN_DP:PL ./.:29:75:28:0,75,1125 ./. -20 10099060 . A . . END=10099065 GT:DP:GQ:MIN_DP:PL ./.:30:81:29:0,81,1118 ./. -20 10099066 . C . . END=10099068 GT:DP:GQ:MIN_DP:PL ./.:31:90:30:0,90,1172 ./. -20 10099069 . A . . . GT:DP:GQ:MIN_DP:PL ./.:32:82:32:0,82,1208 ./. -20 10099070 . G . . END=10099078 GT:DP:GQ:MIN_DP:PL ./.:32:90:32:0,90,1350 ./. +20 10099056 . T . . END=10099061 GT:DP:GQ:MIN_DP:PL ./.:24:60:23:0,60,900 ./. +20 10099062 . A . . END=10099067 GT:DP:GQ:MIN_DP:PL ./.:25:72:24:0,72,921 ./. +20 10099068 . G . . END=10099072 GT:DP:GQ:MIN_DP:PL ./.:27:81:27:0,81,1042 ./. +20 10099073 . T . . END=10099077 GT:DP:GQ:MIN_DP:PL ./.:27:78:27:0,78,1170 ./. +20 10099078 . G . . . GT:DP:GQ:MIN_DP:PL ./.:28:81:28:0,81,1215 ./. 20 10099079 . C T, . . BaseQRankSum=1.43;DP=29;ExcessHet=3.01;MQRankSum=-2.821e+00;RAW_MQ=78698.00;ReadPosRankSum=0.969 GT:AD:DP:GQ:PGT:PID:PL:SB ./.:23,6,0:29:99:0|1:10099029_T_C:145,0,886,217,904,1120:11,12,4,2 ./. -20 10099080 . G . . END=10099087 GT:DP:GQ:MIN_DP:PL ./.:36:90:35:0,90,1350 ./. -20 10099088 . C . . END=10099090 GT:DP:GQ:MIN_DP:PL ./.:37:87:37:0,87,1305 ./. -20 10099091 . C . . . GT:DP:GQ:MIN_DP:PL ./.:39:90:39:0,90,1350 ./. -20 10099092 . A . . END=10099098 GT:DP:GQ:MIN_DP:PL ./.:40:81:39:0,81,1215 ./. -20 10099099 . C . . END=10099105 GT:DP:GQ:MIN_DP:PL ./.:42:72:41:0,72,1080 ./. -20 10099106 . T . . END=10099108 GT:DP:GQ:MIN_DP:PL ./.:45:66:42:0,66,990 ./. -20 10099109 . T . . END=10099110 GT:DP:GQ:MIN_DP:PL ./.:48:72:47:0,72,1080 ./. +20 10099080 . G . . END=10099089 GT:DP:GQ:MIN_DP:PL ./.:30:81:29:0,81,1215 ./. +20 10099090 . A . . END=10099095 GT:DP:GQ:MIN_DP:PL ./.:34:90:31:0,90,1350 ./. +20 10099096 . A . . . GT:DP:GQ:MIN_DP:PL ./.:35:74:35:0,74,1310 ./. +20 10099097 . G . . END=10099100 GT:DP:GQ:MIN_DP:PL ./.:35:93:34:0,93,1395 ./. +20 10099101 . G . . END=10099105 GT:DP:GQ:MIN_DP:PL ./.:37:99:36:0,99,1485 ./. +20 10099106 . T . . . GT:DP:GQ:MIN_DP:PL ./.:36:96:36:0,96,1440 ./. +20 10099107 . T . . END=10099110 GT:DP:GQ:MIN_DP:PL ./.:41:99:39:0,99,1485 ./. 20 10099111 . T TTTTGTTTG, . . BaseQRankSum=-1.207e+00;DP=42;ExcessHet=3.01;MQRankSum=-4.071e+00;RAW_MQ=109737.00;ReadPosRankSum=-2.730e-01 GT:AD:DP:GQ:PL:SB ./.:22,13,0:35:99:694,0,802,763,859,1622:13,9,7,6 ./. -20 10099112 . T . . . GT:DP:GQ:MIN_DP:PL ./.:55:0:55:0,0,194 ./. -20 10099113 . T . . END=10099139 GT:DP:GQ:MIN_DP:PL ./.:63:99:57:0,120,1800 ./. +20 10099112 . T . . END=10099139 GT:DP:GQ:MIN_DP:PL ./.:57:99:49:0,114,1710 ./. 20 10099140 . G T, . . BaseQRankSum=-1.140e-01;DP=62;ExcessHet=3.01;MQRankSum=-2.469e+00;RAW_MQ=192512.00;ReadPosRankSum=0.338 GT:AD:DP:GQ:PL:SB ./.:30,32,0:62:99:1034,0,931,1122,1028,2150:18,12,22,10 ./. 20 10099141 . G . . END=10099189 GT:DP:GQ:MIN_DP:PL ./.:67:99:64:0,120,1800 ./. 20 10099190 . G T, . . BaseQRankSum=-3.400e-02;DP=65;ExcessHet=3.01;MQRankSum=-1.711e+00;RAW_MQ=215351.00;ReadPosRankSum=-1.260e+00 GT:AD:DP:GQ:PL:SB ./.:33,32,0:65:99:1063,0,1154,1162,1251,2413:21,12,21,11 ./. -20 10099191 . C . . END=10099219 GT:DP:GQ:MIN_DP:PL ./.:59:99:46:0,111,1665 ./. +20 10099191 . C . . END=10099219 GT:DP:GQ:MIN_DP:PL ./.:58:99:46:0,111,1665 ./. 20 10099220 . A G, . . BaseQRankSum=-1.664e+00;DP=45;ExcessHet=3.01;MQRankSum=-2.596e+00;RAW_MQ=149477.00;ReadPosRankSum=0.629 GT:AD:DP:GQ:PL:SB ./.:25,20,0:45:99:606,0,873,681,933,1614:15,10,11,9 ./. 20 10099221 . T . . END=10099229 GT:DP:GQ:MIN_DP:PL ./.:44:99:42:0,102,1530 ./. 20 10099230 . T . . END=10099233 GT:DP:GQ:MIN_DP:PL ./.:41:90:41:0,90,1350 ./. @@ -1897,9 +1550,9 @@ 20 10099272 . C . . END=10099534 GT:DP:GQ:MIN_DP:PL ./.:57:99:36:0,99,1485 ./. 20 10099535 . G A, . . BaseQRankSum=5.03;DP=65;ExcessHet=3.01;MQRankSum=-1.418e+00;RAW_MQ=226251.00;ReadPosRankSum=-7.770e-01 GT:AD:DP:GQ:PL:SB ./.:26,39,0:65:99:1364,0,686,1442,803,2245:17,9,22,17 ./. 20 10099536 . T . . END=10099564 GT:DP:GQ:MIN_DP:PL ./.:67:99:63:0,120,1800 ./. -20 10099565 . C T, . . BaseQRankSum=4.60;DP=69;ExcessHet=3.01;MQRankSum=-1.266e+00;RAW_MQ=243410.00;ReadPosRankSum=1.23 GT:AD:DP:GQ:PL:SB ./.:31,38,0:69:99:1375,0,994,1468,1108,2576:23,8,21,17 ./. +20 10099565 . C T, . . BaseQRankSum=4.59;DP=69;ExcessHet=3.01;MQRankSum=-1.266e+00;RAW_MQ=243410.00;ReadPosRankSum=1.23 GT:AD:DP:GQ:PL:SB ./.:31,38,0:69:99:1375,0,994,1468,1108,2576:23,8,21,17 ./. 20 10099566 . T . . END=10099754 GT:DP:GQ:MIN_DP:PL ./.:77:99:66:0,120,1800 ./. 20 10099755 . C T, . . BaseQRankSum=1.55;DP=65;ExcessHet=3.01;MQRankSum=-2.200e-02;RAW_MQ=229010.00;ReadPosRankSum=-2.300e-01 GT:AD:DP:GQ:PL:SB ./.:33,32,0:65:99:1127,0,1148,1226,1245,2470:20,13,17,15 ./. -20 10099756 . C . . END=10099831 GT:DP:GQ:MIN_DP:PL ./.:64:99:59:0,120,1800 ./. +20 10099756 . C . . END=10099831 GT:DP:GQ:MIN_DP:PL ./.:63:99:58:0,120,1800 ./. 20 10099832 . A G, . . BaseQRankSum=-4.563e+00;DP=72;ExcessHet=3.01;MQRankSum=0.869;RAW_MQ=250276.00;ReadPosRankSum=-1.023e+00 GT:AD:DP:GQ:PL:SB ./.:39,33,0:72:99:1102,0,1430,1220,1530,2749:22,17,14,19 ./. 20 10099833 . T . . END=10100000 GT:DP:GQ:MIN_DP:PL ./.:85:99:73:0,120,1800 ./. diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/GenomicsDBImport/expected.testGenomicsDBImportWithNonDiploidData.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/GenomicsDBImport/expected.testGenomicsDBImportWithNonDiploidData.vcf.idx index bf2033347c264651e3d9bd20b57acd7b35154e43..f7516a705a3e7d5968291faed25b365982e4a2e4 100644 GIT binary patch literal 40774 zcmeIyziSg=9DwmRRnb8ls-U2v;viJX+gvU`)InmC#-c{3Y3pDKY4Wx?n&!gY#X1N& z3ZmfPV8NoI5D=ug2!fNHMN!ekO{m~t92G=!{aVE0f8Y~1p7-8_mzS3}pW;yVOhhTQ zru$4fb#q8-J>nbB*Hh(IP;-o@XI*dFZr}Jlpd39{nN;n$p6*7K+O|EvXu^GmpS9g*FqbKg4ChKGa)o^HSm|UgQ&3jg zN=0K<+K$`($;839m0JC?)5UBln;TVDENMlp{zS^Q6A3GBTPj?jw6f@EW_T!57|1C* znM%as@n|v~OLa%~p9Kd_jTDM1W+##=+?Lg^UanW_>1L(gZVC6O)WSNY#`|PUIfw8B zxCh(=?g9S;9KZn_zyTb<0UW>q9KZn_zyTb<0UW>q9KZn_zyTb<0UW>q9KZn_zyTb< z0UW>q9KZn_zyTb<0UW>q9KZn_zyTb<0UW>q9KZn_zyTb<0UW>q9KZn_zyTb<0UW>q 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C . . END=10100467 GT:DP:GQ:MIN_DP:PL 0/0:65:99:52:0,120,1800 +20 10100468 . T C, 785.77 . BaseQRankSum=-2.901;DP=58;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.013;RAW_MQ=202964.00;ReadPosRankSum=-0.471 GT:AD:DP:GQ:PL:SB 0/1:33,25,0:58:99:814,0,901,889,976,1865:17,16,13,12 +20 10100469 . T . . END=10100538 GT:DP:GQ:MIN_DP:PL 0/0:59:99:55:0,120,1800 +20 10100539 . CTTCTAG C, 1156.73 . BaseQRankSum=0.701;DP=64;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.921;RAW_MQ=177502.00;ReadPosRankSum=-0.418 GT:AD:DP:GQ:PL:SB 0/1:31,31,0:62:99:1194,0,1460,1287,1553,2840:18,13,18,13 +20 10100546 . T . . END=10100844 GT:DP:GQ:MIN_DP:PL 0/0:66:99:50:0,120,1800 +20 10100845 . G C, 1215.77 . BaseQRankSum=-1.174;DP=73;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.961;RAW_MQ=237969.00;ReadPosRankSum=-0.913 GT:AD:DP:GQ:PL:SB 0/1:34,39,0:73:99:1244,0,1149,1346,1266,2613:16,18,19,20 +20 10100846 . A . . END=10101267 GT:DP:GQ:MIN_DP:PL 0/0:71:99:63:0,120,1800 +20 10101268 . TAA T, 956.73 . BaseQRankSum=-0.638;DP=71;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.479;RAW_MQ=250451.00;ReadPosRankSum=1.054 GT:AD:DP:GQ:PL:SB 0/1:29,37,0:66:99:994,0,1016,1082,1101,2182:17,12,21,16 +20 10101271 . A . . END=10101287 GT:DP:GQ:MIN_DP:PL 0/0:68:99:66:0,120,1800 +20 10101288 . A G, 887.77 . BaseQRankSum=-2.020;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.868;RAW_MQ=249220.00;ReadPosRankSum=-0.577 GT:AD:DP:GQ:PL:SB 0/1:33,39,0:72:99:916,0,1125,1015,1212,2228:19,14,25,14 +20 10101289 . G . . END=10101664 GT:DP:GQ:MIN_DP:PL 0/0:70:99:48:0,109,1800 +20 10101665 . A . . END=10101665 GT:DP:GQ:MIN_DP:PL 0/0:59:75:59:0,75,2146 +20 10101666 . G . . END=10101667 GT:DP:GQ:MIN_DP:PL 0/0:58:99:58:0,120,1800 +20 10101668 . T . . END=10101668 GT:DP:GQ:MIN_DP:PL 0/0:61:85:61:0,85,2097 +20 10101669 . A . . END=10101670 GT:DP:GQ:MIN_DP:PL 0/0:60:0:59:0,0,1841 +20 10101671 . T . . END=10101673 GT:DP:GQ:MIN_DP:PL 0/0:59:99:58:0,114,1800 +20 10101674 . TTGTGTGTGTGTG T,TTGTGTG,TTGTGTGTG,TTGTGTGTGTGTGTGTGTG,TTGTGTGTGTGTGTGTGTGTG, 1073.73 . DP=65;ExcessHet=3.0103;MLEAC=0,0,1,0,1,0;MLEAF=0.00,0.00,0.500,0.00,0.500,0.00;RAW_MQ=198519.00 GT:AD:DP:GQ:PL:SB 3/5:0,4,3,18,6,4,0:35:70:1111,980,1451,789,756,834,347,251,310,327,834,742,528,70,850,764,673,458,0,770,781,1118,1066,851,393,880,810,1203:0,0,21,14 +20 10101687 . T . . END=10101737 GT:DP:GQ:MIN_DP:PL 0/0:58:99:54:0,120,1800 +20 10101738 . G . . END=10101738 GT:DP:GQ:MIN_DP:PL 0/0:56:17:56:0,17,1795 +20 10101739 . T . . END=10101740 GT:DP:GQ:MIN_DP:PL 0/0:54:99:54:0,120,1800 +20 10101741 . G . . END=10101741 GT:DP:GQ:MIN_DP:PL 0/0:53:17:53:0,17,1696 +20 10101742 . C . . END=10101757 GT:DP:GQ:MIN_DP:PL 0/0:52:99:49:0,120,1800 +20 10101758 . G . . END=10101758 GT:DP:GQ:MIN_DP:PL 0/0:56:95:56:0,95,1986 +20 10101759 . T . . END=10101879 GT:DP:GQ:MIN_DP:PL 0/0:71:99:55:0,102,1779 +20 10101880 . A G, 1742.77 . BaseQRankSum=-1.776;DP=74;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.935;RAW_MQ=260882.00;ReadPosRankSum=-1.911 GT:AD:DP:GQ:PL:SB 0/1:23,51,0:74:99:1771,0,300,1808,452,2260:12,11,24,27 +20 10101881 . G . . END=10101911 GT:DP:GQ:MIN_DP:PL 0/0:78:99:71:0,120,1800 +20 10101912 . C T, 1254.77 . BaseQRankSum=1.124;DP=80;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.566;RAW_MQ=276964.00;ReadPosRankSum=-0.010 GT:AD:DP:GQ:PL:SB 0/1:30,50,0:80:99:1283,0,996,1374,1111,2484:17,13,29,21 +20 10101913 . A . . END=10102233 GT:DP:GQ:MIN_DP:PL 0/0:62:99:42:0,108,1620 +20 10102234 . C T, 833.77 . BaseQRankSum=-1.554;DP=47;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.682;RAW_MQ=158164.00;ReadPosRankSum=-0.217 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:19,28,0:47:99:0|1:10102234_C_T:862,0,2103,920,2170,3089:3,16,4,24 +20 10102235 . A . . END=10102246 GT:DP:GQ:MIN_DP:PL 0/0:48:99:46:0,120,1800 +20 10102247 . G A, 860.77 . BaseQRankSum=1.047;DP=47;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.758;RAW_MQ=158164.00;ReadPosRankSum=1.281 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:20,27,0:47:99:0|1:10102234_C_T:889,0,2176,950,2245,3195:3,17,4,23 +20 10102248 . T C, 832.77 . BaseQRankSum=-0.338;DP=49;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.694;RAW_MQ=165364.00;ReadPosRankSum=0.926 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:20,29,0:49:99:0|1:10102234_C_T:861,0,2179,921,2245,3166:3,17,4,25 +20 10102249 . A . . END=10102362 GT:DP:GQ:MIN_DP:PL 0/0:52:99:45:0,100,1800 +20 10102363 . A T, 811.77 . BaseQRankSum=0.024;DP=59;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.885;RAW_MQ=210169.00;ReadPosRankSum=0.754 GT:AD:DP:GQ:PL:SB 0/1:27,32,0:59:99:840,0,979,921,1052,1973:9,18,13,19 +20 10102364 . T . . END=10102529 GT:DP:GQ:MIN_DP:PL 0/0:54:99:40:0,105,1575 +20 10102530 . C T, 807.77 . BaseQRankSum=-1.280;DP=41;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.669;RAW_MQ=144841.00;ReadPosRankSum=0.633 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:14,27,0:41:99:0|1:10102530_C_T:836,0,1019,878,1082,1960:10,4,20,7 +20 10102531 . A G, 807.77 . BaseQRankSum=-3.192;DP=40;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.641;RAW_MQ=141241.00;ReadPosRankSum=0.159 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:13,27,0:40:99:0|1:10102530_C_T:836,0,1019,878,1082,1960:9,4,20,7 +20 10102532 . T . . END=10102726 GT:DP:GQ:MIN_DP:PL 0/0:56:99:40:0,105,1575 +20 10102727 . G T, 1125.77 . BaseQRankSum=3.846;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=234000.00;ReadPosRankSum=1.662 GT:AD:DP:GQ:PL:SB 0/1:31,34,0:65:99:1154,0,901,1247,1003,2250:18,13,21,13 +20 10102728 . T . . END=10102765 GT:DP:GQ:MIN_DP:PL 0/0:69:99:66:0,120,1800 +20 10102766 . C T, 0.03 . BaseQRankSum=-5.083;DP=67;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=241200.00;ReadPosRankSum=-1.874 GT:AD:DP:GQ:PL:SB 0/1:52,15,0:67:6:6,0,1929,163,1944,2107:28,24,9,6 +20 10102767 . T . . END=10102903 GT:DP:GQ:MIN_DP:PL 0/0:77:99:67:0,120,1800 +20 10102904 . C A, 1390.77 . BaseQRankSum=0.387;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.751;RAW_MQ=317641.00;ReadPosRankSum=0.423 GT:AD:DP:GQ:PL:SB 0/1:33,55,0:88:99:1419,0,1069,1518,1195,2713:17,16,25,30 +20 10102905 . C . . END=10103109 GT:DP:GQ:MIN_DP:PL 0/0:76:99:68:0,120,1800 +20 10103110 . G C, 1257.77 . BaseQRankSum=0.764;DP=74;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.570;RAW_MQ=259707.00;ReadPosRankSum=-0.243 GT:AD:DP:GQ:PL:SB 0/1:37,37,0:74:99:1286,0,1244,1397,1355,2753:17,20,16,21 +20 10103111 . A . . END=10103300 GT:DP:GQ:MIN_DP:PL 0/0:69:99:58:0,120,1800 +20 10103301 . C T, 771.77 . BaseQRankSum=2.466;DP=70;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.752;RAW_MQ=250900.00;ReadPosRankSum=-1.108 GT:AD:DP:GQ:PL:SB 0/1:46,24,0:70:99:800,0,1208,908,1280,2188:21,25,10,14 +20 10103302 . C . . END=10103319 GT:DP:GQ:MIN_DP:PL 0/0:65:99:59:0,120,1800 +20 10103320 . G C, 947.77 . BaseQRankSum=3.043;DP=61;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.017;RAW_MQ=218500.00;ReadPosRankSum=0.462 GT:AD:DP:GQ:PL:SB 0/1:31,30,0:61:99:976,0,964,1070,1054,2123:16,15,13,17 +20 10103321 . A . . END=10103332 GT:DP:GQ:MIN_DP:PL 0/0:60:99:57:0,120,1800 +20 10103333 . G A, 812.77 . BaseQRankSum=1.986;DP=58;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=208800.00;ReadPosRankSum=0.664 GT:AD:DP:GQ:PL:SB 0/1:34,24,0:58:99:841,0,892,919,965,1884:17,17,13,11 +20 10103334 . C . . END=10103551 GT:DP:GQ:MIN_DP:PL 0/0:63:99:53:0,120,1800 +20 10103552 . T G, 935.77 . BaseQRankSum=-2.887;DP=77;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.587;RAW_MQ=270891.00;ReadPosRankSum=0.251 GT:AD:DP:GQ:PL:SB 0/1:35,42,0:77:99:964,0,1223,1069,1316,2386:18,17,32,10 +20 10103553 . T . . END=10103679 GT:DP:GQ:MIN_DP:PL 0/0:71:99:65:0,120,1800 +20 10103680 . G T, 1016.77 . BaseQRankSum=-1.004;DP=78;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.131;RAW_MQ=270245.00;ReadPosRankSum=-1.659 GT:AD:DP:GQ:PL:SB 0/1:34,44,0:78:99:1045,0,1092,1145,1192,2337:17,17,21,23 +20 10103681 . C . . END=10103750 GT:DP:GQ:MIN_DP:PL 0/0:77:99:68:0,120,1800 +20 10103751 . G T, 1045.77 . BaseQRankSum=-0.427;DP=69;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.166;RAW_MQ=244910.00;ReadPosRankSum=0.887 GT:AD:DP:GQ:PL:SB 0/1:25,44,0:69:99:1074,0,786,1149,888,2037:12,13,18,26 +20 10103752 . T . . END=10103827 GT:DP:GQ:MIN_DP:PL 0/0:77:99:64:0,120,1800 +20 10103828 . T A, 978.77 . BaseQRankSum=-3.679;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.360;RAW_MQ=249715.00;ReadPosRankSum=-0.057 GT:AD:DP:GQ:PL:SB 0/1:30,42,0:72:99:1007,0,1077,1097,1174,2271:12,18,20,22 +20 10103829 . T . . END=10103848 GT:DP:GQ:MIN_DP:PL 0/0:76:99:72:0,120,1800 +20 10103849 . T C, 1085.77 . BaseQRankSum=-4.981;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.373;RAW_MQ=260515.00;ReadPosRankSum=-0.452 GT:AD:DP:GQ:PL:SB 0/1:31,44,0:75:99:1114,0,1090,1207,1192,2399:13,18,20,24 +20 10103850 . G A, 1019.77 . BaseQRankSum=4.811;DP=77;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.037;RAW_MQ=264956.00;ReadPosRankSum=-0.251 GT:AD:DP:GQ:PL:SB 0/1:47,30,0:77:99:1048,0,1243,1156,1333,2489:22,25,13,17 +20 10103851 . G . . END=10104017 GT:DP:GQ:MIN_DP:PL 0/0:67:99:60:0,120,1800 +20 10104018 . C T, 1032.77 . BaseQRankSum=3.676;DP=71;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.798;RAW_MQ=250574.00;ReadPosRankSum=-1.212 GT:AD:DP:GQ:PL:SB 0/1:40,31,0:71:99:1061,0,914,1151,1007,2159:24,16,20,11 +20 10104019 . C . . END=10104351 GT:DP:GQ:MIN_DP:PL 0/0:79:99:61:0,120,1800 +20 10104352 . A G, 1261.77 . BaseQRankSum=0.450;DP=82;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.401;RAW_MQ=289646.00;ReadPosRankSum=-1.114 GT:AD:DP:GQ:PL:SB 0/1:45,37,0:82:99:1290,0,1028,1389,1139,2528:17,28,18,19 +20 10104353 . G . . END=10104592 GT:DP:GQ:MIN_DP:PL 0/0:83:99:56:0,120,1800 +20 10104593 . G C, 567.77 . BaseQRankSum=0.103;DP=58;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.809;RAW_MQ=205110.00;ReadPosRankSum=-0.220 GT:AD:DP:GQ:PL:SB 0/1:38,19,0:57:99:596,0,1044,686,1101,1787:18,20,7,12 +20 10104594 . A . . END=10104647 GT:DP:GQ:MIN_DP:PL 0/0:61:99:58:0,120,1800 +20 10104648 . AG A, 654.73 . BaseQRankSum=-0.116;DP=64;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.017;RAW_MQ=228945.00;ReadPosRankSum=-0.086 GT:AD:DP:GQ:PL:SB 0/1:40,23,0:63:99:692,0,998,786,1067,1852:14,26,7,16 +20 10104650 . G . . END=10104693 GT:DP:GQ:MIN_DP:PL 0/0:69:99:59:0,120,1800 +20 10104694 . T G, 1064.77 . BaseQRankSum=2.269;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.122;RAW_MQ=246100.00;ReadPosRankSum=-1.374 GT:AD:DP:GQ:PL:SB 0/1:37,31,0:68:99:1093,0,886,1174,979,2153:10,27,12,19 +20 10104695 . A . . END=10105065 GT:DP:GQ:MIN_DP:PL 0/0:67:99:43:0,100,1665 +20 10105066 . GA G, 567.73 . BaseQRankSum=0.918;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.969;RAW_MQ=191104.00;ReadPosRankSum=0.010 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:33,17,0:50:99:0|1:10105066_GA_G:605,0,1357,686,1408,2094:19,14,6,11 +20 10105068 . C . . END=10105076 GT:DP:GQ:MIN_DP:PL 0/0:47:99:46:0,117,1755 +20 10105077 . G A, 562.77 . BaseQRankSum=4.061;DP=44;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.034;RAW_MQ=158404.00;ReadPosRankSum=-0.273 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:29,15,0:44:99:0|1:10105066_GA_G:591,0,1237,663,1285,1948:16,13,8,7 +20 10105078 . G . . END=10105094 GT:DP:GQ:MIN_DP:PL 0/0:43:99:41:0,111,1665 +20 10105095 . A T, 505.77 . BaseQRankSum=3.594;DP=48;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.032;RAW_MQ=172804.00;ReadPosRankSum=-0.525 GT:AD:DP:GQ:PL:SB 0/1:32,16,0:48:99:534,0,773,609,821,1430:21,11,9,7 +20 10105096 . T . . END=10105233 GT:DP:GQ:MIN_DP:PL 0/0:69:99:45:0,106,1710 +20 10105234 . A T, 886.77 . BaseQRankSum=-0.191;DP=69;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.181;RAW_MQ=246169.00;ReadPosRankSum=0.960 GT:AD:DP:GQ:PL:SB 0/1:41,28,0:69:99:915,0,1037,1008,1121,2130:20,21,13,15 +20 10105235 . A . . END=10105357 GT:DP:GQ:MIN_DP:PL 0/0:73:99:68:0,120,1800 +20 10105358 . A G, 916.77 . BaseQRankSum=-5.736;DP=71;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.754;RAW_MQ=254916.00;ReadPosRankSum=1.535 GT:AD:DP:GQ:PL:SB 0/1:27,44,0:71:99:945,0,928,1026,1029,2056:16,11,26,18 +20 10105359 . A . . END=10106403 GT:DP:GQ:MIN_DP:PL 0/0:73:99:47:0,120,1800 +20 10106404 . T C, 303.77 . BaseQRankSum=2.121;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.724;RAW_MQ=231241.00;ReadPosRankSum=0.688 GT:AD:DP:GQ:PL:SB 0/1:44,21,0:65:99:332,0,1535,464,1571,2035:29,15,10,11 +20 10106405 . A . . END=10106428 GT:DP:GQ:MIN_DP:PL 0/0:70:99:62:0,120,1800 +20 10106429 . C A, 972.77 . BaseQRankSum=3.316;DP=77;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.826;RAW_MQ=274441.00;ReadPosRankSum=-1.082 GT:AD:DP:GQ:PL:SB 0/1:47,30,0:77:99:1001,0,1122,1109,1212,2321:26,21,16,14 +20 10106430 . C . . END=10106801 GT:DP:GQ:MIN_DP:PL 0/0:79:99:68:0,120,1800 +20 10106802 . G A, 985.77 . BaseQRankSum=3.508;DP=73;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=262800.00;ReadPosRankSum=0.632 GT:AD:DP:GQ:PL:SB 0/1:44,29,0:73:99:1014,0,1097,1116,1185,2301:24,20,11,18 +20 10106803 . T . . END=10106857 GT:DP:GQ:MIN_DP:PL 0/0:68:99:63:0,120,1800 +20 10106858 . C G, 696.77 . BaseQRankSum=2.300;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=244800.00;ReadPosRankSum=0.110 GT:AD:DP:GQ:PL:SB 0/1:45,23,0:68:99:725,0,1074,829,1143,1972:23,22,10,13 +20 10106859 . A . . END=10106888 GT:DP:GQ:MIN_DP:PL 0/0:62:99:57:0,120,1800 +20 10106889 . C T, 609.77 . BaseQRankSum=1.898;DP=58;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=208800.00;ReadPosRankSum=-1.506 GT:AD:DP:GQ:PL:SB 0/1:37,21,0:58:99:638,0,898,725,961,1686:16,21,10,11 +20 10106890 . A . . END=10107046 GT:DP:GQ:MIN_DP:PL 0/0:67:99:52:0,120,1800 +20 10107047 . AG A, 1191.73 . BaseQRankSum=-0.967;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.694;RAW_MQ=269841.00;ReadPosRankSum=1.518 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:43,32,0:75:99:0|1:10107047_AG_A:1229,0,2352,1325,2448,3773:16,27,16,16 +20 10107049 . T . . END=10107051 GT:DP:GQ:MIN_DP:PL 0/0:73:99:73:0,120,1800 +20 10107052 . C T, 1167.77 . BaseQRankSum=3.104;DP=74;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.150;RAW_MQ=263641.00;ReadPosRankSum=1.732 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:43,31,0:74:99:0|1:10107047_AG_A:1196,0,2331,1292,2424,3717:16,27,16,15 +20 10107053 . T . . END=10107329 GT:DP:GQ:MIN_DP:PL 0/0:71:99:55:0,120,1800 +20 10107330 . G . . END=10107330 GT:DP:GQ:MIN_DP:PL 0/0:59:98:59:0,98,2194 +20 10107331 . G GT,GTT, 599.73 . BaseQRankSum=1.190;DP=58;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=2.262;RAW_MQ=215242.00;ReadPosRankSum=-1.300 GT:AD:DP:GQ:PL:SB 0/2:17,3,20,0:40:99:637,491,813,0,416,478,604,886,491,1023:9,8,14,9 +20 10107332 . T . . END=10107343 GT:DP:GQ:MIN_DP:PL 0/0:60:99:58:0,105,1575 +20 10107344 . C . . END=10107344 GT:DP:GQ:MIN_DP:PL 0/0:57:97:57:0,97,1999 +20 10107345 . C . . END=10107651 GT:DP:GQ:MIN_DP:PL 0/0:69:99:51:0,120,1800 +20 10107652 . T . . END=10107652 GT:DP:GQ:MIN_DP:PL 0/0:85:0:85:0,0,2774 +20 10107653 . G . . END=10107685 GT:DP:GQ:MIN_DP:PL 0/0:82:99:75:0,120,1800 +20 10107686 . C T, 1095.77 . BaseQRankSum=4.222;DP=76;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=273600.00;ReadPosRankSum=0.409 GT:AD:DP:GQ:PL:SB 0/1:43,33,0:76:99:1124,0,952,1220,1051,2272:26,17,26,7 +20 10107687 . A . . END=10108100 GT:DP:GQ:MIN_DP:PL 0/0:63:99:42:0,101,1647 +20 10108101 . A . . END=10108101 GT:DP:GQ:MIN_DP:PL 0/0:49:98:49:0,98,1736 +20 10108102 . C . . END=10108166 GT:DP:GQ:MIN_DP:PL 0/0:57:99:49:0,102,1755 +20 10108167 . A . . END=10108167 GT:DP:GQ:MIN_DP:PL 0/0:54:90:54:0,90,1993 +20 10108168 . A . . END=10108536 GT:DP:GQ:MIN_DP:PL 0/0:74:99:52:0,113,1800 +20 10108537 . C T, 0 . BaseQRankSum=-4.108;DP=61;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.536;RAW_MQ=217369.00;ReadPosRankSum=0.835 GT:AD:DP:GQ:PL:SB 0/0:49,12,0:61:47:0,47,1855,147,1864,1964:28,21,8,4 +20 10108538 . A . . END=10108753 GT:DP:GQ:MIN_DP:PL 0/0:80:99:61:0,120,1800 +20 10108754 . T G, 1383.77 . BaseQRankSum=1.266;DP=97;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.148;RAW_MQ=346441.00;ReadPosRankSum=-0.351 GT:AD:DP:GQ:PL:SB 0/1:56,41,0:97:99:1412,0,1397,1539,1521,3059:26,30,25,16 +20 10108755 . C . . END=10108865 GT:DP:GQ:MIN_DP:PL 0/0:95:99:71:0,120,1800 +20 10108866 . C T, 949.77 . BaseQRankSum=2.673;DP=76;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.813;RAW_MQ=270841.00;ReadPosRankSum=-0.749 GT:AD:DP:GQ:PL:SB 0/1:47,29,0:76:99:978,0,1192,1086,1279,2366:28,19,19,10 +20 10108867 . A . . END=10108940 GT:DP:GQ:MIN_DP:PL 0/0:65:99:56:0,120,1800 +20 10108941 . T C, 862.77 . BaseQRankSum=-3.128;DP=66;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.445;RAW_MQ=230379.00;ReadPosRankSum=-1.468 GT:AD:DP:GQ:PL:SB 0/1:27,39,0:66:99:891,0,870,971,961,1932:15,12,19,20 +20 10108942 . C . . END=10109708 GT:DP:GQ:MIN_DP:PL 0/0:81:99:65:0,120,1800 +20 10109709 . C G, 1043.77 . BaseQRankSum=-3.654;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=259200.00;ReadPosRankSum=0.553 GT:AD:DP:GQ:PL:SB 0/1:28,43,0:71:99:1072,0,966,1157,1065,2222:12,16,19,24 +20 10109710 . T . . END=10109723 GT:DP:GQ:MIN_DP:PL 0/0:71:99:68:0,120,1800 +20 10109724 . A T, 0.02 . BaseQRankSum=-5.114;DP=67;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.573;RAW_MQ=238969.00;ReadPosRankSum=1.715 GT:AD:DP:GQ:PL:SB 0/1:52,15,0:67:5:5,0,1942,162,1957,2119:18,34,8,7 +20 10109725 . T . . END=10110236 GT:DP:GQ:MIN_DP:PL 0/0:72:99:46:0,120,1800 +20 10110237 . G A, 0.01 . BaseQRankSum=-5.670;DP=90;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.561;RAW_MQ=321241.00;ReadPosRankSum=-1.884 GT:AD:DP:GQ:PL:SB 0/1:70,20,0:90:2:2,0,2592,213,2613,2826:29,41,8,12 +20 10110238 . A . . END=10110565 GT:DP:GQ:MIN_DP:PL 0/0:79:99:40:0,99,1485 +20 10110566 . A . . END=10110566 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1440 +20 10110567 . G . . END=10110725 GT:DP:GQ:MIN_DP:PL 0/0:57:99:39:0,102,1530 +20 10110726 . GT G, 896.73 . BaseQRankSum=0.455;DP=76;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.424;RAW_MQ=269910.00;ReadPosRankSum=-0.262 GT:AD:DP:GQ:PL:SB 0/1:25,44,0:69:99:934,0,638,1009,740,1749:10,15,17,27 +20 10110728 . T . . END=10111256 GT:DP:GQ:MIN_DP:PL 0/0:72:99:39:0,108,1410 +20 10111257 . T . . END=10111257 GT:DP:GQ:MIN_DP:PL 0/0:55:0:55:0,0,1626 +20 10111258 . T . . END=10111345 GT:DP:GQ:MIN_DP:PL 0/0:61:99:48:0,114,1710 +20 10111346 . A G, 801.77 . BaseQRankSum=0.202;DP=67;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.424;RAW_MQ=239741.00;ReadPosRankSum=0.668 GT:AD:DP:GQ:PL:SB 0/1:41,25,0:66:99:830,0,1077,926,1153,2079:21,20,13,12 +20 10111347 . C . . END=10111700 GT:DP:GQ:MIN_DP:PL 0/0:77:99:65:0,120,1800 +20 10111701 . C A, 1338.77 . BaseQRankSum=-1.698;DP=76;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=273600.00;ReadPosRankSum=1.850 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:30,46,0:76:99:0|1:10111701_C_A:1367,0,2289,1463,2398,3861:15,15,26,20 +20 10111702 . C . . END=10111704 GT:DP:GQ:MIN_DP:PL 0/0:78:99:76:0,120,1800 +20 10111705 . T A, 1354.77 . BaseQRankSum=-4.532;DP=77;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=277200.00;ReadPosRankSum=2.317 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:32,45,0:77:99:0|1:10111701_C_A:1383,0,2322,1482,2430,3912:16,16,24,21 +20 10111706 . T . . END=10111918 GT:DP:GQ:MIN_DP:PL 0/0:79:99:70:0,120,1800 +20 10111919 . A G, 1501.77 . BaseQRankSum=-1.208;DP=103;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.326;RAW_MQ=365810.00;ReadPosRankSum=-0.183 GT:AD:DP:GQ:PL:SB 0/1:40,63,0:103:99:1530,0,1315,1650,1458,3108:14,26,28,35 +20 10111920 . C . . END=10112057 GT:DP:GQ:MIN_DP:PL 0/0:70:99:51:0,120,1800 +20 10112058 . A . . END=10112058 GT:DP:GQ:MIN_DP:PL 0/0:54:0:54:0,0,1704 +20 10112059 . C . . END=10112390 GT:DP:GQ:MIN_DP:PL 0/0:63:99:44:0,108,1620 +20 10112391 . G T, 0.04 . BaseQRankSum=0.457;DP=48;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.595;RAW_MQ=170041.00;ReadPosRankSum=-0.699 GT:AD:DP:GQ:PL:SB 0/1:37,11,0:48:8:8,0,1252,119,1264,1383:28,9,4,7 +20 10112392 . C . . END=10112868 GT:DP:GQ:MIN_DP:PL 0/0:59:99:38:0,99,1485 +20 10112869 . T C, 547.77 . BaseQRankSum=-4.752;DP=51;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.226;RAW_MQ=179138.00;ReadPosRankSum=0.438 GT:AD:DP:GQ:PL:SB 0/1:22,29,0:51:99:576,0,744,642,810,1452:11,11,14,15 +20 10112870 . G . . END=10113192 GT:DP:GQ:MIN_DP:PL 0/0:56:99:44:0,100,1665 +20 10113193 . A . . END=10113193 GT:DP:GQ:MIN_DP:PL 0/0:44:96:44:0,96,1414 +20 10113194 . C . . END=10113406 GT:DP:GQ:MIN_DP:PL 0/0:65:99:46:0,120,1800 +20 10113407 . T G, 0 . BaseQRankSum=-4.113;DP=54;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.826;RAW_MQ=191641.00;ReadPosRankSum=0.895 GT:AD:DP:GQ:PL:SB 0/0:42,12,0:54:47:0,47,1422,125,1433,1511:10,32,12,0 +20 10113408 . G . . END=10113420 GT:DP:GQ:MIN_DP:PL 0/0:43:99:41:0,99,1620 +20 10113421 . G A, 461.77 . BaseQRankSum=3.029;DP=44;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=158400.00;ReadPosRankSum=0.198 GT:AD:DP:GQ:PL:SB 0/1:29,15,0:44:99:490,0,691,558,736,1295:9,20,4,11 +20 10113422 . G . . END=10113428 GT:DP:GQ:MIN_DP:PL 0/0:48:99:47:0,120,1800 +20 10113429 . T . . END=10113429 GT:DP:GQ:MIN_DP:PL 0/0:45:94:45:0,94,1559 +20 10113430 . A . . END=10113448 GT:DP:GQ:MIN_DP:PL 0/0:49:99:46:0,114,1701 +20 10113449 . T . . END=10113449 GT:DP:GQ:MIN_DP:PL 0/0:46:63:46:0,63,1464 +20 10113450 . A . . END=10113637 GT:DP:GQ:MIN_DP:PL 0/0:65:99:46:0,99,1800 +20 10113638 . G C, 1102.77 . BaseQRankSum=-1.819;DP=71;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=250082.00;ReadPosRankSum=-0.794 GT:AD:DP:GQ:PL:SB 0/1:36,35,0:71:99:1131,0,1206,1239,1312,2551:18,18,21,14 +20 10113639 . A . . END=10113724 GT:DP:GQ:MIN_DP:PL 0/0:80:99:69:0,120,1800 +20 10113725 . C . . END=10113725 GT:DP:GQ:MIN_DP:PL 0/0:82:0:82:0,0,2624 +20 10113726 . T . . END=10113829 GT:DP:GQ:MIN_DP:PL 0/0:77:99:65:0,120,1800 +20 10113830 . A . . END=10113830 GT:DP:GQ:MIN_DP:PL 0/0:55:94:55:0,94,1725 +20 10113831 . A . . END=10113837 GT:DP:GQ:MIN_DP:PL 0/0:55:99:49:0,120,1800 +20 10113838 . T . . END=10113838 GT:DP:GQ:MIN_DP:PL 0/0:40:49:40:0,49,1387 +20 10113839 . G . . END=10114044 GT:DP:GQ:MIN_DP:PL 0/0:80:99:43:0,103,1505 +20 10114045 . T A, 1213.77 . BaseQRankSum=-4.801;DP=92;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.321;RAW_MQ=323979.00;ReadPosRankSum=0.051 GT:AD:DP:GQ:PL:SB 0/1:39,53,0:92:99:1242,0,1360,1360,1481,2840:22,17,27,26 +20 10114046 . A . . END=10114704 GT:DP:GQ:MIN_DP:PL 0/0:77:99:65:0,120,1800 +20 10114705 . CA C, 590.73 . BaseQRankSum=0.632;DP=74;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.917;RAW_MQ=260710.00;ReadPosRankSum=-1.019 GT:AD:DP:GQ:PL:SB 0/1:36,29,0:65:99:628,0,555,709,643,1352:20,16,16,13 +20 10114707 . A . . END=10115096 GT:DP:GQ:MIN_DP:PL 0/0:80:99:69:0,120,1800 +20 10115097 . C G, 1110.77 . BaseQRankSum=0.399;DP=78;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.558;RAW_MQ=273579.00;ReadPosRankSum=-0.912 GT:AD:DP:GQ:PL:SB 0/1:44,34,0:78:99:1139,0,1099,1239,1201,2440:21,23,18,16 +20 10115098 . C . . END=10115324 GT:DP:GQ:MIN_DP:PL 0/0:78:99:64:0,120,1800 +20 10115325 . C T, 1375.77 . BaseQRankSum=-0.359;DP=85;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=306000.00;ReadPosRankSum=2.220 GT:AD:DP:GQ:PL:SB 0/1:42,43,0:85:99:1404,0,1415,1530,1544,3074:25,17,21,22 +20 10115326 . T . . END=10115598 GT:DP:GQ:MIN_DP:PL 0/0:76:99:65:0,120,1800 +20 10115599 . C A, 1080.77 . BaseQRankSum=0.608;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.071;RAW_MQ=267241.00;ReadPosRankSum=-1.150 GT:AD:DP:GQ:PL:SB 0/1:41,34,0:75:99:1109,0,1006,1199,1109,2308:20,21,14,20 +20 10115600 . A . . END=10119748 GT:DP:GQ:MIN_DP:PL 0/0:74:99:45:0,100,1620 +20 10119749 . G A, 1064.77 . BaseQRankSum=4.049;DP=87;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.256;RAW_MQ=310441.00;ReadPosRankSum=-1.610 GT:AD:DP:GQ:PL:SB 0/1:54,33,0:87:99:1093,0,1233,1216,1332,2548:25,29,17,16 +20 10119750 . G . . END=10120193 GT:DP:GQ:MIN_DP:PL 0/0:78:99:58:0,120,1800 +20 10120194 . T . . END=10120195 GT:DP:GQ:MIN_DP:PL 0/0:73:65:72:0,65,2496 +20 10120196 . A . . END=10120196 GT:DP:GQ:MIN_DP:PL 0/0:72:73:72:0,73,2432 +20 10120197 . T . . END=10120197 GT:DP:GQ:MIN_DP:PL 0/0:75:10:75:0,10,2527 +20 10120198 . T . . END=10120202 GT:DP:GQ:MIN_DP:PL 0/0:76:0:75:0,0,2127 +20 10120203 . C . . END=10120205 GT:DP:GQ:MIN_DP:PL 0/0:75:99:75:0,120,1800 +20 10120206 . C . . END=10120206 GT:DP:GQ:MIN_DP:PL 0/0:76:0:76:0,0,2227 +20 10120207 . C CAGGCCACAA, 1226.73 . BaseQRankSum=-1.117;DP=74;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.794;RAW_MQ=190448.00;ReadPosRankSum=-1.525 GT:AD:DP:GQ:PL:SB 0/1:33,40,0:73:99:1264,0,3255,1364,3354,4718:15,18,23,17 +20 10120208 . A . . END=10120210 GT:DP:GQ:MIN_DP:PL 0/0:78:99:77:0,120,1800 +20 10120211 . T . . END=10120214 GT:DP:GQ:MIN_DP:PL 0/0:81:0:80:0,0,2332 +20 10120215 . A . . END=10120215 GT:DP:GQ:MIN_DP:PL 0/0:81:99:81:0,120,1800 +20 10120216 . G . . END=10120218 GT:DP:GQ:MIN_DP:PL 0/0:82:0:80:0,0,2581 +20 10120219 . A . . END=10120219 GT:DP:GQ:MIN_DP:PL 0/0:82:5:82:0,5,2619 +20 10120220 . C . . END=10120220 GT:DP:GQ:MIN_DP:PL 0/0:79:65:79:0,65,2677 +20 10120221 . T . . END=10120221 GT:DP:GQ:MIN_DP:PL 0/0:79:70:79:0,70,2781 +20 10120222 . A . . END=10120222 GT:DP:GQ:MIN_DP:PL 0/0:80:94:80:0,94,2894 +20 10120223 . G . . END=10120853 GT:DP:GQ:MIN_DP:PL 0/0:70:99:54:0,120,1800 +20 10120854 . G T, 1143.77 . BaseQRankSum=5.607;DP=82;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.626;RAW_MQ=290738.00;ReadPosRankSum=-1.196 GT:AD:DP:GQ:PL:SB 0/1:36,46,0:82:99:1172,0,994,1280,1096,2376:22,14,25,21 +20 10120855 . G . . END=10121177 GT:DP:GQ:MIN_DP:PL 0/0:73:99:61:0,120,1800 +20 10121178 . C T, 997.77 . BaseQRankSum=-1.117;DP=73;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.137;RAW_MQ=257810.00;ReadPosRankSum=-1.392 GT:AD:DP:GQ:PL:SB 0/1:40,33,0:73:99:1026,0,959,1115,1057,2172:21,19,11,22 +20 10121179 . A . . END=10121201 GT:DP:GQ:MIN_DP:PL 0/0:82:99:74:0,120,1800 +20 10121202 . C A, 1279.77 . BaseQRankSum=-0.183;DP=88;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.718;RAW_MQ=309051.00;ReadPosRankSum=0.255 GT:AD:DP:GQ:PL:SB 0/1:47,41,0:88:99:1308,0,1621,1450,1743,3193:21,26,22,19 +20 10121203 . A . . END=10121271 GT:DP:GQ:MIN_DP:PL 0/0:83:99:76:0,120,1800 +20 10121272 . G A, 1441.77 . BaseQRankSum=-1.120;DP=91;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.745;RAW_MQ=320379.00;ReadPosRankSum=-0.866 GT:AD:DP:GQ:PL:SB 0/1:46,45,0:91:99:1470,0,1551,1609,1687,3295:23,23,22,23 +20 10121273 . C . . END=10121683 GT:DP:GQ:MIN_DP:PL 0/0:77:99:62:0,120,1800 +20 10121684 . C T, 1631.77 . BaseQRankSum=2.889;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.936;RAW_MQ=332041.00;ReadPosRankSum=-0.375 GT:AD:DP:GQ:PL:SB 0/1:44,48,0:92:99:1660,0,1400,1793,1545,3338:20,24,23,25 +20 10121685 . T . . END=10122274 GT:DP:GQ:MIN_DP:PL 0/0:78:99:53:0,120,1800 +20 10122275 . A G, 1062.77 . BaseQRankSum=-0.432;DP=82;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.181;RAW_MQ=292969.00;ReadPosRankSum=-1.808 GT:AD:DP:GQ:PL:SB 0/1:48,33,0:81:99:1091,0,1194,1199,1293,2492:27,21,19,14 +20 10122276 . G . . END=10122668 GT:DP:GQ:MIN_DP:PL 0/0:72:99:47:0,117,1684 +20 10122669 . G T, 821.77 . BaseQRankSum=0.689;DP=47;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.826;RAW_MQ=153629.00;ReadPosRankSum=-0.543 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:24,23,0:47:99:0|1:10122669_G_T:850,0,1660,922,1729,2651:15,9,8,15 +20 10122670 . G . . END=10122671 GT:DP:GQ:MIN_DP:PL 0/0:47:99:46:0,117,1755 +20 10122672 . A G, 821.77 . BaseQRankSum=-2.011;DP=47;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.826;RAW_MQ=153629.00;ReadPosRankSum=-0.821 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:24,23,0:47:99:0|1:10122669_G_T:850,0,1660,922,1729,2651:15,9,8,15 +20 10122673 . G . . END=10124074 GT:DP:GQ:MIN_DP:PL 0/0:73:99:46:0,101,1606 +20 10124075 . G C, 880.77 . BaseQRankSum=-0.229;DP=71;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.132;RAW_MQ=252841.00;ReadPosRankSum=-0.087 GT:AD:DP:GQ:PL:SB 0/1:32,39,0:71:99:909,0,1039,1005,1126,2131:16,16,13,26 +20 10124076 . C . . END=10124266 GT:DP:GQ:MIN_DP:PL 0/0:74:99:68:0,120,1800 +20 10124267 . C T, 1369.77 . BaseQRankSum=6.068;DP=77;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=277200.00;ReadPosRankSum=-0.857 GT:AD:DP:GQ:PL:SB 0/1:37,40,0:77:99:1398,0,1050,1509,1170,2679:13,24,16,24 +20 10124268 . G . . END=10126302 GT:DP:GQ:MIN_DP:PL 0/0:78:99:50:0,111,1665 +20 10126303 . GAAAA G,GA,GAA,GAAA, 74.73 . BaseQRankSum=-1.900;DP=76;ExcessHet=3.0103;MLEAC=0,0,0,1,0;MLEAF=0.00,0.00,0.00,0.500,0.00;MQRankSum=1.994;RAW_MQ=251528.00;ReadPosRankSum=-0.202 GT:AD:DP:GQ:PL:SB 0/4:22,2,3,8,8,0:43:41:112,172,1630,161,1236,1156,41,721,734,631,0,324,337,238,251,201,1058,1026,723,369,990:12,10,6,15 +20 10126308 . A . . END=10126323 GT:DP:GQ:MIN_DP:PL 0/0:76:99:70:0,120,1800 +20 10126324 . C . . END=10126324 GT:DP:GQ:MIN_DP:PL 0/0:70:69:70:0,69,2152 +20 10126325 . A . . END=10126397 GT:DP:GQ:MIN_DP:PL 0/0:79:99:63:0,120,1800 +20 10126398 . T A, 1520.77 . BaseQRankSum=2.482;DP=87;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.084;RAW_MQ=310969.00;ReadPosRankSum=0.181 GT:AD:DP:GQ:PL:SB 0/1:40,45,0:85:99:1549,0,1294,1669,1429,3098:21,19,28,17 +20 10126399 . C . . END=10128280 GT:DP:GQ:MIN_DP:PL 0/0:71:99:41:0,108,1620 +20 10128281 . C . . END=10128281 GT:DP:GQ:MIN_DP:PL 0/0:53:84:53:0,84,1778 +20 10128282 . G . . END=10128282 GT:DP:GQ:MIN_DP:PL 0/0:51:99:51:0,106,1409 +20 10128283 . C . . END=10128283 GT:DP:GQ:MIN_DP:PL 0/0:53:0:53:0,0,1619 +20 10128284 . A . . END=10128419 GT:DP:GQ:MIN_DP:PL 0/0:80:99:55:0,120,1800 +20 10128420 . T . . END=10128420 GT:DP:GQ:MIN_DP:PL 0/0:55:29:55:0,29,1749 +20 10128421 . C . . END=10128633 GT:DP:GQ:MIN_DP:PL 0/0:62:99:54:0,120,1800 +20 10128634 . T G, 984.77 . BaseQRankSum=-5.038;DP=77;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=277200.00;ReadPosRankSum=-2.073 GT:AD:DP:GQ:PL:SB 0/1:45,32,0:77:99:1013,0,1219,1115,1316,2431:14,31,10,22 +20 10128635 . T . . END=10128651 GT:DP:GQ:MIN_DP:PL 0/0:84:99:80:0,120,1800 +20 10128652 . T C, 3462.77 . DP=86;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=309600.00 GT:AD:DP:GQ:PL:SB 1/1:0,86,0:86:99:3491,258,0,3491,258,3491:0,0,26,60 +20 10128653 . A . . END=10129395 GT:DP:GQ:MIN_DP:PL 0/0:73:99:51:0,120,1800 +20 10129396 . A G, 1194.77 . BaseQRankSum=-0.195;DP=74;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=266400.00;ReadPosRankSum=0.584 GT:AD:DP:GQ:PL:SB 0/1:38,36,0:74:99:1223,0,1296,1337,1405,2742:15,23,18,18 +20 10129397 . C . . END=10129599 GT:DP:GQ:MIN_DP:PL 0/0:78:99:59:0,120,1800 +20 10129600 . A G, 3396.77 . DP=97;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=343682.00 GT:AD:DP:GQ:PL:SB 1/1:0,97,0:97:99:3425,290,0,3425,290,3425:0,0,43,54 +20 10129601 . T . . END=10130016 GT:DP:GQ:MIN_DP:PL 0/0:81:99:65:0,120,1800 +20 10130017 . G A, 3907.77 . DP=99;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=326051.00 GT:AD:DP:GQ:PL:SB 1/1:0,99,0:99:99:3936,298,0,3936,298,3936:0,0,55,44 +20 10130018 . A . . END=10130138 GT:DP:GQ:MIN_DP:PL 0/0:72:99:45:0,102,1795 +20 10130139 . G . . END=10130139 GT:DP:GQ:MIN_DP:PL 0/0:46:98:46:0,98,1738 +20 10130140 . A . . END=10130147 GT:DP:GQ:MIN_DP:PL 0/0:44:99:42:0,103,1620 +20 10130148 . C . . END=10130148 GT:DP:GQ:MIN_DP:PL 0/0:43:91:43:0,91,1606 +20 10130149 . A . . END=10130152 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,102,1530 +20 10130153 . T . . END=10130153 GT:DP:GQ:MIN_DP:PL 0/0:42:96:42:0,96,1440 +20 10130154 . G . . END=10130154 GT:DP:GQ:MIN_DP:PL 0/0:40:79:40:0,79,1488 +20 10130155 . A . . END=10130157 GT:DP:GQ:MIN_DP:PL 0/0:40:93:39:0,93,1395 +20 10130158 . T . . END=10130163 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,100,1530 +20 10130164 . A . . END=10130164 GT:DP:GQ:MIN_DP:PL 0/0:41:85:41:0,85,1590 +20 10130165 . A . . END=10130180 GT:DP:GQ:MIN_DP:PL 0/0:40:99:37:0,102,1530 +20 10130181 . T . . END=10130197 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1350 +20 10130198 . T . . END=10130248 GT:DP:GQ:MIN_DP:PL 0/0:42:99:35:0,99,1485 +20 10130249 . AACAC A,AAC, 1237.73 . BaseQRankSum=-0.893;DP=60;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;MQRankSum=-0.647;RAW_MQ=179055.00;ReadPosRankSum=0.532 GT:AD:DP:GQ:PL:SB 1/2:2,21,19,0:42:99:1275,565,609,572,0,470,1227,620,570,1239:1,1,9,31 +20 10130254 . A . . END=10130305 GT:DP:GQ:MIN_DP:PL 0/0:73:99:58:0,120,1800 +20 10130306 . A ATG, 1063.73 . BaseQRankSum=-1.446;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.621;RAW_MQ=228333.00;ReadPosRankSum=1.620 GT:AD:DP:GQ:PL:SB 0/1:34,34,0:68:99:1101,0,1095,1204,1197,2401:5,29,8,26 +20 10130307 . T . . END=10130344 GT:DP:GQ:MIN_DP:PL 0/0:70:99:62:0,120,1800 +20 10130345 . G GTA, 638.73 . BaseQRankSum=1.003;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.479;RAW_MQ=196871.00;ReadPosRankSum=-0.335 GT:AD:DP:GQ:PL:SB 0/1:28,20,0:48:99:676,0,680,739,743,1482:8,20,7,13 +20 10130346 . T . . END=10130447 GT:DP:GQ:MIN_DP:PL 0/0:47:99:40:0,102,1530 +20 10130448 . T . . END=10130448 GT:DP:GQ:MIN_DP:PL 0/0:41:91:41:0,91,1611 +20 10130449 . C . . END=10130459 GT:DP:GQ:MIN_DP:PL 0/0:43:99:41:0,102,1530 +20 10130460 . C . . END=10130460 GT:DP:GQ:MIN_DP:PL 0/0:40:83:40:0,83,1502 +20 10130461 . A . . END=10130466 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,105,1575 +20 10130467 . C . . END=10130467 GT:DP:GQ:MIN_DP:PL 0/0:44:90:44:0,90,1638 +20 10130468 . C . . END=10130485 GT:DP:GQ:MIN_DP:PL 0/0:43:99:38:0,99,1485 +20 10130486 . T . . END=10130489 GT:DP:GQ:MIN_DP:PL 0/0:40:96:39:0,96,1440 +20 10130490 . A . . END=10130496 GT:DP:GQ:MIN_DP:PL 0/0:37:99:35:0,102,1390 +20 10130497 . A . . END=10130499 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 +20 10130500 . T . . END=10130503 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 +20 10130504 . T . . END=10130507 GT:DP:GQ:MIN_DP:PL 0/0:37:93:35:0,93,1395 +20 10130508 . G . . END=10130548 GT:DP:GQ:MIN_DP:PL 0/0:38:99:35:0,99,1485 +20 10130549 . T . . END=10130550 GT:DP:GQ:MIN_DP:PL 0/0:39:96:38:0,96,1440 +20 10130551 . A . . END=10130556 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,102,1530 +20 10130557 . T . . END=10130563 GT:DP:GQ:MIN_DP:PL 0/0:40:90:39:0,90,1350 +20 10130564 . A . . END=10130572 GT:DP:GQ:MIN_DP:PL 0/0:37:99:35:0,99,1485 +20 10130573 . T . . END=10130575 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 +20 10130576 . T . . END=10130577 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,99,1485 +20 10130578 . T . . END=10130578 GT:DP:GQ:MIN_DP:PL 0/0:39:88:39:0,88,1481 +20 10130579 . C . . END=10130610 GT:DP:GQ:MIN_DP:PL 0/0:43:99:40:0,111,1665 +20 10130611 . C . . END=10130611 GT:DP:GQ:MIN_DP:PL 0/0:45:97:45:0,97,1751 +20 10130612 . T . . END=10130721 GT:DP:GQ:MIN_DP:PL 0/0:54:99:45:0,117,1755 +20 10130722 . G A, 1137.77 . BaseQRankSum=2.253;DP=60;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.229;RAW_MQ=193207.00;ReadPosRankSum=1.303 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:29,31,0:60:99:0|1:10130722_G_A:1166,0,1831,1253,1924,3177:12,17,21,10 +20 10130723 . T . . END=10130765 GT:DP:GQ:MIN_DP:PL 0/0:56:99:49:0,108,1620 +20 10130766 . T . . END=10130766 GT:DP:GQ:MIN_DP:PL 0/0:49:96:49:0,96,1440 +20 10130767 . ATGTATG A, 723.73 . BaseQRankSum=0.220;DP=45;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.326;RAW_MQ=131764.00;ReadPosRankSum=-1.040 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:20,25,0:45:99:0|1:10130722_G_A:761,0,1889,827,1949,2776:7,13,19,6 +20 10130774 . T . . END=10130776 GT:DP:GQ:MIN_DP:PL 0/0:37:90:36:0,90,1350 +20 10130777 . A . . END=10130785 GT:DP:GQ:MIN_DP:PL 0/0:35:81:32:0,81,1215 +20 10130786 . A . . END=10130796 GT:DP:GQ:MIN_DP:PL 0/0:29:72:26:0,72,1080 +20 10130797 . T . . END=10130799 GT:DP:GQ:MIN_DP:PL 0/0:27:60:26:0,60,900 +20 10130800 . G . . END=10130803 GT:DP:GQ:MIN_DP:PL 0/0:25:57:24:0,57,855 +20 10130804 . G . . END=10130804 GT:DP:GQ:MIN_DP:PL 0/0:24:54:24:0,54,810 +20 10130805 . T . . END=10130807 GT:DP:GQ:MIN_DP:PL 0/0:24:51:23:0,51,765 +20 10130808 . A . . END=10130809 GT:DP:GQ:MIN_DP:PL 0/0:24:48:24:0,48,720 +20 10130810 . G . . END=10130811 GT:DP:GQ:MIN_DP:PL 0/0:24:42:23:0,42,630 +20 10130812 . A . . END=10130813 GT:DP:GQ:MIN_DP:PL 0/0:21:39:19:0,39,585 +20 10130814 . A . . END=10130816 GT:DP:GQ:MIN_DP:PL 0/0:17:36:17:0,36,540 +20 10130817 . A . . END=10130818 GT:DP:GQ:MIN_DP:PL 0/0:17:24:17:0,24,360 +20 10130819 . A . . END=10130824 GT:DP:GQ:MIN_DP:PL 0/0:16:21:15:0,21,315 +20 10130825 . G . . END=10130827 GT:DP:GQ:MIN_DP:PL 0/0:14:18:11:0,18,270 +20 10130828 . T . . END=10130835 GT:DP:GQ:MIN_DP:PL 0/0:9:9:7:0,9,135 +20 10130836 . T . . END=10130837 GT:DP:GQ:MIN_DP:PL 0/0:7:6:7:0,6,90 +20 10130838 . T . . END=10130840 GT:DP:GQ:MIN_DP:PL 0/0:6:3:5:0,3,45 +20 10130841 . G . . END=10130841 GT:DP:GQ:MIN_DP:PL 0/0:6:6:6:0,6,90 +20 10130842 . T . . END=10130844 GT:DP:GQ:MIN_DP:PL 0/0:4:3:4:0,3,45 +20 10130845 . A . . END=10130846 GT:DP:GQ:MIN_DP:PL 0/0:5:6:5:0,6,90 +20 10130847 . A . . END=10130849 GT:DP:GQ:MIN_DP:PL 0/0:5:9:5:0,9,135 +20 10130850 . A . . END=10130851 GT:DP:GQ:MIN_DP:PL 0/0:6:12:5:0,12,180 +20 10130852 . A . . END=10130852 GT:DP:GQ:MIN_DP:PL 0/0:6:15:6:0,15,225 +20 10130853 . T . . END=10130856 GT:DP:GQ:MIN_DP:PL 0/0:7:21:7:0,21,250 +20 10130857 . T . . END=10130857 GT:DP:GQ:MIN_DP:PL 0/0:8:24:8:0,24,331 +20 10130858 . A . . END=10130858 GT:DP:GQ:MIN_DP:PL 0/0:11:33:11:0,33,456 +20 10130859 . T . . END=10130861 GT:DP:GQ:MIN_DP:PL 0/0:12:36:12:0,36,500 +20 10130862 . G . . END=10130863 GT:DP:GQ:MIN_DP:PL 0/0:13:39:13:0,39,517 +20 10130864 . A . . END=10130866 GT:DP:GQ:MIN_DP:PL 0/0:14:42:14:0,42,567 +20 10130867 . T . . END=10130867 GT:DP:GQ:MIN_DP:PL 0/0:15:45:15:0,45,625 +20 10130868 . G . . END=10130869 GT:DP:GQ:MIN_DP:PL 0/0:16:48:16:0,48,642 +20 10130870 . A . . END=10130872 GT:DP:GQ:MIN_DP:PL 0/0:17:51:17:0,51,693 +20 10130873 . T . . END=10130873 GT:DP:GQ:MIN_DP:PL 0/0:19:57:19:0,57,792 +20 10130874 . A . . END=10130883 GT:DP:GQ:MIN_DP:PL 0/0:22:60:20:0,60,828 +20 10130884 . T . . END=10130886 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,937 +20 10130887 . G . . END=10130888 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,1031 +20 10130889 . A . . END=10130893 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,1232 +20 10130894 . T . . END=10131195 GT:DP:GQ:MIN_DP:PL 0/0:60:99:33:0,99,1372 +20 10131196 . T C, 1561.77 . DP=43;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=145348.00 GT:AD:DP:GQ:PL:SB 1/1:0,42,0:42:99:1590,126,0,1590,126,1590:0,0,22,20 +20 10131197 . T . . END=10131979 GT:DP:GQ:MIN_DP:PL 0/0:72:99:37:0,99,1485 +20 10131980 . T C, 3248.77 . DP=80;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=274205.00 GT:AD:DP:GQ:PL:SB 1/1:0,80,0:80:99:3277,241,0,3277,241,3277:0,0,37,43 +20 10131981 . T . . END=10131997 GT:DP:GQ:MIN_DP:PL 0/0:76:99:72:0,120,1800 +20 10131998 . G A, 1416.77 . BaseQRankSum=1.236;DP=77;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.578;RAW_MQ=260646.00;ReadPosRankSum=-0.561 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:38,39,0:77:99:0|1:10131998_G_A:1445,0,1391,1559,1509,3068:17,21,16,23 +20 10131999 . T . . END=10132022 GT:DP:GQ:MIN_DP:PL 0/0:73:99:68:0,120,1800 +20 10132023 . T C, 1220.77 . BaseQRankSum=-4.209;DP=71;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.949;RAW_MQ=236287.00;ReadPosRankSum=0.788 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:36,35,0:71:99:0|1:10131998_G_A:1249,0,1377,1360,1482,2843:19,17,11,24 +20 10132024 . G . . END=10132090 GT:DP:GQ:MIN_DP:PL 0/0:64:99:60:0,120,1800 +20 10132091 . A G, 792.77 . BaseQRankSum=-0.956;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.615;RAW_MQ=216292.00;ReadPosRankSum=-1.722 GT:AD:DP:GQ:PL:SB 0/1:38,25,0:63:99:821,0,979,908,1054,1962:24,14,9,16 +20 10132092 . A . . END=10132300 GT:DP:GQ:MIN_DP:PL 0/0:68:99:49:0,116,1800 +20 10132301 . GACACACACAC G, 851.73 . BaseQRankSum=-0.259;DP=51;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.040;RAW_MQ=144617.00;ReadPosRankSum=-1.258 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:21,22,0:43:99:0|1:10132301_GACACACACAC_G:889,0,2525,952,2595,3547:14,7,9,13 +20 10132312 . A . . END=10132339 GT:DP:GQ:MIN_DP:PL 0/0:52:99:45:0,120,1800 +20 10132340 . A G, 841.77 . BaseQRankSum=-2.887;DP=56;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.525;RAW_MQ=148050.00;ReadPosRankSum=-0.622 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:24,32,0:56:99:0|1:10132301_GACACACACAC_G:870,0,2516,945,2588,3533:15,9,14,18 +20 10132341 . T . . END=10132681 GT:DP:GQ:MIN_DP:PL 0/0:65:99:50:0,120,1800 +20 10132682 . A . . END=10132682 GT:DP:GQ:MIN_DP:PL 0/0:63:96:63:0,96,1440 +20 10132683 . T . . END=10132696 GT:DP:GQ:MIN_DP:PL 0/0:60:0:49:0,0,1213 +20 10132697 . T . . END=10132704 GT:DP:GQ:MIN_DP:PL 0/0:48:90:43:0,90,1350 +20 10132705 . T . . END=10132705 GT:DP:GQ:MIN_DP:PL 0/0:43:87:43:0,87,1305 +20 10132706 . G GAC, 70.73 . BaseQRankSum=-0.397;DP=43;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.509;RAW_MQ=102405.00;ReadPosRankSum=1.504 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:22,9,0:31:99:0|1:10132706_G_GAC:108,0,915,179,930,1109:7,15,6,3 +20 10132707 . T A, 76.77 . BaseQRankSum=-0.460;DP=45;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.509;RAW_MQ=104087.00;ReadPosRankSum=1.482 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:22,9,0:31:99:0|1:10132706_G_GAC:105,0,957,179,972,1151:7,15,6,3 +20 10132708 . G . . END=10132708 GT:DP:GQ:MIN_DP:PL 0/0:46:96:46:0,96,1440 +20 10132709 . T A, 92.77 . BaseQRankSum=0.615;DP=47;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.614;RAW_MQ=111287.00;ReadPosRankSum=1.254 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:24,9,0:33:99:0|1:10132706_G_GAC:121,0,957,194,972,1167:7,17,6,3 +20 10132710 . G . . END=10132710 GT:DP:GQ:MIN_DP:PL 0/0:47:93:47:0,93,1395 +20 10132711 . T A, 76.77 . BaseQRankSum=1.155;DP=47;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.614;RAW_MQ=111287.00;ReadPosRankSum=0.850 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:24,9,0:33:99:0|1:10132706_G_GAC:105,0,957,179,972,1151:7,17,6,3 +20 10132712 . G . . END=10132712 GT:DP:GQ:MIN_DP:PL 0/0:46:90:46:0,90,1350 +20 10132713 . T A, 92.77 . BaseQRankSum=1.799;DP=46;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.770;RAW_MQ=110446.00;ReadPosRankSum=0.378 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:23,9,0:32:99:0|1:10132706_G_GAC:121,0,957,195,972,1167:6,17,6,3 +20 10132714 . G . . END=10132714 GT:DP:GQ:MIN_DP:PL 0/0:45:87:45:0,87,1305 +20 10132715 . T A, 80.77 . BaseQRankSum=0.176;DP=45;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.720;RAW_MQ=106846.00;ReadPosRankSum=-0.131 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:22,9,0:31:99:0|1:10132706_G_GAC:109,0,914,180,930,1110:6,16,6,3 +20 10132716 . G . . END=10132716 GT:DP:GQ:MIN_DP:PL 0/0:46:87:46:0,87,1305 +20 10132717 . T A, 83.77 . BaseQRankSum=0.593;DP=47;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.720;RAW_MQ=114046.00;ReadPosRankSum=-0.480 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:22,9,0:31:99:0|1:10132706_G_GAC:112,0,872,179,888,1068:6,16,6,3 +20 10132718 . G . . END=10132718 GT:DP:GQ:MIN_DP:PL 0/0:48:90:48:0,90,1350 +20 10132719 . T A, 99.77 . BaseQRankSum=0.592;DP=48;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.720;RAW_MQ=117646.00;ReadPosRankSum=-0.829 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:22,9,0:31:99:0|1:10132706_G_GAC:128,0,872,195,888,1084:6,16,6,3 +20 10132720 . G . . END=10132720 GT:DP:GQ:MIN_DP:PL 0/0:48:90:48:0,90,1350 +20 10132721 . A . . END=10132721 GT:DP:GQ:MIN_DP:PL 0/0:47:81:47:0,81,1215 +20 10132722 . CAG C,GAG,CAGAGAGAGAGAGAGAGAG, 951.73 . DP=48;ExcessHet=3.0103;MLEAC=1,1,0,0;MLEAF=0.500,0.500,0.00,0.00;RAW_MQ=117646.00 GT:AD:DP:GQ:PL:SB 1/2:0,15,9,1,0:25:99:989,671,679,357,0,685,675,373,439,1166,1028,718,465,831,1176:0,0,9,16 +20 10132725 . A . . END=10132726 GT:DP:GQ:MIN_DP:PL 0/0:52:72:51:0,72,1080 +20 10132727 . A . . END=10132728 GT:DP:GQ:MIN_DP:PL 0/0:53:81:52:0,81,1215 +20 10132729 . A . . END=10132730 GT:DP:GQ:MIN_DP:PL 0/0:54:90:53:0,90,1350 +20 10132731 . A . . END=10132751 GT:DP:GQ:MIN_DP:PL 0/0:61:99:55:0,99,1485 +20 10132752 . A . . END=10132752 GT:DP:GQ:MIN_DP:PL 0/0:59:0:59:0,0,1498 +20 10132753 . A . . END=10132754 GT:DP:GQ:MIN_DP:PL 0/0:57:99:57:0,120,1800 +20 10132755 . C . . END=10132756 GT:DP:GQ:MIN_DP:PL 0/0:57:0:56:0,0,1580 +20 10132757 . A . . END=10132759 GT:DP:GQ:MIN_DP:PL 0/0:58:99:56:0,120,1800 +20 10132760 . T . . END=10132760 GT:DP:GQ:MIN_DP:PL 0/0:57:19:57:0,19,1857 +20 10132761 . C . . END=10132761 GT:DP:GQ:MIN_DP:PL 0/0:57:51:57:0,51,1965 +20 10132762 . T . . END=10132762 GT:DP:GQ:MIN_DP:PL 0/0:58:65:58:0,65,2049 +20 10132763 . C . . END=10132763 GT:DP:GQ:MIN_DP:PL 0/0:58:54:58:0,54,2010 +20 10132764 . A . . END=10132764 GT:DP:GQ:MIN_DP:PL 0/0:58:91:58:0,91,2086 +20 10132765 . A . . END=10132765 GT:DP:GQ:MIN_DP:PL 0/0:58:99:58:0,120,1800 +20 10132766 . C . . END=10132767 GT:DP:GQ:MIN_DP:PL 0/0:59:90:58:0,90,2089 +20 10132768 . C . . END=10132768 GT:DP:GQ:MIN_DP:PL 0/0:56:73:56:0,73,1984 +20 10132769 . T . . END=10132769 GT:DP:GQ:MIN_DP:PL 0/0:55:80:55:0,80,1970 +20 10132770 . A . . END=10132770 GT:DP:GQ:MIN_DP:PL 0/0:56:99:56:0,120,1800 +20 10132771 . C . . END=10132771 GT:DP:GQ:MIN_DP:PL 0/0:57:86:57:0,86,2066 +20 10132772 . T . . END=10132772 GT:DP:GQ:MIN_DP:PL 0/0:57:60:57:0,60,2026 +20 10132773 . A . . END=10132774 GT:DP:GQ:MIN_DP:PL 0/0:56:99:55:0,120,1800 +20 10132775 . G . . END=10132775 GT:DP:GQ:MIN_DP:PL 0/0:57:97:57:0,97,2040 +20 10132776 . G . . END=10134202 GT:DP:GQ:MIN_DP:PL 0/0:79:99:48:0,118,1800 +20 10134203 . C . . END=10134203 GT:DP:GQ:MIN_DP:PL 0/0:63:64:63:0,64,1847 +20 10134204 . G . . END=10134409 GT:DP:GQ:MIN_DP:PL 0/0:67:99:57:0,120,1800 +20 10134410 . AAAAGAAAG A,AAAAG, 765.73 . DP=67;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;RAW_MQ=220547.00 GT:AD:DP:GQ:PL:SB 1/2:0,15,8,0:23:99:803,318,522,480,0,451,819,449,496,928:0,0,17,6 +20 10134419 . A . . END=10134419 GT:DP:GQ:MIN_DP:PL 0/0:61:69:61:0,69,1035 +20 10134420 . A . . END=10134423 GT:DP:GQ:MIN_DP:PL 0/0:60:72:59:0,72,1080 +20 10134424 . A . . END=10134431 GT:DP:GQ:MIN_DP:PL 0/0:56:81:53:0,81,1215 +20 10134432 . A . . END=10134439 GT:DP:GQ:MIN_DP:PL 0/0:55:90:54:0,90,1350 +20 10134440 . A . . END=10134478 GT:DP:GQ:MIN_DP:PL 0/0:60:99:55:0,99,1485 +20 10134479 . A C, 1140.77 . BaseQRankSum=-3.058;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.254;RAW_MQ=219478.00;ReadPosRankSum=-1.622 GT:AD:DP:GQ:PL:SB 0/1:32,33,0:65:99:1169,0,1115,1266,1214,2480:23,9,29,4 +20 10134480 . A . . END=10134480 GT:DP:GQ:MIN_DP:PL 0/0:68:99:68:0,120,1800 +20 10134481 . A . . END=10134481 GT:DP:GQ:MIN_DP:PL 0/0:68:54:68:0,54,2396 +20 10134482 . G . . END=10135473 GT:DP:GQ:MIN_DP:PL 0/0:66:99:47:0,105,1575 +20 10135474 . T . . END=10135474 GT:DP:GQ:MIN_DP:PL 0/0:80:0:80:0,0,2812 +20 10135475 . G . . END=10135589 GT:DP:GQ:MIN_DP:PL 0/0:74:99:67:0,120,1800 +20 10135590 . C . . END=10135590 GT:DP:GQ:MIN_DP:PL 0/0:77:0:77:0,0,2410 +20 10135591 . A . . END=10136401 GT:DP:GQ:MIN_DP:PL 0/0:73:99:54:0,120,1800 +20 10136402 . C . . END=10136402 GT:DP:GQ:MIN_DP:PL 0/0:58:0:58:0,0,1460 +20 10136403 . G . . END=10137926 GT:DP:GQ:MIN_DP:PL 0/0:71:99:48:0,113,1681 +20 10137927 . C . . END=10137927 GT:DP:GQ:MIN_DP:PL 0/0:59:0:59:0,0,1592 +20 10137928 . G . . END=10138549 GT:DP:GQ:MIN_DP:PL 0/0:80:99:42:0,117,1800 +20 10138550 . T . . END=10138550 GT:DP:GQ:MIN_DP:PL 0/0:58:83:58:0,83,1975 +20 10138551 . T . . END=10139503 GT:DP:GQ:MIN_DP:PL 0/0:72:99:57:0,120,1800 +20 10139504 . A T, 9.31 . BaseQRankSum=-5.626;DP=76;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.588;RAW_MQ=270841.00;ReadPosRankSum=1.681 GT:AD:DP:GQ:PL:SB 0/1:58,18,0:76:37:37,0,2172,211,2193,2404:18,40,8,10 +20 10139505 . C . . END=10139767 GT:DP:GQ:MIN_DP:PL 0/0:63:99:41:0,108,1620 +20 10139768 . G . . END=10139768 GT:DP:GQ:MIN_DP:PL 0/0:46:76:46:0,76,1542 +20 10139769 . A . . END=10140053 GT:DP:GQ:MIN_DP:PL 0/0:58:99:42:0,100,1530 +20 10140054 . T . . END=10140054 GT:DP:GQ:MIN_DP:PL 0/0:36:94:36:0,94,1298 +20 10140055 . C . . END=10140124 GT:DP:GQ:MIN_DP:PL 0/0:43:99:38:0,99,1427 +20 10140125 . TGG T, 171.73 . BaseQRankSum=-3.995;DP=53;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.567;RAW_MQ=189341.00;ReadPosRankSum=-1.801 GT:AD:DP:GQ:PL:SB 0/1:36,15,0:51:99:209,0,1392,317,1417,1734:23,13,7,8 +20 10140128 . G . . END=10140145 GT:DP:GQ:MIN_DP:PL 0/0:55:99:52:0,120,1800 +20 10140146 . T . . END=10140146 GT:DP:GQ:MIN_DP:PL 0/0:54:87:54:0,87,1305 +20 10140147 . T . . END=10140155 GT:DP:GQ:MIN_DP:PL 0/0:50:90:48:0,90,1350 +20 10140156 . T . . END=10140157 GT:DP:GQ:MIN_DP:PL 0/0:53:99:51:0,111,1665 +20 10140158 . G . . END=10140158 GT:DP:GQ:MIN_DP:PL 0/0:42:91:42:0,91,1399 +20 10140159 . A . . END=10141258 GT:DP:GQ:MIN_DP:PL 0/0:81:99:41:0,114,1540 +20 10141259 . G . . END=10141259 GT:DP:GQ:MIN_DP:PL 0/0:98:0:98:0,0,2798 +20 10141260 . C . . END=10141439 GT:DP:GQ:MIN_DP:PL 0/0:76:99:67:0,120,1800 +20 10141440 . T . . END=10141440 GT:DP:GQ:MIN_DP:PL 0/0:75:0:75:0,0,1964 +20 10141441 . G . . END=10141691 GT:DP:GQ:MIN_DP:PL 0/0:74:99:59:0,120,1800 +20 10141692 . A G, 0 . BaseQRankSum=-4.974;DP=72;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=1.855;RAW_MQ=229044.00;ReadPosRankSum=-0.185 GT:AD:DP:GQ:PGT:PID:PL:SB 0/0:58,14,0:72:55:0|1:10141692_A_G:0,55,3517,181,3526,3652:35,23,8,6 +20 10141693 . A . . END=10141699 GT:DP:GQ:MIN_DP:PL 0/0:74:99:72:0,120,1800 +20 10141700 . C T, 0 . BaseQRankSum=-4.747;DP=76;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=1.863;RAW_MQ=243444.00;ReadPosRankSum=0.379 GT:AD:DP:GQ:PGT:PID:PL:SB 0/0:61,15,0:76:29:0|1:10141692_A_G:0,29,3559,187,3571,3729:39,22,9,6 +20 10141701 . A . . END=10142022 GT:DP:GQ:MIN_DP:PL 0/0:81:99:55:0,106,1800 +20 10142023 . G . . END=10142023 GT:DP:GQ:MIN_DP:PL 0/0:59:89:59:0,89,2109 +20 10142024 . C . . END=10142024 GT:DP:GQ:MIN_DP:PL 0/0:58:98:58:0,98,2064 +20 10142025 . A . . END=10142027 GT:DP:GQ:MIN_DP:PL 0/0:62:99:61:0,120,1800 +20 10142028 . G . . END=10142029 GT:DP:GQ:MIN_DP:PL 0/0:61:0:60:0,0,1800 +20 10142030 . A . . END=10142031 GT:DP:GQ:MIN_DP:PL 0/0:66:54:66:0,54,810 +20 10142032 . A . . END=10142032 GT:DP:GQ:MIN_DP:PL 0/0:71:69:71:0,69,1035 +20 10142033 . A . . END=10142033 GT:DP:GQ:MIN_DP:PL 0/0:71:78:71:0,78,1170 +20 10142034 . A AC, 111.73 . BaseQRankSum=-5.713;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.829;RAW_MQ=169080.00;ReadPosRankSum=-1.149 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:45,16,0:61:99:0|1:10142034_A_AC:149,0,5339,294,5360,5654:28,17,9,7 +20 10142035 . A . . END=10142037 GT:DP:GQ:MIN_DP:PL 0/0:63:63:63:0,63,945 +20 10142038 . A . . END=10142039 GT:DP:GQ:MIN_DP:PL 0/0:66:75:65:0,75,1125 +20 10142040 . A . . END=10142041 GT:DP:GQ:MIN_DP:PL 0/0:65:84:65:0,84,1260 +20 10142042 . A C, 57.77 . BaseQRankSum=-5.362;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.816;RAW_MQ=179874.00;ReadPosRankSum=-1.051 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:53,15,0:68:86:0|1:10142034_A_AC:86,0,6085,252,6103,6355:30,23,8,7 +20 10142043 . A . . END=10142048 GT:DP:GQ:MIN_DP:PL 0/0:72:99:68:0,99,1485 +20 10142049 . A ACAAACAAAC, 2.02 . BaseQRankSum=-5.324;DP=73;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=4.108;RAW_MQ=199262.00;ReadPosRankSum=-1.614 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:57,16,0:73:35:0|1:10142034_A_AC:35,0,6211,210,6226,6436:32,25,7,9 +20 10142050 . A . . END=10142059 GT:DP:GQ:MIN_DP:PL 0/0:85:99:69:0,107,1800 +20 10142060 . G . . END=10142060 GT:DP:GQ:MIN_DP:PL 0/0:70:22:70:0,22,2166 +20 10142061 . T . . END=10142061 GT:DP:GQ:MIN_DP:PL 0/0:70:33:70:0,33,2189 +20 10142062 . A . . END=10142653 GT:DP:GQ:MIN_DP:PL 0/0:86:99:63:0,120,1800 +20 10142654 . T . . END=10142654 GT:DP:GQ:MIN_DP:PL 0/0:122:0:122:0,0,3463 +20 10142655 . C . . END=10144243 GT:DP:GQ:MIN_DP:PL 0/0:75:99:41:0,105,1575 +20 10144244 . CAAAA C,CAAA,CAAAAA, 197.73 . BaseQRankSum=-1.283;DP=79;ExcessHet=3.0103;MLEAC=0,1,1,0;MLEAF=0.00,0.500,0.500,0.00;MQRankSum=0.141;RAW_MQ=231835.00;ReadPosRankSum=0.371 GT:AD:DP:GQ:PL:SB 2/3:5,3,5,12,0:25:65:235,279,1601,196,464,404,65,132,0,99,303,614,426,149,572:5,0,14,6 +20 10144249 . A . . END=10144273 GT:DP:GQ:MIN_DP:PL 0/0:76:99:69:0,120,1800 +20 10144274 . G . . END=10144274 GT:DP:GQ:MIN_DP:PL 0/0:69:14:69:0,14,1849 +20 10144275 . A . . END=10144278 GT:DP:GQ:MIN_DP:PL 0/0:70:99:69:0,120,1800 +20 10144279 . G . . END=10144279 GT:DP:GQ:MIN_DP:PL 0/0:67:50:67:0,50,1768 +20 10144280 . A . . END=10144283 GT:DP:GQ:MIN_DP:PL 0/0:83:99:81:0,120,1800 +20 10144284 . C . . END=10144284 GT:DP:GQ:MIN_DP:PL 0/0:76:0:76:0,0,1828 +20 10144285 . A . . END=10145937 GT:DP:GQ:MIN_DP:PL 0/0:83:99:43:0,108,1620 +20 10145938 . G . . END=10145938 GT:DP:GQ:MIN_DP:PL 0/0:42:95:42:0,95,1590 +20 10145939 . G . . END=10145943 GT:DP:GQ:MIN_DP:PL 0/0:42:99:39:0,99,1485 +20 10145944 . A . . END=10145946 GT:DP:GQ:MIN_DP:PL 0/0:39:93:39:0,93,1395 +20 10145947 . A . . END=10145947 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,99,1485 +20 10145948 . C . . END=10145950 GT:DP:GQ:MIN_DP:PL 0/0:41:90:38:0,90,1350 +20 10145951 . A . . END=10145961 GT:DP:GQ:MIN_DP:PL 0/0:36:81:32:0,81,1215 +20 10145962 . T . . END=10145962 GT:DP:GQ:MIN_DP:PL 0/0:31:79:31:0,79,1165 +20 10145963 . T . . END=10145964 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 +20 10145965 . T . . END=10145966 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,1350 +20 10145967 . A . . END=10145967 GT:DP:GQ:MIN_DP:PL 0/0:32:78:32:0,78,1138 +20 10145968 . C . . END=10145969 GT:DP:GQ:MIN_DP:PL 0/0:32:87:31:0,87,1305 +20 10145970 . C . . END=10145977 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,1257 +20 10145978 . G . . END=10145983 GT:DP:GQ:MIN_DP:PL 0/0:34:99:33:0,99,1300 +20 10145984 . G . . END=10145991 GT:DP:GQ:MIN_DP:PL 0/0:36:90:35:0,90,1267 +20 10145992 . A . . END=10145994 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,99,1485 +20 10145995 . A . . END=10145998 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 +20 10145999 . A . . END=10146001 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 +20 10146002 . G . . END=10146009 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1350 +20 10146010 . G . . END=10146015 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,99,1485 +20 10146016 . A . . END=10146027 GT:DP:GQ:MIN_DP:PL 0/0:36:90:35:0,90,1249 +20 10146028 . T . . END=10146028 GT:DP:GQ:MIN_DP:PL 0/0:34:88:34:0,88,1222 +20 10146029 . G . . END=10146478 GT:DP:GQ:MIN_DP:PL 0/0:61:99:36:0,99,1485 +20 10146479 . A C, 0 . BaseQRankSum=-5.146;DP=71;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=1.533;RAW_MQ=242513.00;ReadPosRankSum=1.247 GT:AD:DP:GQ:PGT:PID:PL:SB 0/0:57,13,0:70:7:0|1:10146479_A_C:0,7,3867,175,3879,4047:24,33,6,7 +20 10146480 . G . . END=10146480 GT:DP:GQ:MIN_DP:PL 0/0:69:99:69:0,120,1800 +20 10146481 . C T, 0 . BaseQRankSum=-0.208;DP=68;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=1.310;RAW_MQ=236526.00;ReadPosRankSum=0.653 GT:AD:DP:GQ:PGT:PID:PL:SB 0/0:54,14,0:68:7:0|1:10146479_A_C:0,7,3867,175,3879,4047:22,32,7,7 +20 10146482 . G . . END=10147298 GT:DP:GQ:MIN_DP:PL 0/0:68:99:54:0,120,1800 +20 10147299 . A . . END=10147299 GT:DP:GQ:MIN_DP:PL 0/0:68:66:68:0,66,2427 +20 10147300 . A . . END=10148539 GT:DP:GQ:MIN_DP:PL 0/0:78:99:54:0,120,1800 +20 10148540 . A . . END=10148540 GT:DP:GQ:MIN_DP:PL 0/0:86:0:86:0,0,2573 +20 10148541 . T . . END=10148802 GT:DP:GQ:MIN_DP:PL 0/0:86:99:63:0,120,1800 +20 10148803 . A G, 0.93 . BaseQRankSum=-5.387;DP=71;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.792;RAW_MQ=250082.00;ReadPosRankSum=-1.583 GT:AD:DP:GQ:PL:SB 0/1:55,16,0:71:22:22,0,2035,187,2053,2241:22,33,8,8 +20 10148804 . C . . END=10149175 GT:DP:GQ:MIN_DP:PL 0/0:75:99:60:0,120,1800 +20 10149176 . A . . END=10149176 GT:DP:GQ:MIN_DP:PL 0/0:73:0:73:0,0,2257 +20 10149177 . T . . END=10149663 GT:DP:GQ:MIN_DP:PL 0/0:73:99:56:0,120,1800 +20 10149664 . G . . END=10149664 GT:DP:GQ:MIN_DP:PL 0/0:54:0:54:0,0,1594 +20 10149665 . A . . END=10150000 GT:DP:GQ:MIN_DP:PL 0/0:79:99:51:0,120,1800 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf index adc8e148e46..3c4b47050b2 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf @@ -103,7 +103,7 @@ 20 10000211 . C T, 941.77 . AS_RAW_BaseQRankSum=|1.8,1|NaN;AS_RAW_MQ=91369.00|97200.00|0.00;AS_RAW_MQRankSum=|1.0,1|NaN;AS_RAW_ReadPosRankSum=|0.7,1|NaN;AS_SB_TABLE=15,11|11,16|0,0;BaseQRankSum=1.867;DP=53;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.057;RAW_MQ=188569.00;ReadPosRankSum=0.703 GT:AD:DP:GQ:PL:SB 0/1:26,27,0:53:99:970,0,906,1049,988,2036:15,11,11,16 20 10000212 . A . . END=10000438 GT:DP:GQ:MIN_DP:PL 0/0:79:99:55:0,120,1800 20 10000439 . T G, 2804.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|279076.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|49,31|0,0;DP=80;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=279076.00 GT:AD:DP:GQ:PL:SB 1/1:0,80,0:80:99:2833,240,0,2833,240,2833:0,0,49,31 -20 10000440 . T . . END=10000585 GT:DP:GQ:MIN_DP:PL 0/0:55:99:41:0,100,1530 +20 10000440 . T . . END=10000585 GT:DP:GQ:MIN_DP:PL 0/0:55:99:41:0,102,1530 20 10000586 . C . . END=10000586 GT:DP:GQ:MIN_DP:PL 0/0:44:93:44:0,93,1503 20 10000587 . G . . END=10000597 GT:DP:GQ:MIN_DP:PL 0/0:46:99:42:0,108,1620 20 10000598 . T A, 1941.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|149628.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|19,30|0,0;DP=49;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=149628.00 GT:AD:DP:GQ:PL:SB 1/1:0,49,0:49:99:1970,147,0,1970,147,1970:0,0,19,30 @@ -115,40 +115,28 @@ 20 10001019 . T G, 650.77 . AS_RAW_BaseQRankSum=|-2.6,1|NaN;AS_RAW_MQ=137329.00|21866.00|0.00;AS_RAW_MQRankSum=|-7.5,1|NaN;AS_RAW_ReadPosRankSum=|-1.0,1|NaN;AS_SB_TABLE=17,22|14,12|0,0;BaseQRankSum=-2.541;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-7.498;RAW_MQ=159195.00;ReadPosRankSum=-0.925 GT:AD:DP:GQ:PL:SB 0/1:39,26,0:65:99:679,0,1426,796,1504,2300:17,22,14,12 20 10001020 . C . . END=10001297 GT:DP:GQ:MIN_DP:PL 0/0:68:99:46:0,117,1755 20 10001298 . T A, 2917.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|217124.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|41,32|0,0;DP=74;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=218493.00 GT:AD:DP:GQ:PL:SB 1/1:0,73,0:73:99:2946,220,0,2946,220,2946:0,0,41,32 -20 10001299 . C . . END=10001402 GT:DP:GQ:MIN_DP:PL 0/0:71:99:51:0,99,1485 -20 10001403 . A . . END=10001403 GT:DP:GQ:MIN_DP:PL 0/0:50:93:50:0,93,1395 -20 10001404 . A . . END=10001406 GT:DP:GQ:MIN_DP:PL 0/0:50:81:50:0,81,1215 -20 10001407 . T . . END=10001407 GT:DP:GQ:MIN_DP:PL 0/0:50:78:50:0,78,1170 -20 10001408 . C . . END=10001410 GT:DP:GQ:MIN_DP:PL 0/0:50:63:49:0,63,945 -20 10001411 . T . . END=10001411 GT:DP:GQ:MIN_DP:PL 0/0:50:54:50:0,54,810 -20 10001412 . A . . END=10001412 GT:DP:GQ:MIN_DP:PL 0/0:50:48:50:0,48,720 -20 10001413 . T . . END=10001414 GT:DP:GQ:MIN_DP:PL 0/0:51:42:51:0,42,630 -20 10001415 . T . . END=10001415 GT:DP:GQ:MIN_DP:PL 0/0:50:39:50:0,39,585 -20 10001416 . A . . END=10001420 GT:DP:GQ:MIN_DP:PL 0/0:50:33:49:0,33,495 -20 10001421 . G . . END=10001422 GT:DP:GQ:MIN_DP:PL 0/0:50:30:49:0,30,450 -20 10001423 . T . . END=10001426 GT:DP:GQ:MIN_DP:PL 0/0:50:24:49:0,24,360 +20 10001299 . C . . END=10001426 GT:DP:GQ:MIN_DP:PL 0/0:63:99:49:0,111,1800 20 10001427 . T . . END=10001427 GT:DP:GQ:MIN_DP:PL 0/0:53:5:53:0,5,1899 -20 10001428 . T . . END=10001429 GT:DP:GQ:MIN_DP:PL 0/0:54:21:53:0,21,315 +20 10001428 . T . . END=10001429 GT:DP:GQ:MIN_DP:PL 0/0:54:99:53:0,120,1800 20 10001430 . G . . END=10001431 GT:DP:GQ:MIN_DP:PL 0/0:56:0:56:0,0,1743 -20 10001432 . A . . END=10001432 GT:DP:GQ:MIN_DP:PL 0/0:56:18:56:0,18,270 +20 10001432 . A . . END=10001432 GT:DP:GQ:MIN_DP:PL 0/0:56:99:56:0,120,1800 20 10001433 . T . . END=10001433 GT:DP:GQ:MIN_DP:PL 0/0:56:0:56:0,0,1779 -20 10001434 . G . . END=10001434 GT:DP:GQ:MIN_DP:PL 0/0:56:18:56:0,18,270 +20 10001434 . G . . END=10001434 GT:DP:GQ:MIN_DP:PL 0/0:56:99:56:0,120,1800 20 10001435 . A . . END=10001435 GT:DP:GQ:MIN_DP:PL 0/0:55:0:55:0,0,1790 20 10001436 . A AAGGCT, 2301.73 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|76986.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|43,7|0,0;DP=55;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=92755.00 GT:AD:DP:GQ:PL:SB 1/1:0,50,0:50:99:2339,156,0,2340,157,2340:0,0,43,7 -20 10001437 . A . . END=10001437 GT:DP:GQ:MIN_DP:PL 0/0:57:0:57:0,0,0 -20 10001438 . G . . END=10001473 GT:DP:GQ:MIN_DP:PL 0/0:62:99:51:0,118,1800 +20 10001437 . A . . END=10001473 GT:DP:GQ:MIN_DP:PL 0/0:61:99:51:0,120,1800 20 10001474 . C T, 2640.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|140615.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|48,25|0,0;DP=73;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=140615.00 GT:AD:DP:GQ:PL:SB 1/1:0,73,0:73:99:2669,219,0,2669,219,2669:0,0,48,25 20 10001475 . G . . END=10001616 GT:DP:GQ:MIN_DP:PL 0/0:95:99:72:0,120,1800 20 10001617 . C A, 1731.77 . AS_RAW_BaseQRankSum=|1.2,1|NaN;AS_RAW_MQ=177220.00|181369.00|0.00;AS_RAW_MQRankSum=|1.3,1|NaN;AS_RAW_ReadPosRankSum=|-0.3,1|NaN;AS_SB_TABLE=23,29|33,18|0,0;BaseQRankSum=1.261;DP=103;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.373;RAW_MQ=358589.00;ReadPosRankSum=-0.280 GT:AD:DP:GQ:PL:SB 0/1:52,51,0:103:99:1760,0,1781,1916,1935,3851:23,29,33,18 -20 10001618 . T . . END=10001627 GT:DP:GQ:MIN_DP:PL 0/0:101:99:95:0,120,1800 +20 10001618 . T . . END=10001627 GT:DP:GQ:MIN_DP:PL 0/0:100:99:94:0,120,1800 20 10001628 . G A, 3898.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|332548.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|55,40|0,0;DP=95;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=332548.00 GT:AD:DP:GQ:PL:SB 1/1:0,95,0:95:99:3927,285,0,3927,285,3927:0,0,55,40 -20 10001629 . G . . END=10001660 GT:DP:GQ:MIN_DP:PL 0/0:82:99:76:0,120,1800 +20 10001629 . G . . END=10001660 GT:DP:GQ:MIN_DP:PL 0/0:81:99:76:0,120,1800 20 10001661 . T C, 3606.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|275574.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|49,32|0,0;DP=81;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=275574.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,81,0:81:99:0|1:10001661_T_C:3635,249,0,3635,249,3635:0,0,49,32 -20 10001662 . T . . END=10001669 GT:DP:GQ:MIN_DP:PL 0/0:83:99:82:0,120,1800 +20 10001662 . T . . END=10001669 GT:DP:GQ:MIN_DP:PL 0/0:82:99:81:0,120,1800 20 10001670 . T G, 3673.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|267297.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|46,35|0,0;DP=81;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=267297.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,81,0:81:99:0|1:10001661_T_C:3702,253,0,3702,253,3702:0,0,46,35 20 10001671 . G . . END=10002057 GT:DP:GQ:MIN_DP:PL 0/0:76:99:57:0,120,1800 20 10002058 . T G, 2963.77 . AS_RAW_BaseQRankSum=|1.9,1|NaN;AS_RAW_MQ=841.00|249365.00|0.00;AS_RAW_MQRankSum=|3.0,1|NaN;AS_RAW_ReadPosRankSum=|0.6,1|NaN;AS_SB_TABLE=1,0|51,23|0,0;BaseQRankSum=1.931;DP=75;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=3.068;RAW_MQ=250206.00;ReadPosRankSum=0.624 GT:AD:DP:GQ:PL:SB 1/1:1,74,0:75:99:2992,216,0,2994,223,3001:1,0,51,23 -20 10002059 . A . . END=10002098 GT:DP:GQ:MIN_DP:PL 0/0:78:99:65:0,120,1800 +20 10002059 . A . . END=10002098 GT:DP:GQ:MIN_DP:PL 0/0:77:99:65:0,120,1800 20 10002099 . C T, 1194.77 . AS_RAW_BaseQRankSum=|-0.3,1|NaN;AS_RAW_MQ=88923.00|117006.00|0.00;AS_RAW_MQRankSum=|-0.9,1|NaN;AS_RAW_ReadPosRankSum=|0.1,1|NaN;AS_SB_TABLE=19,8|23,15|0,0;BaseQRankSum=-0.282;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.850;RAW_MQ=205929.00;ReadPosRankSum=0.173 GT:AD:DP:GQ:PL:SB 0/1:27,38,0:65:99:1223,0,844,1304,958,2262:19,8,23,15 20 10002100 . T . . END=10002137 GT:DP:GQ:MIN_DP:PL 0/0:59:99:49:0,120,1800 20 10002138 . C G, 2443.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|168463.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|27,26|0,0;DP=53;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=168463.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,53,0:53:99:0|1:10002138_C_G:2472,169,0,2472,169,2472:0,0,27,26 @@ -158,16 +146,16 @@ 20 10002202 . G . . END=10002203 GT:DP:GQ:MIN_DP:PL 0/0:49:96:47:0,96,1440 20 10002204 . G . . END=10002212 GT:DP:GQ:MIN_DP:PL 0/0:46:99:45:0,99,1485 20 10002213 . T . . END=10002213 GT:DP:GQ:MIN_DP:PL 0/0:45:65:45:0,65,1504 -20 10002214 . G . . END=10002448 GT:DP:GQ:MIN_DP:PL 0/0:74:99:44:0,102,1530 -20 10002449 . T . . END=10002450 GT:DP:GQ:MIN_DP:PL 0/0:52:90:51:0,90,1350 -20 10002451 . T . . END=10002454 GT:DP:GQ:MIN_DP:PL 0/0:50:81:48:0,81,1215 -20 10002455 . A . . END=10002455 GT:DP:GQ:MIN_DP:PL 0/0:50:72:50:0,72,1080 -20 10002456 . T . . END=10002456 GT:DP:GQ:MIN_DP:PL 0/0:52:48:52:0,48,720 +20 10002214 . G . . END=10002454 GT:DP:GQ:MIN_DP:PL 0/0:74:99:44:0,102,1530 +20 10002455 . A . . END=10002455 GT:DP:GQ:MIN_DP:PL 0/0:50:93:50:0,93,1395 +20 10002456 . T . . END=10002456 GT:DP:GQ:MIN_DP:PL 0/0:52:78:52:0,78,1170 20 10002457 . A . . END=10002457 GT:DP:GQ:MIN_DP:PL 0/0:52:0:52:0,0,1572 20 10002458 . G GT,GTTT,GTTTTT, 2135.73 . AS_RAW_BaseQRankSum=||||;AS_RAW_MQ=0.00|18441.00|16082.00|3364.00|0.00;AS_RAW_MQRankSum=||||;AS_RAW_ReadPosRankSum=||||;AS_SB_TABLE=0,0|3,3|5,1|4,0|0,0;DP=47;ExcessHet=3.0103;MLEAC=1,1,0,0;MLEAF=0.500,0.500,0.00,0.00;RAW_MQ=127415.00 GT:AD:DP:GQ:PL:SB 1/2:0,6,6,4,0:16:9:2172,654,493,249,0,82,353,33,9,214,876,512,168,254,730:0,0,12,4 -20 10002459 . T . . END=10002459 GT:DP:GQ:MIN_DP:PL 0/0:59:0:59:0,0,1511 -20 10002460 . T . . END=10002466 GT:DP:GQ:MIN_DP:PL 0/0:62:72:61:0,72,1080 -20 10002467 . T . . END=10002469 GT:DP:GQ:MIN_DP:PL 0/0:64:81:63:0,81,1215 +20 10002459 . T . . END=10002459 GT:DP:GQ:MIN_DP:PL 0/0:58:78:58:0,78,1170 +20 10002460 . T . . END=10002460 GT:DP:GQ:MIN_DP:PL 0/0:60:87:60:0,87,1305 +20 10002461 . T . . END=10002467 GT:DP:GQ:MIN_DP:PL 0/0:62:90:60:0,90,1350 +20 10002468 . T . . END=10002468 GT:DP:GQ:MIN_DP:PL 0/0:64:99:64:0,99,1485 +20 10002469 . T . . END=10002469 GT:DP:GQ:MIN_DP:PL 0/0:62:81:62:0,81,1215 20 10002470 . C T, 2522.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|144226.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|34,27|0,0;DP=61;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=144226.00 GT:AD:DP:GQ:PL:SB 1/1:0,61,0:61:99:2551,189,0,2551,189,2551:0,0,34,27 20 10002471 . T . . END=10002471 GT:DP:GQ:MIN_DP:PL 0/0:63:84:63:0,84,1260 20 10002472 . T . . END=10002474 GT:DP:GQ:MIN_DP:PL 0/0:63:90:63:0,90,1350 @@ -216,18 +204,15 @@ 20 10003832 . G A, 2705.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|215436.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|23,43|0,0;DP=66;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=215436.00 GT:AD:DP:GQ:PL:SB 1/1:0,66,0:66:99:2734,199,0,2734,199,2734:0,0,23,43 20 10003833 . T . . END=10004093 GT:DP:GQ:MIN_DP:PL 0/0:69:99:43:0,108,1620 20 10004094 . A C, 1825.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|147492.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|35,18|0,0;DP=53;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=147492.00 GT:AD:DP:GQ:PL:SB 1/1:0,53,0:53:99:1854,157,0,1854,157,1854:0,0,35,18 -20 10004095 . C . . END=10004146 GT:DP:GQ:MIN_DP:PL 0/0:52:99:45:0,109,1596 +20 10004095 . C . . END=10004146 GT:DP:GQ:MIN_DP:PL 0/0:51:99:45:0,109,1596 20 10004147 . A G, 1837.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|157262.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|21,31|0,0;DP=52;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=157262.00 GT:AD:DP:GQ:PL:SB 1/1:0,52,0:52:99:1866,156,0,1866,156,1866:0,0,21,31 -20 10004148 . G . . END=10004192 GT:DP:GQ:MIN_DP:PL 0/0:51:99:47:0,112,1687 +20 10004148 . G . . END=10004192 GT:DP:GQ:MIN_DP:PL 0/0:49:99:45:0,106,1637 20 10004193 . G T, 918.77 . AS_RAW_BaseQRankSum=|-0.6,1|NaN;AS_RAW_MQ=70129.00|112740.00|0.00;AS_RAW_MQRankSum=|3.4,1|NaN;AS_RAW_ReadPosRankSum=|1.5,1|NaN;AS_SB_TABLE=12,11|12,17|0,0;BaseQRankSum=-0.504;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.421;RAW_MQ=182869.00;ReadPosRankSum=1.512 GT:AD:DP:GQ:PL:SB 0/1:23,29,0:52:99:947,0,775,1016,860,1876:12,11,12,17 -20 10004194 . C . . END=10004214 GT:DP:GQ:MIN_DP:PL 0/0:53:99:49:0,102,1530 -20 10004215 . C . . END=10004215 GT:DP:GQ:MIN_DP:PL 0/0:53:96:53:0,96,1440 -20 10004216 . T . . END=10004218 GT:DP:GQ:MIN_DP:PL 0/0:53:84:53:0,84,1260 -20 10004219 . C . . END=10004221 GT:DP:GQ:MIN_DP:PL 0/0:52:72:51:0,72,1080 +20 10004194 . C . . END=10004221 GT:DP:GQ:MIN_DP:PL 0/0:50:99:46:0,105,1575 20 10004222 . C CA, 12.96 . AS_RAW_BaseQRankSum=|0.3,1|NaN;AS_RAW_MQ=121951.00|23791.00|0.00;AS_RAW_MQRankSum=|-2.1,1|NaN;AS_RAW_ReadPosRankSum=|1.2,1|NaN;AS_SB_TABLE=18,13|4,4|0,0;BaseQRankSum=0.335;DP=54;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.042;RAW_MQ=194729.00;ReadPosRankSum=1.271 GT:AD:DP:GQ:PL:SB 0/1:31,8,0:39:50:50,0,923,153,952,1105:18,13,4,4 20 10004223 . A AG, 47.73 . AS_RAW_BaseQRankSum=|-0.5,1|NaN;AS_RAW_MQ=108277.00|39441.00|0.00;AS_RAW_MQRankSum=|1.8,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=16,20|5,6|0,0;BaseQRankSum=-0.480;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.886;RAW_MQ=210769.00;ReadPosRankSum=0.339 GT:AD:DP:GQ:PL:SB 0/1:36,11,0:47:85:85,0,982,193,1017,1210:16,20,5,6 -20 10004224 . A . . END=10004224 GT:DP:GQ:MIN_DP:PL 0/0:70:0:70:0,0,450 -20 10004225 . A . . END=10004240 GT:DP:GQ:MIN_DP:PL 0/0:70:99:65:0,114,1710 +20 10004224 . A . . END=10004224 GT:DP:GQ:MIN_DP:PL 0/0:66:0:66:0,0,1403 +20 10004225 . A . . END=10004240 GT:DP:GQ:MIN_DP:PL 0/0:70:99:65:0,117,1755 20 10004241 . G . . END=10004241 GT:DP:GQ:MIN_DP:PL 0/0:66:0:66:0,0,1965 20 10004242 . A . . END=10004350 GT:DP:GQ:MIN_DP:PL 0/0:73:99:58:0,120,1800 20 10004351 . C G, 2755.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|243987.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|38,32|0,0;DP=70;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=243987.00 GT:AD:DP:GQ:PL:SB 1/1:0,70,0:70:99:2784,211,0,2784,211,2784:0,0,38,32 @@ -237,10 +222,9 @@ 20 10004610 . A C, 3625.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|306605.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|46,43|0,0;DP=89;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=306605.00 GT:AD:DP:GQ:PL:SB 1/1:0,89,0:89:99:3654,267,0,3654,267,3654:0,0,46,43 20 10004611 . C . . END=10004724 GT:DP:GQ:MIN_DP:PL 0/0:75:99:64:0,120,1800 20 10004725 . A G, 951.77 . AS_RAW_BaseQRankSum=|-2.2,1|NaN;AS_RAW_MQ=92793.00|105769.00|0.00;AS_RAW_MQRankSum=|3.0,1|NaN;AS_RAW_ReadPosRankSum=|2.0,1|NaN;AS_SB_TABLE=10,25|17,13|0,0;BaseQRankSum=-2.154;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.008;RAW_MQ=198562.00;ReadPosRankSum=2.087 GT:AD:DP:GQ:PL:SB 0/1:35,30,0:65:99:980,0,1168,1085,1258,2343:10,25,17,13 -20 10004726 . T . . END=10004768 GT:DP:GQ:MIN_DP:PL 0/0:67:99:63:0,105,1575 +20 10004726 . T . . END=10004768 GT:DP:GQ:MIN_DP:PL 0/0:66:99:62:0,120,1800 20 10004769 . TAAAACTATGC T, 981.73 . AS_RAW_BaseQRankSum=|1.6,1|NaN;AS_RAW_MQ=133200.00|32185.00|0.00;AS_RAW_MQRankSum=|-6.7,1|NaN;AS_RAW_ReadPosRankSum=|1.8,1|NaN;AS_SB_TABLE=14,23|7,20|0,0;BaseQRankSum=1.603;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-6.625;RAW_MQ=216626.00;ReadPosRankSum=1.879 GT:AD:DP:GQ:PL:SB 0/1:37,27,0:64:99:1019,0,1471,1130,1554,2684:14,23,7,20 -20 10004780 . A . . END=10004780 GT:DP:GQ:MIN_DP:PL 0/0:70:0:70:0,0,795 -20 10004781 . A . . END=10004873 GT:DP:GQ:MIN_DP:PL 0/0:77:99:69:0,120,1800 +20 10004780 . A . . END=10004873 GT:DP:GQ:MIN_DP:PL 0/0:77:99:69:0,120,1800 20 10004874 . A C, 3602.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|306223.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|54,33|0,0;DP=87;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=306223.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,87,0:87:99:0|1:10004874_A_C:3631,261,0,3631,261,3631:0,0,54,33 20 10004875 . T . . END=10004886 GT:DP:GQ:MIN_DP:PL 0/0:86:99:85:0,120,1800 20 10004887 . A G, 1323.77 . AS_RAW_BaseQRankSum=|0.3,1|NaN;AS_RAW_MQ=159241.00|141241.00|0.00;AS_RAW_MQRankSum=|-0.1,1|NaN;AS_RAW_ReadPosRankSum=|-1.2,1|NaN;AS_SB_TABLE=24,21|24,16|0,0;BaseQRankSum=0.356;DP=85;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.067;RAW_MQ=300482.00;ReadPosRankSum=-1.114 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:45,40,0:85:99:0|1:10004874_A_C:1352,0,1542,1487,1662,3149:24,21,24,16 @@ -248,7 +232,7 @@ 20 10005010 . C T, 2934.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|256441.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|44,28|0,0;DP=72;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=256441.00 GT:AD:DP:GQ:PL:SB 1/1:0,72,0:72:99:2963,217,0,2963,217,2963:0,0,44,28 20 10005011 . G . . END=10005426 GT:DP:GQ:MIN_DP:PL 0/0:72:99:51:0,120,1800 20 10005427 . C T, 2214.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|195241.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|27,28|0,0;DP=55;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=195241.00 GT:AD:DP:GQ:PL:SB 1/1:0,55,0:55:99:2243,165,0,2243,165,2243:0,0,27,28 -20 10005428 . A . . END=10005498 GT:DP:GQ:MIN_DP:PL 0/0:71:99:58:0,120,1800 +20 10005428 . A . . END=10005498 GT:DP:GQ:MIN_DP:PL 0/0:71:99:57:0,120,1800 20 10005499 . A G, 3053.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|273600.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|45,31|0,0;DP=76;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=273600.00 GT:AD:DP:GQ:PL:SB 1/1:0,76,0:76:99:3082,229,0,3082,229,3082:0,0,45,31 20 10005500 . T . . END=10005586 GT:DP:GQ:MIN_DP:PL 0/0:71:99:66:0,120,1800 20 10005587 . A G, 1229.77 . AS_RAW_BaseQRankSum=|-0.9,1|NaN;AS_RAW_MQ=129600.00|127369.00|0.00;AS_RAW_MQRankSum=|-1.0,1|NaN;AS_RAW_ReadPosRankSum=|0.2,1|NaN;AS_SB_TABLE=19,17|16,20|0,0;BaseQRankSum=-0.834;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.972;RAW_MQ=256969.00;ReadPosRankSum=0.248 GT:AD:DP:GQ:PL:SB 0/1:36,36,0:72:99:1258,0,1236,1366,1345,2710:19,17,16,20 @@ -260,17 +244,9 @@ 20 10006404 . A C, 2928.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|268082.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|27,49|0,0;DP=77;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=269451.00 GT:AD:DP:GQ:PL:SB 1/1:0,76,0:76:99:2957,228,0,2957,228,2957:0,0,27,49 20 10006405 . C . . END=10006681 GT:DP:GQ:MIN_DP:PL 0/0:78:99:65:0,120,1800 20 10006682 . T A, 2874.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|257810.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|44,29|0,0;DP=73;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=257810.00 GT:AD:DP:GQ:PL:SB 1/1:0,73,0:73:99:2903,219,0,2903,219,2903:0,0,44,29 -20 10006683 . A . . END=10006807 GT:DP:GQ:MIN_DP:PL 0/0:65:99:61:0,99,1485 -20 10006808 . C . . END=10006808 GT:DP:GQ:MIN_DP:PL 0/0:75:78:75:0,78,1170 -20 10006809 . C . . END=10006813 GT:DP:GQ:MIN_DP:PL 0/0:76:60:75:0,60,900 -20 10006814 . T . . END=10006814 GT:DP:GQ:MIN_DP:PL 0/0:79:57:79:0,57,855 -20 10006815 . C . . END=10006815 GT:DP:GQ:MIN_DP:PL 0/0:80:51:80:0,51,765 -20 10006816 . T . . END=10006816 GT:DP:GQ:MIN_DP:PL 0/0:80:45:80:0,45,675 -20 10006817 . A . . END=10006817 GT:DP:GQ:MIN_DP:PL 0/0:80:33:80:0,33,495 -20 10006818 . A . . END=10006818 GT:DP:GQ:MIN_DP:PL 0/0:77:30:77:0,30,450 +20 10006683 . A . . END=10006818 GT:DP:GQ:MIN_DP:PL 0/0:65:99:61:0,120,1800 20 10006819 . AAAAC A, 2531.73 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|219200.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|30,28|0,0;DP=76;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=284000.00 GT:AD:DP:GQ:PL:SB 1/1:0,58,0:58:99:2569,176,0,2569,176,2569:0,0,30,28 -20 10006824 . A . . END=10006824 GT:DP:GQ:MIN_DP:PL 0/0:75:0:75:0,0,0 -20 10006825 . A . . END=10007149 GT:DP:GQ:MIN_DP:PL 0/0:77:99:59:0,120,1800 +20 10006824 . A . . END=10007149 GT:DP:GQ:MIN_DP:PL 0/0:77:99:59:0,120,1800 20 10007150 . G C, 669.77 . AS_RAW_BaseQRankSum=|-4.5,1|NaN;AS_RAW_MQ=136800.00|90000.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=16,22|14,11|0,0;BaseQRankSum=-4.476;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=226800.00;ReadPosRankSum=-0.077 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:38,25,0:63:99:0|1:10007150_G_C:698,0,1479,813,1554,2366:16,22,14,11 20 10007151 . G . . END=10007174 GT:DP:GQ:MIN_DP:PL 0/0:57:99:56:0,120,1800 20 10007175 . C T, 1350.77 . AS_RAW_BaseQRankSum=|2.2,1|NaN;AS_RAW_MQ=80041.00|136800.00|0.00;AS_RAW_MQRankSum=|1.3,1|NaN;AS_RAW_ReadPosRankSum=|-1.3,1|NaN;AS_SB_TABLE=9,14|18,20|0,0;BaseQRankSum=2.249;DP=61;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.319;RAW_MQ=216841.00;ReadPosRankSum=-1.213 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:23,38,0:61:99:1|0:10007150_G_C:1379,0,780,1448,894,2343:9,14,18,20 @@ -280,72 +256,34 @@ 20 10007531 . A G, 2920.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|256969.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|48,24|0,0;DP=72;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=256969.00 GT:AD:DP:GQ:PL:SB 1/1:0,72,0:72:99:2949,217,0,2949,217,2949:0,0,48,24 20 10007532 . G . . END=10007979 GT:DP:GQ:MIN_DP:PL 0/0:80:99:65:0,120,1800 20 10007980 . A C, 3524.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|331800.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|39,51|0,0;DP=90;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=331800.00 GT:AD:DP:GQ:PL:SB 1/1:0,90,0:90:99:3553,270,0,3553,270,3553:0,0,39,51 -20 10007981 . A . . END=10008013 GT:DP:GQ:MIN_DP:PL 0/0:85:99:81:0,99,1485 -20 10008014 . C . . END=10008014 GT:DP:GQ:MIN_DP:PL 0/0:85:90:85:0,90,1350 -20 10008015 . C . . END=10008015 GT:DP:GQ:MIN_DP:PL 0/0:88:87:88:0,87,1305 -20 10008016 . A . . END=10008020 GT:DP:GQ:MIN_DP:PL 0/0:90:72:89:0,72,1080 -20 10008021 . G . . END=10008021 GT:DP:GQ:MIN_DP:PL 0/0:86:54:86:0,54,810 -20 10008022 . A . . END=10008023 GT:DP:GQ:MIN_DP:PL 0/0:85:33:85:0,33,495 -20 10008024 . A . . END=10008028 GT:DP:GQ:MIN_DP:PL 0/0:87:9:86:0,9,135 +20 10007981 . A . . END=10008028 GT:DP:GQ:MIN_DP:PL 0/0:86:99:80:0,120,1800 20 10008029 . T TA, 1986.73 . AS_RAW_BaseQRankSum=|0.4,1|NaN;AS_RAW_MQ=10800.00|268510.00|0.00;AS_RAW_MQRankSum=|0.5,1|NaN;AS_RAW_ReadPosRankSum=|-1.4,1|NaN;AS_SB_TABLE=1,2|27,45|0,0;BaseQRankSum=0.409;DP=88;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=0.576;RAW_MQ=327251.00;ReadPosRankSum=-1.326 GT:AD:DP:GQ:PL:SB 1/1:3,72,0:75:99:2024,145,0,2033,222,2110:1,2,27,45 -20 10008030 . A . . END=10008030 GT:DP:GQ:MIN_DP:PL 0/0:91:0:91:0,0,0 -20 10008031 . A . . END=10008127 GT:DP:GQ:MIN_DP:PL 0/0:82:99:77:0,105,1575 -20 10008128 . T . . END=10008129 GT:DP:GQ:MIN_DP:PL 0/0:79:93:78:0,93,1395 -20 10008130 . T . . END=10008131 GT:DP:GQ:MIN_DP:PL 0/0:78:78:77:0,78,1170 -20 10008132 . C . . END=10008133 GT:DP:GQ:MIN_DP:PL 0/0:77:60:76:0,60,900 -20 10008134 . A . . END=10008134 GT:DP:GQ:MIN_DP:PL 0/0:79:54:79:0,54,810 -20 10008135 . G . . END=10008135 GT:DP:GQ:MIN_DP:PL 0/0:79:48:79:0,48,720 -20 10008136 . A . . END=10008136 GT:DP:GQ:MIN_DP:PL 0/0:78:24:78:0,24,360 -20 10008137 . T . . END=10008139 GT:DP:GQ:MIN_DP:PL 0/0:77:21:76:0,21,315 -20 10008140 . T . . END=10008140 GT:DP:GQ:MIN_DP:PL 0/0:78:18:78:0,18,270 -20 10008141 . C . . END=10008141 GT:DP:GQ:MIN_DP:PL 0/0:79:9:79:0,9,135 -20 10008142 . T . . END=10008142 GT:DP:GQ:MIN_DP:PL 0/0:77:6:77:0,6,90 -20 10008143 . C . . END=10008145 GT:DP:GQ:MIN_DP:PL 0/0:77:3:76:0,3,45 +20 10008030 . A . . END=10008145 GT:DP:GQ:MIN_DP:PL 0/0:82:99:76:0,120,1800 20 10008146 . TA T, 2141.73 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|257200.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|38,32|0,0;DP=73;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=268000.00 GT:AD:DP:GQ:PL:SB 1/1:0,70,0:70:99:2179,211,0,2179,211,2179:0,0,38,32 -20 10008148 . A . . END=10008148 GT:DP:GQ:MIN_DP:PL 0/0:74:0:74:0,0,0 -20 10008149 . A . . END=10008220 GT:DP:GQ:MIN_DP:PL 0/0:81:99:74:0,120,1800 +20 10008148 . A . . END=10008220 GT:DP:GQ:MIN_DP:PL 0/0:80:99:72:0,120,1800 20 10008221 . T C, 3224.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|289669.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|43,37|0,0;DP=80;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=289669.00 GT:AD:DP:GQ:PL:SB 1/1:0,80,0:80:99:3253,240,0,3253,240,3253:0,0,43,37 20 10008222 . T . . END=10008457 GT:DP:GQ:MIN_DP:PL 0/0:64:99:45:0,108,1620 20 10008458 . T G, 2654.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|191842.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|30,39|0,0;DP=69;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=191842.00 GT:AD:DP:GQ:PL:SB 1/1:0,69,0:69:99:2683,207,0,2683,207,2683:0,0,30,39 20 10008459 . A . . END=10008732 GT:DP:GQ:MIN_DP:PL 0/0:70:99:40:0,105,1575 -20 10008733 . T . . END=10008737 GT:DP:GQ:MIN_DP:PL 0/0:47:90:47:0,90,1350 -20 10008738 . C . . END=10008740 GT:DP:GQ:MIN_DP:PL 0/0:50:81:49:0,81,1215 -20 10008741 . C . . END=10008741 GT:DP:GQ:MIN_DP:PL 0/0:52:78:52:0,78,1170 +20 10008733 . T . . END=10008733 GT:DP:GQ:MIN_DP:PL 0/0:47:94:47:0,94,1689 +20 10008734 . G . . END=10008741 GT:DP:GQ:MIN_DP:PL 0/0:48:99:47:0,120,1800 20 10008742 . G T, 715.77 . AS_RAW_BaseQRankSum=|3.8,1|NaN;AS_RAW_MQ=37586.00|30288.00|0.00;AS_RAW_MQRankSum=|-1.6,1|NaN;AS_RAW_ReadPosRankSum=|0.1,1|NaN;AS_SB_TABLE=10,13|11,15|0,0;BaseQRankSum=3.893;DP=49;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.502;RAW_MQ=67874.00;ReadPosRankSum=0.190 GT:AD:DP:GQ:PL:SB 0/1:23,26,0:49:99:744,0,580,813,658,1471:10,13,11,15 -20 10008743 . T . . END=10008744 GT:DP:GQ:MIN_DP:PL 0/0:52:72:52:0,72,1080 -20 10008745 . T . . END=10008746 GT:DP:GQ:MIN_DP:PL 0/0:52:63:52:0,63,945 -20 10008747 . T . . END=10008749 GT:DP:GQ:MIN_DP:PL 0/0:49:57:48:0,57,855 -20 10008750 . T . . END=10008750 GT:DP:GQ:MIN_DP:PL 0/0:47:51:47:0,51,765 -20 10008751 . A . . END=10008751 GT:DP:GQ:MIN_DP:PL 0/0:49:30:49:0,30,450 -20 10008752 . A . . END=10008754 GT:DP:GQ:MIN_DP:PL 0/0:51:33:51:0,33,495 -20 10008755 . A . . END=10008755 GT:DP:GQ:MIN_DP:PL 0/0:51:36:51:0,36,540 -20 10008756 . T . . END=10008756 GT:DP:GQ:MIN_DP:PL 0/0:45:33:45:0,33,495 -20 10008757 . A . . END=10008757 GT:DP:GQ:MIN_DP:PL 0/0:48:24:48:0,24,360 +20 10008743 . T . . END=10008757 GT:DP:GQ:MIN_DP:PL 0/0:46:99:42:0,99,1485 20 10008758 . C CA, 684.14 . AS_RAW_BaseQRankSum=|0.1,1|NaN;AS_RAW_MQ=6578.00|37631.00|0.00;AS_RAW_MQRankSum=|-1.2,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=3,1|16,15|0,0;BaseQRankSum=0.130;DP=44;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=-1.168;RAW_MQ=54656.00;ReadPosRankSum=-0.052 GT:AD:DP:GQ:PL:SB 1/1:4,31,0:35:10:721,10,0,733,102,825:3,1,16,15 -20 10008759 . A . . END=10008759 GT:DP:GQ:MIN_DP:PL 0/0:55:0:55:0,0,0 -20 10008760 . A . . END=10008772 GT:DP:GQ:MIN_DP:PL 0/0:55:99:53:0,120,1800 +20 10008759 . A . . END=10008772 GT:DP:GQ:MIN_DP:PL 0/0:55:99:53:0,120,1800 20 10008773 . T . . END=10008773 GT:DP:GQ:MIN_DP:PL 0/0:54:0:54:0,0,1660 20 10008774 . T . . END=10008774 GT:DP:GQ:MIN_DP:PL 0/0:55:99:55:0,117,1755 20 10008775 . A . . END=10008775 GT:DP:GQ:MIN_DP:PL 0/0:55:60:55:0,60,1923 -20 10008776 . G . . END=10008910 GT:DP:GQ:MIN_DP:PL 0/0:55:99:45:0,100,1530 -20 10008911 . G . . END=10008911 GT:DP:GQ:MIN_DP:PL 0/0:45:93:45:0,93,1395 -20 10008912 . A . . END=10008916 GT:DP:GQ:MIN_DP:PL 0/0:46:84:45:0,84,1260 -20 10008917 . G . . END=10008917 GT:DP:GQ:MIN_DP:PL 0/0:46:78:46:0,78,1170 -20 10008918 . T . . END=10008920 GT:DP:GQ:MIN_DP:PL 0/0:50:66:48:0,66,990 +20 10008776 . G . . END=10008920 GT:DP:GQ:MIN_DP:PL 0/0:54:99:45:0,99,1480 20 10008921 . C CA, 253.73 . AS_RAW_BaseQRankSum=|0.6,1|NaN;AS_RAW_MQ=62041.00|43805.00|0.00;AS_RAW_MQRankSum=|-2.0,1|NaN;AS_RAW_ReadPosRankSum=|0.1,1|NaN;AS_SB_TABLE=10,8|8,8|0,0;BaseQRankSum=0.610;DP=49;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.906;RAW_MQ=155512.00;ReadPosRankSum=0.173 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:18,16,0:34:99:0|1:10008921_C_CA:291,0,366,345,415,761:10,8,8,8 -20 10008922 . A . . END=10008922 GT:DP:GQ:MIN_DP:PL 0/0:51:0:51:0,0,714 -20 10008923 . A . . END=10008934 GT:DP:GQ:MIN_DP:PL 0/0:58:99:55:0,117,1755 -20 10008935 . T . . END=10008936 GT:DP:GQ:MIN_DP:PL 0/0:54:73:52:0,73,1586 -20 10008937 . A . . END=10008938 GT:DP:GQ:MIN_DP:PL 0/0:55:99:54:0,111,1665 -20 10008939 . T . . END=10008940 GT:DP:GQ:MIN_DP:PL 0/0:52:93:51:0,93,1395 -20 10008941 . A . . END=10008942 GT:DP:GQ:MIN_DP:PL 0/0:50:84:49:0,84,1260 -20 10008943 . A . . END=10008946 GT:DP:GQ:MIN_DP:PL 0/0:49:72:49:0,72,1080 -20 10008947 . T . . END=10008947 GT:DP:GQ:MIN_DP:PL 0/0:48:66:48:0,66,990 +20 10008922 . A . . END=10008942 GT:DP:GQ:MIN_DP:PL 0/0:53:99:47:0,114,1710 +20 10008943 . A . . END=10008944 GT:DP:GQ:MIN_DP:PL 0/0:47:78:47:0,78,1170 +20 10008945 . A . . END=10008947 GT:DP:GQ:MIN_DP:PL 0/0:47:81:46:0,81,1215 20 10008948 . TA T, 2057.73 . AS_RAW_BaseQRankSum=|0.9,1|NaN;AS_RAW_MQ=625.00|134397.00|0.00;AS_RAW_MQRankSum=|2.0,1|NaN;AS_RAW_ReadPosRankSum=|0.8,1|NaN;AS_SB_TABLE=1,0|35,15|0,0;BaseQRankSum=0.994;DP=52;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=2.047;RAW_MQ=138622.00;ReadPosRankSum=0.884 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:1,50,0:51:99:0|1:10008921_C_CA:2095,107,0,2098,159,2150:1,0,35,15 -20 10008950 . A . . END=10008951 GT:DP:GQ:MIN_DP:PL 0/0:48:0:48:0,0,0 +20 10008950 . A . . END=10008950 GT:DP:GQ:MIN_DP:PL 0/0:52:99:52:0,99,1485 +20 10008951 . A . . END=10008951 GT:DP:GQ:MIN_DP:PL 0/0:51:93:51:0,93,1395 20 10008952 . CACACACACACACA C,CCA,CCACACACACA,CCACACACACACA, 1666.73 . AS_RAW_BaseQRankSum=|0.3,1|0.3,1|0.6,1|1.9,1|NaN;AS_RAW_MQ=625.00|2523.00|11774.00|12125.00|39600.00|0.00;AS_RAW_MQRankSum=|1.1,1|4.0,1|0.6,1|3.6,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|1.0,1|-0.3,1|0.8,1|NaN;AS_SB_TABLE=1,0|2,1|8,6|4,1|11,0|0,0;BaseQRankSum=0.941;DP=59;ExcessHet=3.0103;MLEAC=0,1,0,1,0;MLEAF=0.00,0.500,0.00,0.500,0.00;MQRankSum=1.844;RAW_MQ=154068.00;ReadPosRankSum=0.716 GT:AD:DP:GQ:PL:SB 2/4:1,3,14,5,11,0:34:99:1704,876,1258,525,811,845,726,514,173,703,582,342,0,443,530,1135,1092,744,779,607,1321:1,0,25,8 -20 10008966 . C . . END=10008966 GT:DP:GQ:MIN_DP:PL 0/0:56:95:56:0,95,1995 -20 10008967 . A . . END=10008986 GT:DP:GQ:MIN_DP:PL 0/0:58:99:56:0,120,1800 +20 10008966 . C . . END=10008986 GT:DP:GQ:MIN_DP:PL 0/0:58:99:56:0,120,1800 20 10008987 . A . . END=10008989 GT:DP:GQ:MIN_DP:PL 0/0:59:94:59:0,94,2181 20 10008990 . C . . END=10009226 GT:DP:GQ:MIN_DP:PL 0/0:61:99:38:0,102,1530 20 10009227 . A G, 1369.77 . AS_RAW_BaseQRankSum=|-2.3,1|NaN;AS_RAW_MQ=70061.00|132527.00|0.00;AS_RAW_MQRankSum=|1.4,1|NaN;AS_RAW_ReadPosRankSum=|-1.2,1|NaN;AS_SB_TABLE=16,7|19,20|0,0;BaseQRankSum=-2.220;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.428;RAW_MQ=202588.00;ReadPosRankSum=-1.159 GT:AD:DP:GQ:PL:SB 0/1:23,39,0:62:99:1398,0,740,1468,857,2325:16,7,19,20 @@ -359,42 +297,30 @@ 20 10009719 . A G, 1895.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|207410.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|26,33|0,0;DP=59;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=207410.00 GT:AD:DP:GQ:PL:SB 1/1:0,59,0:59:99:1924,175,0,1924,175,1924:0,0,26,33 20 10009720 . T . . END=10009794 GT:DP:GQ:MIN_DP:PL 0/0:54:99:47:0,120,1800 20 10009795 . A G, 1880.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|166969.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|16,31|0,0;DP=47;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=166969.00 GT:AD:DP:GQ:PL:SB 1/1:0,47,0:47:99:1909,141,0,1909,141,1909:0,0,16,31 -20 10009796 . C . . END=10009828 GT:DP:GQ:MIN_DP:PL 0/0:48:99:44:0,120,1800 -20 10009829 . A . . END=10009829 GT:DP:GQ:MIN_DP:PL 0/0:54:69:54:0,69,1035 -20 10009830 . G . . END=10009830 GT:DP:GQ:MIN_DP:PL 0/0:54:72:54:0,72,1080 -20 10009831 . A . . END=10009832 GT:DP:GQ:MIN_DP:PL 0/0:54:63:53:0,63,945 -20 10009833 . A . . END=10009833 GT:DP:GQ:MIN_DP:PL 0/0:53:27:53:0,27,405 -20 10009834 . G . . END=10009834 GT:DP:GQ:MIN_DP:PL 0/0:53:30:53:0,30,450 -20 10009835 . A . . END=10009838 GT:DP:GQ:MIN_DP:PL 0/0:55:33:54:0,33,495 -20 10009839 . A . . END=10009839 GT:DP:GQ:MIN_DP:PL 0/0:54:30:54:0,30,450 -20 10009840 . A . . END=10009840 GT:DP:GQ:MIN_DP:PL 0/0:54:33:54:0,33,495 -20 10009841 . A . . END=10009841 GT:DP:GQ:MIN_DP:PL 0/0:55:27:55:0,27,405 +20 10009796 . C . . END=10009832 GT:DP:GQ:MIN_DP:PL 0/0:49:99:44:0,99,1485 +20 10009833 . A . . END=10009840 GT:DP:GQ:MIN_DP:PL 0/0:53:66:51:0,66,990 +20 10009841 . A . . END=10009841 GT:DP:GQ:MIN_DP:PL 0/0:51:39:51:0,39,585 20 10009842 . G GAA, 532.73 . AS_RAW_BaseQRankSum=|0.8,1|NaN;AS_RAW_MQ=51846.00|37046.00|0.00;AS_RAW_MQRankSum=|-0.7,1|NaN;AS_RAW_ReadPosRankSum=|1.7,1|NaN;AS_SB_TABLE=9,10|8,7|0,0;BaseQRankSum=0.872;DP=51;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.603;RAW_MQ=150092.00;ReadPosRankSum=1.720 GT:AD:DP:GQ:PL:SB 0/1:19,15,0:34:99:570,0,690,629,738,1367:9,10,8,7 -20 10009843 . A . . END=10009843 GT:DP:GQ:MIN_DP:PL 0/0:56:27:56:0,27,405 +20 10009843 . A . . END=10009843 GT:DP:GQ:MIN_DP:PL 0/0:51:36:51:0,36,540 20 10009844 . G A, 661.77 . AS_RAW_BaseQRankSum=|1.0,1|NaN;AS_RAW_MQ=37722.00|51846.00|0.00;AS_RAW_MQRankSum=|0.9,1|NaN;AS_RAW_ReadPosRankSum=|-1.6,1|NaN;AS_SB_TABLE=8,8|9,10|0,0;BaseQRankSum=1.048;DP=51;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.975;RAW_MQ=147168.00;ReadPosRankSum=-1.555 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:16,19,0:35:99:0|1:10009844_G_A:690,0,586,739,644,1382:8,8,9,10 -20 10009845 . A . . END=10009847 GT:DP:GQ:MIN_DP:PL 0/0:55:30:55:0,30,450 -20 10009848 . G . . END=10009848 GT:DP:GQ:MIN_DP:PL 0/0:58:39:58:0,39,585 -20 10009849 . A . . END=10009850 GT:DP:GQ:MIN_DP:PL 0/0:59:45:58:0,45,675 -20 10009851 . A . . END=10009851 GT:DP:GQ:MIN_DP:PL 0/0:60:51:60:0,51,765 -20 10009852 . G . . END=10009852 GT:DP:GQ:MIN_DP:PL 0/0:60:54:60:0,54,810 -20 10009853 . A . . END=10009853 GT:DP:GQ:MIN_DP:PL 0/0:61:57:61:0,57,855 -20 10009854 . G . . END=10009860 GT:DP:GQ:MIN_DP:PL 0/0:61:60:60:0,60,900 -20 10009861 . A . . END=10009867 GT:DP:GQ:MIN_DP:PL 0/0:58:72:56:0,72,1080 -20 10009868 . G . . END=10009870 GT:DP:GQ:MIN_DP:PL 0/0:57:81:56:0,81,1215 +20 10009845 . A . . END=10009847 GT:DP:GQ:MIN_DP:PL 0/0:51:42:51:0,42,630 +20 10009848 . G . . END=10009848 GT:DP:GQ:MIN_DP:PL 0/0:54:51:54:0,51,765 +20 10009849 . A . . END=10009850 GT:DP:GQ:MIN_DP:PL 0/0:55:57:54:0,57,855 +20 10009851 . A . . END=10009853 GT:DP:GQ:MIN_DP:PL 0/0:56:63:56:0,63,945 +20 10009854 . G . . END=10009860 GT:DP:GQ:MIN_DP:PL 0/0:57:72:56:0,72,1080 +20 10009861 . A . . END=10009864 GT:DP:GQ:MIN_DP:PL 0/0:58:84:56:0,84,1260 +20 10009865 . A . . END=10009869 GT:DP:GQ:MIN_DP:PL 0/0:57:90:56:0,90,1350 +20 10009870 . G . . END=10009870 GT:DP:GQ:MIN_DP:PL 0/0:57:99:57:0,99,1485 20 10009871 . A G, 658.77 . AS_RAW_BaseQRankSum=|-0.9,1|NaN;AS_RAW_MQ=35804.00|51846.00|0.00;AS_RAW_MQRankSum=|1.4,1|NaN;AS_RAW_ReadPosRankSum=|1.5,1|NaN;AS_SB_TABLE=10,7|9,10|0,0;BaseQRankSum=-0.803;DP=60;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.495;RAW_MQ=154737.00;ReadPosRankSum=1.539 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:17,19,0:36:99:0|1:10009844_G_A:687,0,594,739,652,1391:10,7,9,10 -20 10009872 . G . . END=10009873 GT:DP:GQ:MIN_DP:PL 0/0:57:96:55:0,96,1440 -20 10009874 . G . . END=10009874 GT:DP:GQ:MIN_DP:PL 0/0:58:99:58:0,102,1530 +20 10009872 . G . . END=10009874 GT:DP:GQ:MIN_DP:PL 0/0:57:99:55:0,108,1620 20 10009875 . A G,AGGGAGG, 2369.73 . AS_RAW_BaseQRankSum=|1.3,1|-0.7,1|NaN;AS_RAW_MQ=1682.00|40205.00|26922.00|0.00;AS_RAW_MQRankSum=|1.8,1|0.8,1|NaN;AS_RAW_ReadPosRankSum=|1.4,1|0.5,1|NaN;AS_SB_TABLE=2,0|6,9|6,7|0,0;BaseQRankSum=0.378;DP=57;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;MQRankSum=1.361;RAW_MQ=143937.00;ReadPosRankSum=1.040 GT:AD:DP:GQ:PL:SB 1/2:2,15,13,0:30:99:2407,645,533,697,0,574,1881,655,700,1805:2,0,12,16 -20 10009876 . G . . END=10009876 GT:DP:GQ:MIN_DP:PL 0/0:57:99:57:0,108,2100 -20 10009877 . A . . END=10009877 GT:DP:GQ:MIN_DP:PL 0/0:55:85:55:0,85,1858 -20 10009878 . G . . END=10009878 GT:DP:GQ:MIN_DP:PL 0/0:55:99:55:0,108,1620 +20 10009876 . G . . END=10009878 GT:DP:GQ:MIN_DP:PL 0/0:52:99:51:0,114,1710 20 10009879 . A G, 2244.77 . AS_RAW_BaseQRankSum=|1.5,1|NaN;AS_RAW_MQ=1682.00|118979.00|0.00;AS_RAW_MQRankSum=|1.5,1|NaN;AS_RAW_ReadPosRankSum=|1.1,1|NaN;AS_SB_TABLE=2,0|15,32|0,0;BaseQRankSum=1.534;DP=49;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=1.570;RAW_MQ=120661.00;ReadPosRankSum=1.113 GT:AD:DP:GQ:PL:SB 1/1:2,47,0:49:99:2273,150,0,2276,154,2279:2,0,15,32 -20 10009880 . G . . END=10009880 GT:DP:GQ:MIN_DP:PL 0/0:52:80:52:0,80,1858 -20 10009881 . A . . END=10009882 GT:DP:GQ:MIN_DP:PL 0/0:51:99:50:0,108,1755 +20 10009880 . G . . END=10009882 GT:DP:GQ:MIN_DP:PL 0/0:49:99:48:0,120,1800 20 10009883 . A G, 2151.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|127656.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|15,32|0,0;DP=49;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=129338.00 GT:AD:DP:GQ:PL:SB 1/1:0,47,0:47:99:2180,147,0,2180,147,2181:0,0,15,32 20 10009884 . G . . END=10009884 GT:DP:GQ:MIN_DP:PL 0/0:53:99:53:0,120,1800 -20 10009885 . A . . END=10009885 GT:DP:GQ:MIN_DP:PL 0/0:52:58:52:0,58,1739 -20 10009886 . A . . END=10009886 GT:DP:GQ:MIN_DP:PL 0/0:53:0:53:0,0,1490 +20 10009885 . A . . END=10009885 GT:DP:GQ:MIN_DP:PL 0/0:52:96:52:0,96,1815 +20 10009886 . A . . END=10009886 GT:DP:GQ:MIN_DP:PL 0/0:53:0:53:0,0,1567 20 10009887 . G . . END=10009887 GT:DP:GQ:MIN_DP:PL 0/0:50:99:50:0,109,1906 20 10009888 . A . . END=10009888 GT:DP:GQ:MIN_DP:PL 0/0:51:0:51:0,0,1610 20 10009889 . A . . END=10009891 GT:DP:GQ:MIN_DP:PL 0/0:49:99:49:0,106,1800 @@ -403,20 +329,9 @@ 20 10009894 . G . . END=10009894 GT:DP:GQ:MIN_DP:PL 0/0:53:48:53:0,48,1842 20 10009895 . G . . END=10010392 GT:DP:GQ:MIN_DP:PL 0/0:70:99:45:0,111,1665 20 10010393 . T G, 1464.77 . AS_RAW_BaseQRankSum=|-3.4,1|NaN;AS_RAW_MQ=129600.00|149282.00|0.00;AS_RAW_MQRankSum=|-1.3,1|NaN;AS_RAW_ReadPosRankSum=|-1.8,1|NaN;AS_SB_TABLE=24,12|19,24|0,0;BaseQRankSum=-3.351;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.284;RAW_MQ=278882.00;ReadPosRankSum=-1.738 GT:AD:DP:GQ:PL:SB 0/1:36,43,0:79:99:1493,0,1230,1601,1359,2961:24,12,19,24 -20 10010394 . T . . END=10010518 GT:DP:GQ:MIN_DP:PL 0/0:82:99:67:0,102,1530 -20 10010519 . T . . END=10010522 GT:DP:GQ:MIN_DP:PL 0/0:90:81:89:0,81,1215 -20 10010523 . G . . END=10010526 GT:DP:GQ:MIN_DP:PL 0/0:92:63:90:0,63,945 -20 10010527 . A . . END=10010527 GT:DP:GQ:MIN_DP:PL 0/0:88:54:88:0,54,810 -20 10010528 . T . . END=10010528 GT:DP:GQ:MIN_DP:PL 0/0:88:51:88:0,51,765 -20 10010529 . T . . END=10010529 GT:DP:GQ:MIN_DP:PL 0/0:88:48:88:0,48,720 -20 10010530 . T . . END=10010531 GT:DP:GQ:MIN_DP:PL 0/0:87:45:86:0,45,675 -20 10010532 . A . . END=10010532 GT:DP:GQ:MIN_DP:PL 0/0:84:39:84:0,39,585 -20 10010533 . G . . END=10010533 GT:DP:GQ:MIN_DP:PL 0/0:83:33:83:0,33,495 -20 10010534 . A . . END=10010534 GT:DP:GQ:MIN_DP:PL 0/0:84:24:84:0,24,360 -20 10010535 . A . . END=10010535 GT:DP:GQ:MIN_DP:PL 0/0:85:12:85:0,12,180 +20 10010394 . T . . END=10010535 GT:DP:GQ:MIN_DP:PL 0/0:83:99:67:0,120,1800 20 10010536 . G GA, 2462.73 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|301300.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|36,43|0,0;DP=85;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=322900.00 GT:AD:DP:GQ:PL:SB 1/1:0,79,0:79:99:2500,243,0,2500,244,2500:0,0,36,43 -20 10010537 . A . . END=10010537 GT:DP:GQ:MIN_DP:PL 0/0:88:0:88:0,0,0 -20 10010538 . A . . END=10010765 GT:DP:GQ:MIN_DP:PL 0/0:79:99:68:0,120,1800 +20 10010537 . A . . END=10010765 GT:DP:GQ:MIN_DP:PL 0/0:79:99:68:0,120,1800 20 10010766 . T G, 2411.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|237600.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|35,31|0,0;DP=67;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=241200.00 GT:AD:DP:GQ:PL:SB 1/1:0,66,0:66:99:2440,199,0,2440,199,2440:0,0,35,31 20 10010767 . G . . END=10010831 GT:DP:GQ:MIN_DP:PL 0/0:74:99:61:0,120,1800 20 10010832 . T C, 2951.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|265538.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|31,44|0,0;DP=75;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=265538.00 GT:AD:DP:GQ:PL:SB 1/1:0,75,0:75:99:2980,226,0,2980,226,2980:0,0,31,44 @@ -430,45 +345,25 @@ 20 10011666 . C T, 2961.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|254523.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|43,30|0,0;DP=73;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=254523.00 GT:AD:DP:GQ:PL:SB 1/1:0,73,0:73:99:2990,220,0,2990,220,2990:0,0,43,30 20 10011667 . A . . END=10011938 GT:DP:GQ:MIN_DP:PL 0/0:87:99:64:0,111,1665 20 10011939 . C T, 2469.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|193043.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|23,38|0,0;DP=61;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=193043.00 GT:AD:DP:GQ:PL:SB 1/1:0,61,0:61:99:2498,184,0,2498,184,2498:0,0,23,38 -20 10011940 . G . . END=10011944 GT:DP:GQ:MIN_DP:PL 0/0:62:99:54:0,114,1710 -20 10011945 . G . . END=10011945 GT:DP:GQ:MIN_DP:PL 0/0:50:84:50:0,84,1730 -20 10011946 . T . . END=10011992 GT:DP:GQ:MIN_DP:PL 0/0:53:99:44:0,102,1530 -20 10011993 . C . . END=10011996 GT:DP:GQ:MIN_DP:PL 0/0:59:90:57:0,90,1350 -20 10011997 . A . . END=10011998 GT:DP:GQ:MIN_DP:PL 0/0:59:75:59:0,75,1125 -20 10011999 . T . . END=10012000 GT:DP:GQ:MIN_DP:PL 0/0:60:63:59:0,63,945 -20 10012001 . A . . END=10012001 GT:DP:GQ:MIN_DP:PL 0/0:60:57:60:0,57,855 -20 10012002 . C . . END=10012002 GT:DP:GQ:MIN_DP:PL 0/0:61:51:61:0,51,765 -20 10012003 . T . . END=10012005 GT:DP:GQ:MIN_DP:PL 0/0:61:48:61:0,48,720 -20 10012006 . T . . END=10012006 GT:DP:GQ:MIN_DP:PL 0/0:63:39:63:0,39,585 -20 10012007 . A . . END=10012007 GT:DP:GQ:MIN_DP:PL 0/0:64:36:64:0,36,540 -20 10012008 . G . . END=10012010 GT:DP:GQ:MIN_DP:PL 0/0:64:33:63:0,33,495 -20 10012011 . T . . END=10012011 GT:DP:GQ:MIN_DP:PL 0/0:65:24:65:0,24,360 -20 10012012 . C . . END=10012012 GT:DP:GQ:MIN_DP:PL 0/0:65:21:65:0,21,315 -20 10012013 . C . . END=10012013 GT:DP:GQ:MIN_DP:PL 0/0:66:18:66:0,18,270 -20 10012014 . A . . END=10012015 GT:DP:GQ:MIN_DP:PL 0/0:66:9:66:0,9,135 -20 10012016 . T . . END=10012016 GT:DP:GQ:MIN_DP:PL 0/0:68:3:68:0,3,45 -20 10012017 . A . . END=10012020 GT:DP:GQ:MIN_DP:PL 0/0:68:0:68:0,0,0 +20 10011940 . G . . END=10012020 GT:DP:GQ:MIN_DP:PL 0/0:56:99:42:0,101,1575 20 10012021 . CA C, 1975.73 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|215907.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|26,40|0,0;DP=70;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=228076.00 GT:AD:DP:GQ:PL:SB 1/1:0,66,0:66:99:2013,198,0,2013,198,2013:0,0,26,40 -20 10012023 . A . . END=10012023 GT:DP:GQ:MIN_DP:PL 0/0:69:0:69:0,0,0 -20 10012024 . A . . END=10012147 GT:DP:GQ:MIN_DP:PL 0/0:70:99:38:0,99,1485 +20 10012023 . A . . END=10012147 GT:DP:GQ:MIN_DP:PL 0/0:70:99:38:0,99,1485 20 10012148 . G . . END=10012157 GT:DP:GQ:MIN_DP:PL 0/0:38:90:37:0,90,1350 20 10012158 . A . . END=10012159 GT:DP:GQ:MIN_DP:PL 0/0:35:84:34:0,84,1260 20 10012160 . C . . END=10012162 GT:DP:GQ:MIN_DP:PL 0/0:34:78:34:0,78,1170 20 10012163 . G . . END=10012167 GT:DP:GQ:MIN_DP:PL 0/0:34:81:33:0,81,1215 20 10012168 . C . . END=10012170 GT:DP:GQ:MIN_DP:PL 0/0:31:78:29:0,78,1170 -20 10012171 . T . . END=10012174 GT:DP:GQ:MIN_DP:PL 0/0:29:61:29:0,61,1035 -20 10012175 . C . . END=10012175 GT:DP:GQ:MIN_DP:PL 0/0:30:72:30:0,72,1080 -20 10012176 . A . . END=10012176 GT:DP:GQ:MIN_DP:PL 0/0:29:69:29:0,69,1035 -20 10012177 . C . . END=10012179 GT:DP:GQ:MIN_DP:PL 0/0:31:72:30:0,72,1080 -20 10012180 . C . . END=10012181 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20 10012182 . C . . END=10012183 GT:DP:GQ:MIN_DP:PL 0/0:30:78:29:0,78,1170 -20 10012184 . C . . END=10012196 GT:DP:GQ:MIN_DP:PL 0/0:32:81:30:0,81,1215 -20 10012197 . C . . END=10012197 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20 10012198 . G . . END=10012200 GT:DP:GQ:MIN_DP:PL 0/0:33:84:32:0,84,1260 -20 10012201 . T . . END=10012201 GT:DP:GQ:MIN_DP:PL 0/0:30:53:30:0,53,1087 +20 10012171 . T . . END=10012171 GT:DP:GQ:MIN_DP:PL 0/0:29:61:29:0,61,1086 +20 10012172 . C . . END=10012178 GT:DP:GQ:MIN_DP:PL 0/0:29:72:29:0,72,1080 +20 10012179 . G . . END=10012188 GT:DP:GQ:MIN_DP:PL 0/0:31:81:29:0,81,1157 +20 10012189 . G . . END=10012189 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 +20 10012190 . C . . END=10012196 GT:DP:GQ:MIN_DP:PL 0/0:32:87:30:0,87,1305 +20 10012197 . C . . END=10012197 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 +20 10012198 . G . . END=10012198 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 +20 10012199 . C . . END=10012200 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 +20 10012201 . T . . END=10012201 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 20 10012202 . C . . END=10012202 GT:DP:GQ:MIN_DP:PL 0/0:32:62:32:0,62,1157 -20 10012203 . C . . END=10012203 GT:DP:GQ:MIN_DP:PL 0/0:32:53:32:0,53,1153 -20 10012204 . T . . END=10012211 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,1350 +20 10012203 . C . . END=10012211 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,1350 20 10012212 . G . . END=10012215 GT:DP:GQ:MIN_DP:PL 0/0:31:84:30:0,84,1260 20 10012216 . C . . END=10012221 GT:DP:GQ:MIN_DP:PL 0/0:33:72:32:0,72,1080 20 10012222 . T . . END=10012224 GT:DP:GQ:MIN_DP:PL 0/0:32:69:32:0,69,1035 @@ -520,10 +415,7 @@ 20 10012399 . G . . END=10012402 GT:DP:GQ:MIN_DP:PL 0/0:16:45:15:0,45,561 20 10012403 . T . . END=10012403 GT:DP:GQ:MIN_DP:PL 0/0:15:17:15:0,17,521 20 10012404 . G . . END=10012404 GT:DP:GQ:MIN_DP:PL 0/0:14:42:14:0,42,564 -20 10012405 . G . . END=10012405 GT:DP:GQ:MIN_DP:PL 0/0:15:39:15:0,39,585 -20 10012406 . C . . END=10012406 GT:DP:GQ:MIN_DP:PL 0/0:15:3:15:0,3,396 -20 10012407 . G . . END=10012407 GT:DP:GQ:MIN_DP:PL 0/0:15:2:15:0,2,481 -20 10012408 . G . . END=10012409 GT:DP:GQ:MIN_DP:PL 0/0:15:39:15:0,39,585 +20 10012405 . G . . END=10012409 GT:DP:GQ:MIN_DP:PL 0/0:15:39:15:0,39,585 20 10012410 . C . . END=10012410 GT:DP:GQ:MIN_DP:PL 0/0:15:33:15:0,33,495 20 10012411 . C . . END=10012412 GT:DP:GQ:MIN_DP:PL 0/0:15:30:14:0,30,450 20 10012413 . C . . END=10012416 GT:DP:GQ:MIN_DP:PL 0/0:16:33:14:0,33,495 @@ -558,63 +450,56 @@ 20 10012475 . C . . END=10012476 GT:DP:GQ:MIN_DP:PL 0/0:20:36:19:0,36,540 20 10012477 . G . . END=10012478 GT:DP:GQ:MIN_DP:PL 0/0:18:33:17:0,33,495 20 10012479 . A G, 592.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|45990.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|9,8|0,0;DP=17;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=45990.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,17,0:17:50:0|1:10012479_A_G:621,50,0,621,50,621:0,0,9,8 -20 10012480 . G . . END=10012482 GT:DP:GQ:MIN_DP:PL 0/0:17:24:16:0,24,360 +20 10012480 . G . . END=10012482 GT:DP:GQ:MIN_DP:PL 0/0:16:24:15:0,24,360 20 10012483 . G . . END=10012489 GT:DP:GQ:MIN_DP:PL 0/0:13:27:12:0,27,405 20 10012490 . G . . END=10012490 GT:DP:GQ:MIN_DP:PL 0/0:11:22:11:0,22,359 20 10012491 . T . . END=10012491 GT:DP:GQ:MIN_DP:PL 0/0:8:24:8:0,24,269 -20 10012492 . G . . END=10012494 GT:DP:GQ:MIN_DP:PL 0/0:9:27:9:0,27,304 -20 10012495 . C . . END=10012497 GT:DP:GQ:MIN_DP:PL 0/0:11:30:11:0,30,450 +20 10012492 . G . . END=10012497 GT:DP:GQ:MIN_DP:PL 0/0:10:27:9:0,27,304 20 10012498 . C G, 466.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|22302.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|4,7|0,0;DP=11;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=22302.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,11,0:11:33:0|1:10012479_A_G:495,33,0,495,33,495:0,0,4,7 -20 10012499 . G . . END=10012501 GT:DP:GQ:MIN_DP:PL 0/0:12:30:10:0,30,350 -20 10012502 . C . . END=10012503 GT:DP:GQ:MIN_DP:PL 0/0:12:27:12:0,27,405 -20 10012504 . C . . END=10012508 GT:DP:GQ:MIN_DP:PL 0/0:11:24:10:0,24,360 -20 10012509 . A . . END=10012513 GT:DP:GQ:MIN_DP:PL 0/0:12:30:11:0,30,450 -20 10012514 . C . . END=10012514 GT:DP:GQ:MIN_DP:PL 0/0:11:24:11:0,24,360 -20 10012515 . A . . END=10012515 GT:DP:GQ:MIN_DP:PL 0/0:12:27:12:0,27,405 -20 10012516 . G . . END=10012517 GT:DP:GQ:MIN_DP:PL 0/0:12:24:11:0,24,360 +20 10012499 . G . . END=10012501 GT:DP:GQ:MIN_DP:PL 0/0:11:27:9:0,27,334 +20 10012502 . C . . END=10012503 GT:DP:GQ:MIN_DP:PL 0/0:11:24:11:0,24,360 +20 10012504 . C . . END=10012508 GT:DP:GQ:MIN_DP:PL 0/0:10:21:10:0,21,315 +20 10012509 . A . . END=10012513 GT:DP:GQ:MIN_DP:PL 0/0:11:27:10:0,27,405 +20 10012514 . C . . END=10012515 GT:DP:GQ:MIN_DP:PL 0/0:10:21:10:0,21,315 +20 10012516 . G . . END=10012517 GT:DP:GQ:MIN_DP:PL 0/0:10:18:9:0,18,270 20 10012518 . T C, 406.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|15102.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|4,5|0,0;DP=9;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=15102.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,9,0:9:30:0|1:10012479_A_G:435,30,0,435,30,435:0,0,4,5 -20 10012519 . C . . END=10012519 GT:DP:GQ:MIN_DP:PL 0/0:12:27:12:0,27,405 -20 10012520 . A . . END=10012520 GT:DP:GQ:MIN_DP:PL 0/0:12:24:12:0,24,400 +20 10012519 . C . . END=10012520 GT:DP:GQ:MIN_DP:PL 0/0:10:21:10:0,21,315 20 10012521 . C T, 46.77 . AS_RAW_BaseQRankSum=|2.3,1|NaN;AS_RAW_MQ=13910.00|5282.00|0.00;AS_RAW_MQRankSum=|-0.1,1|NaN;AS_RAW_ReadPosRankSum=|1.9,1|NaN;AS_SB_TABLE=4,4|2,1|0,0;BaseQRankSum=2.362;DP=11;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.038;RAW_MQ=19192.00;ReadPosRankSum=1.973 GT:AD:DP:GQ:PL:SB 0/1:8,3,0:11:75:75,0,224,99,233,332:4,4,2,1 -20 10012522 . A . . END=10012525 GT:DP:GQ:MIN_DP:PL 0/0:12:30:11:0,30,450 -20 10012526 . G . . END=10012526 GT:DP:GQ:MIN_DP:PL 0/0:10:27:10:0,27,405 -20 10012527 . C . . END=10012527 GT:DP:GQ:MIN_DP:PL 0/0:10:24:10:0,24,360 -20 10012528 . T . . END=10012536 GT:DP:GQ:MIN_DP:PL 0/0:10:21:9:0,21,315 -20 10012537 . T . . END=10012541 GT:DP:GQ:MIN_DP:PL 0/0:8:18:8:0,18,270 -20 10012542 . C . . END=10012544 GT:DP:GQ:MIN_DP:PL 0/0:8:15:8:0,15,225 -20 10012545 . C . . END=10012546 GT:DP:GQ:MIN_DP:PL 0/0:7:12:6:0,12,180 -20 10012547 . G . . END=10012547 GT:DP:GQ:MIN_DP:PL 0/0:8:7:8:0,7,219 -20 10012548 . G . . END=10012548 GT:DP:GQ:MIN_DP:PL 0/0:8:12:8:0,12,180 -20 10012549 . C . . END=10012549 GT:DP:GQ:MIN_DP:PL 0/0:8:7:8:0,7,255 -20 10012550 . C . . END=10012552 GT:DP:GQ:MIN_DP:PL 0/0:10:12:10:0,12,180 -20 10012553 . A . . END=10012555 GT:DP:GQ:MIN_DP:PL 0/0:10:9:10:0,9,135 -20 10012556 . T . . END=10012557 GT:DP:GQ:MIN_DP:PL 0/0:9:6:9:0,6,90 -20 10012558 . C . . END=10012558 GT:DP:GQ:MIN_DP:PL 0/0:9:3:9:0,3,45 -20 10012559 . C . . END=10012569 GT:DP:GQ:MIN_DP:PL 0/0:9:0:8:0,0,0 +20 10012522 . A . . END=10012525 GT:DP:GQ:MIN_DP:PL 0/0:11:24:9:0,24,360 +20 10012526 . G . . END=10012526 GT:DP:GQ:MIN_DP:PL 0/0:8:21:8:0,21,315 +20 10012527 . C . . END=10012545 GT:DP:GQ:MIN_DP:PL 0/0:7:18:6:0,18,188 +20 10012546 . G . . END=10012546 GT:DP:GQ:MIN_DP:PL 0/0:5:15:5:0,15,174 +20 10012547 . G . . END=10012548 GT:DP:GQ:MIN_DP:PL 0/0:6:18:6:0,18,207 +20 10012549 . C . . END=10012549 GT:DP:GQ:MIN_DP:PL 0/0:6:1:6:0,1,186 +20 10012550 . C . . END=10012562 GT:DP:GQ:MIN_DP:PL 0/0:8:24:8:0,24,296 +20 10012563 . G . . END=10012564 GT:DP:GQ:MIN_DP:PL 0/0:8:21:8:0,21,315 +20 10012565 . G . . END=10012567 GT:DP:GQ:MIN_DP:PL 0/0:9:24:8:0,24,261 +20 10012568 . G . . END=10012569 GT:DP:GQ:MIN_DP:PL 0/0:9:21:8:0,21,315 20 10012570 . G GCA, 457.73 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|12736.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|8,1|0,0;DP=9;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=12736.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,9,0:9:33:0|1:10012570_G_GCA:495,33,0,495,33,495:0,0,8,1 -20 10012571 . G . . END=10012571 GT:DP:GQ:MIN_DP:PL 0/0:11:0:11:0,0,0 +20 10012571 . G . . END=10012571 GT:DP:GQ:MIN_DP:PL 0/0:11:27:11:0,27,405 20 10012572 . GT G, 457.73 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|17177.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|10,1|0,0;DP=11;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=17177.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,11,0:11:33:0|1:10012570_G_GCA:495,33,0,495,33,495:0,0,10,1 -20 10012574 . G . . END=10012575 GT:DP:GQ:MIN_DP:PL 0/0:12:0:12:0,0,0 -20 10012576 . T . . END=10012576 GT:DP:GQ:MIN_DP:PL 0/0:12:4:12:0,4,413 -20 10012577 . C . . END=10012577 GT:DP:GQ:MIN_DP:PL 0/0:12:9:12:0,9,419 -20 10012578 . G . . END=10012578 GT:DP:GQ:MIN_DP:PL 0/0:12:2:12:0,2,328 +20 10012574 . G . . END=10012575 GT:DP:GQ:MIN_DP:PL 0/0:12:30:11:0,30,450 +20 10012576 . T . . END=10012577 GT:DP:GQ:MIN_DP:PL 0/0:12:33:12:0,33,495 +20 10012578 . G . . END=10012578 GT:DP:GQ:MIN_DP:PL 0/0:11:30:11:0,30,450 20 10012579 . G . . END=10012581 GT:DP:GQ:MIN_DP:PL 0/0:12:33:12:0,33,495 20 10012582 . C . . END=10012587 GT:DP:GQ:MIN_DP:PL 0/0:13:36:13:0,36,540 -20 10012588 . G . . END=10012589 GT:DP:GQ:MIN_DP:PL 0/0:13:33:12:0,33,495 -20 10012590 . C . . END=10012591 GT:DP:GQ:MIN_DP:PL 0/0:14:36:14:0,36,540 +20 10012588 . G . . END=10012588 GT:DP:GQ:MIN_DP:PL 0/0:12:33:12:0,33,495 +20 10012589 . C . . END=10012589 GT:DP:GQ:MIN_DP:PL 0/0:13:36:13:0,36,540 +20 10012590 . C . . END=10012591 GT:DP:GQ:MIN_DP:PL 0/0:14:39:14:0,39,585 20 10012592 . G . . END=10012592 GT:DP:GQ:MIN_DP:PL 0/0:14:14:14:0,14,377 -20 10012593 . C . . END=10012595 GT:DP:GQ:MIN_DP:PL 0/0:14:36:14:0,36,540 -20 10012596 . T . . END=10012597 GT:DP:GQ:MIN_DP:PL 0/0:14:33:14:0,33,495 -20 10012598 . C . . END=10012600 GT:DP:GQ:MIN_DP:PL 0/0:14:30:14:0,30,450 -20 10012601 . G . . END=10012605 GT:DP:GQ:MIN_DP:PL 0/0:15:33:15:0,33,495 -20 10012606 . C . . END=10012606 GT:DP:GQ:MIN_DP:PL 0/0:15:30:15:0,30,450 -20 10012607 . C . . END=10012609 GT:DP:GQ:MIN_DP:PL 0/0:15:27:14:0,27,405 -20 10012610 . C . . END=10012618 GT:DP:GQ:MIN_DP:PL 0/0:17:30:17:0,30,450 -20 10012619 . T . . END=10012624 GT:DP:GQ:MIN_DP:PL 0/0:19:21:17:0,21,315 -20 10012625 . C . . END=10012630 GT:DP:GQ:MIN_DP:PL 0/0:21:24:20:0,24,360 +20 10012593 . C . . END=10012600 GT:DP:GQ:MIN_DP:PL 0/0:14:39:14:0,39,585 +20 10012601 . G . . END=10012606 GT:DP:GQ:MIN_DP:PL 0/0:15:42:15:0,42,630 +20 10012607 . C . . END=10012607 GT:DP:GQ:MIN_DP:PL 0/0:15:39:15:0,39,585 +20 10012608 . C . . END=10012609 GT:DP:GQ:MIN_DP:PL 0/0:15:42:14:0,42,545 +20 10012610 . C . . END=10012618 GT:DP:GQ:MIN_DP:PL 0/0:17:48:17:0,48,720 +20 10012619 . T . . END=10012620 GT:DP:GQ:MIN_DP:PL 0/0:17:51:17:0,51,653 +20 10012621 . G . . END=10012621 GT:DP:GQ:MIN_DP:PL 0/0:19:57:19:0,57,672 +20 10012622 . G . . END=10012624 GT:DP:GQ:MIN_DP:PL 0/0:19:54:19:0,54,810 +20 10012625 . C . . END=10012625 GT:DP:GQ:MIN_DP:PL 0/0:20:57:20:0,57,855 +20 10012626 . C . . END=10012630 GT:DP:GQ:MIN_DP:PL 0/0:21:60:21:0,60,900 20 10012631 . C CG, 484.73 . AS_RAW_BaseQRankSum=|-1.1,1|NaN;AS_RAW_MQ=23282.00|25783.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|-1.9,1|NaN;AS_SB_TABLE=8,0|9,4|0,0;BaseQRankSum=-1.030;DP=21;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.670;RAW_MQ=49065.00;ReadPosRankSum=-1.813 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:8,13,0:21:99:0|1:10012631_C_CG:522,0,297,546,336,882:8,0,9,4 -20 10012632 . G . . END=10012632 GT:DP:GQ:MIN_DP:PL 0/0:21:0:21:0,0,0 -20 10012633 . C . . END=10012633 GT:DP:GQ:MIN_DP:PL 0/0:20:35:20:0,35,707 +20 10012632 . G . . END=10012632 GT:DP:GQ:MIN_DP:PL 0/0:21:54:21:0,54,810 +20 10012633 . C . . END=10012633 GT:DP:GQ:MIN_DP:PL 0/0:20:51:20:0,51,765 20 10012634 . C . . END=10012635 GT:DP:GQ:MIN_DP:PL 0/0:22:54:22:0,54,810 20 10012636 . G C, 527.77 . AS_RAW_BaseQRankSum=|2.7,1|NaN;AS_RAW_MQ=23282.00|29383.00|0.00;AS_RAW_MQRankSum=|-1.6,1|NaN;AS_RAW_ReadPosRankSum=|-2.0,1|NaN;AS_SB_TABLE=8,0|10,4|0,0;BaseQRankSum=2.711;DP=22;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.513;RAW_MQ=52665.00;ReadPosRankSum=-1.915 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:8,14,0:22:99:0|1:10012631_C_CG:556,0,294,580,336,916:8,0,10,4 20 10012637 . A . . END=10012639 GT:DP:GQ:MIN_DP:PL 0/0:20:54:20:0,54,810 @@ -645,7 +530,9 @@ 20 10012733 . G . . END=10012736 GT:DP:GQ:MIN_DP:PL 0/0:31:72:27:0,72,1080 20 10012737 . G . . END=10012739 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 20 10012740 . C . . END=10012742 GT:DP:GQ:MIN_DP:PL 0/0:29:75:29:0,75,1125 -20 10012743 . C . . END=10012750 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 +20 10012743 . C . . END=10012746 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 +20 10012747 . C . . END=10012747 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,1170 +20 10012748 . A . . END=10012750 GT:DP:GQ:MIN_DP:PL 0/0:31:81:29:0,81,1215 20 10012751 . T C, 937.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|78546.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|17,13|0,0;DP=30;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=78546.00 GT:AD:DP:GQ:PL:SB 1/1:0,30,0:30:89:966,89,0,966,89,966:0,0,17,13 20 10012752 . C . . END=10012752 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 20 10012753 . T . . END=10012753 GT:DP:GQ:MIN_DP:PL 0/0:29:74:29:0,74,1014 @@ -690,8 +577,7 @@ 20 10014590 . A . . END=10014590 GT:DP:GQ:MIN_DP:PL 0/0:44:93:44:0,93,1625 20 10014591 . T . . END=10014989 GT:DP:GQ:MIN_DP:PL 0/0:72:99:42:0,116,1732 20 10014990 . C CAT, 1237.73 . AS_RAW_BaseQRankSum=|1.9,1|NaN;AS_RAW_MQ=134569.00|147200.00|0.00;AS_RAW_MQRankSum=|3.1,1|NaN;AS_RAW_ReadPosRankSum=|-0.5,1|NaN;AS_SB_TABLE=28,10|25,13|0,0;BaseQRankSum=1.930;DP=87;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.107;RAW_MQ=321369.00;ReadPosRankSum=-0.437 GT:AD:DP:GQ:PL:SB 0/1:38,38,0:76:99:1275,0,1248,1389,1365,2755:28,10,25,13 -20 10014991 . A . . END=10014991 GT:DP:GQ:MIN_DP:PL 0/0:88:0:88:0,0,402 -20 10014992 . T . . END=10015385 GT:DP:GQ:MIN_DP:PL 0/0:73:99:41:0,102,1530 +20 10014991 . A . . END=10015385 GT:DP:GQ:MIN_DP:PL 0/0:73:99:41:0,102,1530 20 10015386 . G . . END=10015388 GT:DP:GQ:MIN_DP:PL 0/0:39:90:39:0,90,1350 20 10015389 . A . . END=10015390 GT:DP:GQ:MIN_DP:PL 0/0:38:81:38:0,81,1215 20 10015391 . G . . END=10015392 GT:DP:GQ:MIN_DP:PL 0/0:37:78:36:0,78,1170 @@ -754,17 +640,11 @@ 20 10015662 . G . . END=10015675 GT:DP:GQ:MIN_DP:PL 0/0:13:33:11:0,33,418 20 10015676 . G . . END=10015678 GT:DP:GQ:MIN_DP:PL 0/0:11:27:11:0,27,405 20 10015679 . C T, 140.77 . AS_RAW_BaseQRankSum=|0.2,1|NaN;AS_RAW_MQ=18000.00|18000.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=5,0|5,0|0,0;BaseQRankSum=0.200;DP=10;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=36000.00;ReadPosRankSum=0.497 GT:AD:DP:GQ:PL:SB 0/1:5,5,0:10:99:169,0,166,184,181,365:5,0,5,0 -20 10015680 . G . . END=10015683 GT:DP:GQ:MIN_DP:PL 0/0:11:27:11:0,27,405 -20 10015684 . C . . END=10015687 GT:DP:GQ:MIN_DP:PL 0/0:12:30:11:0,30,450 -20 10015688 . C . . END=10015688 GT:DP:GQ:MIN_DP:PL 0/0:11:33:11:0,33,400 -20 10015689 . G . . END=10015689 GT:DP:GQ:MIN_DP:PL 0/0:10:30:10:0,30,292 -20 10015690 . G . . END=10015690 GT:DP:GQ:MIN_DP:PL 0/0:11:33:11:0,33,406 -20 10015691 . C . . END=10015693 GT:DP:GQ:MIN_DP:PL 0/0:11:30:11:0,30,450 -20 10015694 . C . . END=10015694 GT:DP:GQ:MIN_DP:PL 0/0:12:23:12:0,23,389 -20 10015695 . C . . END=10015697 GT:DP:GQ:MIN_DP:PL 0/0:12:27:12:0,27,405 -20 10015698 . C . . END=10015698 GT:DP:GQ:MIN_DP:PL 0/0:12:23:12:0,23,401 -20 10015699 . C . . END=10015701 GT:DP:GQ:MIN_DP:PL 0/0:12:27:11:0,27,405 -20 10015702 . C . . END=10015707 GT:DP:GQ:MIN_DP:PL 0/0:12:30:11:0,30,450 +20 10015680 . G . . END=10015683 GT:DP:GQ:MIN_DP:PL 0/0:10:24:10:0,24,360 +20 10015684 . C . . END=10015687 GT:DP:GQ:MIN_DP:PL 0/0:11:27:10:0,27,405 +20 10015688 . C . . END=10015690 GT:DP:GQ:MIN_DP:PL 0/0:10:30:10:0,30,292 +20 10015691 . C . . END=10015701 GT:DP:GQ:MIN_DP:PL 0/0:11:27:10:0,27,405 +20 10015702 . C . . END=10015707 GT:DP:GQ:MIN_DP:PL 0/0:11:30:11:0,30,450 20 10015708 . G . . END=10015708 GT:DP:GQ:MIN_DP:PL 0/0:12:33:12:0,33,495 20 10015709 . C . . END=10015714 GT:DP:GQ:MIN_DP:PL 0/0:13:36:13:0,36,540 20 10015715 . C . . END=10015716 GT:DP:GQ:MIN_DP:PL 0/0:13:33:13:0,33,495 @@ -817,9 +697,7 @@ 20 10020890 . A . . END=10020896 GT:DP:GQ:MIN_DP:PL 0/0:42:93:40:0,93,1395 20 10020897 . C . . END=10020918 GT:DP:GQ:MIN_DP:PL 0/0:41:99:37:0,102,1530 20 10020919 . T . . END=10020919 GT:DP:GQ:MIN_DP:PL 0/0:45:95:45:0,95,1765 -20 10020920 . T . . END=10021606 GT:DP:GQ:MIN_DP:PL 0/0:79:99:46:0,105,1721 -20 10021607 . C . . END=10021607 GT:DP:GQ:MIN_DP:PL 0/0:98:98:98:0,98,3341 -20 10021608 . T . . END=10023688 GT:DP:GQ:MIN_DP:PL 0/0:80:99:54:0,110,1800 +20 10020920 . T . . END=10023688 GT:DP:GQ:MIN_DP:PL 0/0:80:99:46:0,105,1721 20 10023689 . G A, 1852.77 . AS_RAW_BaseQRankSum=|2.1,1|NaN;AS_RAW_MQ=102169.00|183600.00|0.00;AS_RAW_MQRankSum=|1.3,1|NaN;AS_RAW_ReadPosRankSum=|1.1,1|NaN;AS_SB_TABLE=16,13|26,25|0,0;BaseQRankSum=2.144;DP=80;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.352;RAW_MQ=285769.00;ReadPosRankSum=1.162 GT:AD:DP:GQ:PL:SB 0/1:29,51,0:80:99:1881,0,946,1968,1099,3067:16,13,26,25 20 10023690 . G . . END=10024106 GT:DP:GQ:MIN_DP:PL 0/0:70:99:57:0,120,1800 20 10024107 . C T, 1694.77 . AS_RAW_BaseQRankSum=|5.7,1|NaN;AS_RAW_MQ=136800.00|166763.00|0.00;AS_RAW_MQRankSum=|-1.6,1|NaN;AS_RAW_ReadPosRankSum=|0.1,1|NaN;AS_SB_TABLE=21,17|28,20|0,0;BaseQRankSum=5.770;DP=86;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.546;RAW_MQ=303563.00;ReadPosRankSum=0.148 GT:AD:DP:GQ:PL:SB 0/1:38,48,0:86:99:1723,0,1086,1837,1230,3068:21,17,28,20 @@ -829,20 +707,18 @@ 20 10024288 . C . . END=10024288 GT:DP:GQ:MIN_DP:PL 0/0:71:0:71:0,0,1411 20 10024289 . T . . END=10024293 GT:DP:GQ:MIN_DP:PL 0/0:72:99:70:0,120,1800 20 10024294 . C . . END=10024294 GT:DP:GQ:MIN_DP:PL 0/0:69:0:69:0,0,1358 -20 10024295 . T . . END=10024295 GT:DP:GQ:MIN_DP:PL 0/0:69:99:69:0,120,1800 -20 10024296 . T . . END=10024296 GT:DP:GQ:MIN_DP:PL 0/0:67:82:67:0,82,2254 +20 10024295 . T . . END=10024296 GT:DP:GQ:MIN_DP:PL 0/0:68:99:67:0,120,1800 20 10024297 . T . . END=10024297 GT:DP:GQ:MIN_DP:PL 0/0:68:65:68:0,65,2188 -20 10024298 . T . . END=10024298 GT:DP:GQ:MIN_DP:PL 0/0:66:37:66:0,37,2037 -20 10024299 . C . . END=10024299 GT:DP:GQ:MIN_DP:PL 0/0:62:0:62:0,0,1430 +20 10024298 . T . . END=10024298 GT:DP:GQ:MIN_DP:PL 0/0:66:59:66:0,59,2080 +20 10024299 . C . . END=10024299 GT:DP:GQ:MIN_DP:PL 0/0:62:0:62:0,0,1480 20 10024300 . CTT C,CT,CTTTT, 87.76 . AS_RAW_BaseQRankSum=|1.7,1|1.4,1|2.3,1|NaN;AS_RAW_MQ=8041.00|5858.00|5282.00|20523.00|0.00;AS_RAW_MQRankSum=|-1.1,1|-0.6,1|-0.1,1|NaN;AS_RAW_ReadPosRankSum=|-0.9,1|-2.0,1|-0.5,1|NaN;AS_SB_TABLE=1,2|3,1|2,1|6,2|0,0;BaseQRankSum=2.446;DP=50;ExcessHet=3.0103;MLEAC=1,0,1,0;MLEAF=0.500,0.00,0.500,0.00;MQRankSum=-0.600;RAW_MQ=134695.00;ReadPosRankSum=-1.073 GT:AD:DP:GQ:PL:SB 1/3:3,4,3,8,0:18:1:122,67,400,91,215,231,19,0,1,156,161,279,257,107,347:1,2,11,4 20 10024303 . T . . END=10024303 GT:DP:GQ:MIN_DP:PL 0/0:67:57:67:0,57,855 20 10024304 . T . . END=10024307 GT:DP:GQ:MIN_DP:PL 0/0:69:63:68:0,63,945 20 10024308 . T . . END=10024310 GT:DP:GQ:MIN_DP:PL 0/0:70:78:70:0,78,1170 -20 10024311 . T . . END=10024315 GT:DP:GQ:MIN_DP:PL 0/0:66:81:66:0,81,1215 -20 10024316 . T . . END=10024316 GT:DP:GQ:MIN_DP:PL 0/0:66:69:66:0,69,1035 -20 10024317 . T . . END=10024317 GT:DP:GQ:MIN_DP:PL 0/0:64:72:64:0,72,1080 -20 10024318 . T . . END=10024318 GT:DP:GQ:MIN_DP:PL 0/0:62:63:62:0,63,945 -20 10024319 . T . . END=10024320 GT:DP:GQ:MIN_DP:PL 0/0:63:75:62:0,75,1125 +20 10024311 . T . . END=10024314 GT:DP:GQ:MIN_DP:PL 0/0:66:81:66:0,81,1215 +20 10024315 . T . . END=10024315 GT:DP:GQ:MIN_DP:PL 0/0:66:72:66:0,72,1080 +20 10024316 . T . . END=10024318 GT:DP:GQ:MIN_DP:PL 0/0:64:60:62:0,60,900 +20 10024319 . T . . END=10024320 GT:DP:GQ:MIN_DP:PL 0/0:63:72:62:0,72,1080 20 10024321 . T . . END=10024321 GT:DP:GQ:MIN_DP:PL 0/0:62:90:62:0,90,1350 20 10024322 . T . . END=10024322 GT:DP:GQ:MIN_DP:PL 0/0:60:69:60:0,69,2100 20 10024323 . T . . END=10024323 GT:DP:GQ:MIN_DP:PL 0/0:56:27:56:0,27,1860 @@ -853,28 +729,21 @@ 20 10026357 . T C, 1166.77 . AS_RAW_BaseQRankSum=|-1.7,1|NaN;AS_RAW_MQ=95810.00|119307.00|0.00;AS_RAW_MQRankSum=|-0.2,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=10,18|20,15|0,0;BaseQRankSum=-1.700;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.148;RAW_MQ=215117.00;ReadPosRankSum=-0.076 GT:AD:DP:GQ:PL:SB 0/1:28,35,0:63:99:1195,0,932,1279,1037,2316:10,18,20,15 20 10026358 . A . . END=10026793 GT:DP:GQ:MIN_DP:PL 0/0:72:99:41:0,102,1530 20 10026794 . C T, 1084.77 . AS_RAW_BaseQRankSum=|2.8,1|NaN;AS_RAW_MQ=68400.00|116041.00|0.00;AS_RAW_MQRankSum=|-0.8,1|NaN;AS_RAW_ReadPosRankSum=|-0.6,1|NaN;AS_SB_TABLE=7,12|15,18|0,0;BaseQRankSum=2.828;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.719;RAW_MQ=184441.00;ReadPosRankSum=-0.533 GT:AD:DP:GQ:PL:SB 0/1:19,33,0:52:99:1113,0,529,1170,627,1798:7,12,15,18 -20 10026795 . G . . END=10027227 GT:DP:GQ:MIN_DP:PL 0/0:71:99:52:0,105,1575 -20 10027228 . G . . END=10027228 GT:DP:GQ:MIN_DP:PL 0/0:66:96:66:0,96,1440 -20 10027229 . A . . END=10027229 GT:DP:GQ:MIN_DP:PL 0/0:67:99:67:0,99,1485 -20 10027230 . A . . END=10027230 GT:DP:GQ:MIN_DP:PL 0/0:66:96:66:0,96,1440 -20 10027231 . A . . END=10027233 GT:DP:GQ:MIN_DP:PL 0/0:70:99:68:0,102,1530 +20 10026795 . G . . END=10027233 GT:DP:GQ:MIN_DP:PL 0/0:70:99:52:0,115,1800 20 10027234 . A ATTAG, 1320.73 . AS_RAW_BaseQRankSum=|-0.5,1|NaN;AS_RAW_MQ=119641.00|106210.00|0.00;AS_RAW_MQRankSum=|-0.9,1|NaN;AS_RAW_ReadPosRankSum=|-1.0,1|NaN;AS_SB_TABLE=18,16|15,20|0,0;BaseQRankSum=-0.406;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.845;RAW_MQ=236651.00;ReadPosRankSum=-0.979 GT:AD:DP:GQ:PL:SB 0/1:34,35,0:69:99:1358,0,1964,1461,2069,3531:18,16,15,20 -20 10027235 . T . . END=10027235 GT:DP:GQ:MIN_DP:PL 0/0:72:0:72:0,0,334 -20 10027236 . T . . END=10027867 GT:DP:GQ:MIN_DP:PL 0/0:78:99:56:0,120,1800 +20 10027235 . T . . END=10027867 GT:DP:GQ:MIN_DP:PL 0/0:78:99:56:0,120,1800 20 10027868 . A G, 1739.77 . AS_RAW_BaseQRankSum=|-5.8,1|NaN;AS_RAW_MQ=155641.00|159241.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|1.8,1|NaN;AS_SB_TABLE=19,25|26,19|0,0;BaseQRankSum=-5.793;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.032;RAW_MQ=314882.00;ReadPosRankSum=1.872 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:44,45,0:89:99:0|1:10027868_A_G:1768,0,3201,1901,3340,5240:19,25,26,19 20 10027869 . A . . END=10027871 GT:DP:GQ:MIN_DP:PL 0/0:86:99:85:0,120,1800 20 10027872 . A G, 1724.77 . AS_RAW_BaseQRankSum=|-5.5,1|NaN;AS_RAW_MQ=141241.00|159241.00|0.00;AS_RAW_MQRankSum=|0.1,1|NaN;AS_RAW_ReadPosRankSum=|1.0,1|NaN;AS_SB_TABLE=16,24|26,19|0,0;BaseQRankSum=-5.491;DP=85;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.101;RAW_MQ=300482.00;ReadPosRankSum=1.053 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:40,45,0:85:99:0|1:10027868_A_G:1753,0,3136,1879,3272,5151:16,24,26,19 20 10027873 . G . . END=10028866 GT:DP:GQ:MIN_DP:PL 0/0:80:99:55:0,120,1800 20 10028867 . A ATG, 1106.73 . AS_RAW_BaseQRankSum=|-0.9,1|NaN;AS_RAW_MQ=115200.00|150800.00|0.00;AS_RAW_MQRankSum=|2.7,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=11,21|18,21|0,0;BaseQRankSum=-0.874;DP=92;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.711;RAW_MQ=338841.00;ReadPosRankSum=0.364 GT:AD:DP:GQ:PL:SB 0/1:32,39,0:71:99:1144,0,916,1242,1033,2275:11,21,18,21 -20 10028868 . T . . END=10028868 GT:DP:GQ:MIN_DP:PL 0/0:92:0:92:0,0,401 -20 10028869 . G . . END=10030187 GT:DP:GQ:MIN_DP:PL 0/0:80:99:60:0,120,1800 +20 10028868 . T . . END=10030187 GT:DP:GQ:MIN_DP:PL 0/0:80:99:60:0,120,1800 20 10030188 . T A, 1372.77 . AS_RAW_BaseQRankSum=|0.7,1|NaN;AS_RAW_MQ=151200.00|137641.00|0.00;AS_RAW_MQRankSum=|-1.1,1|NaN;AS_RAW_ReadPosRankSum=|-0.6,1|NaN;AS_SB_TABLE=24,18|15,24|0,0;BaseQRankSum=0.711;DP=81;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.013;RAW_MQ=288841.00;ReadPosRankSum=-0.553 GT:AD:DP:GQ:PL:SB 0/1:42,39,0:81:99:1401,0,1524,1527,1641,3168:24,18,15,24 20 10030189 . G . . END=10030566 GT:DP:GQ:MIN_DP:PL 0/0:71:99:41:0,103,1575 20 10030567 . G . . END=10030567 GT:DP:GQ:MIN_DP:PL 0/0:41:90:41:0,90,1511 -20 10030568 . C . . END=10031253 GT:DP:GQ:MIN_DP:PL 0/0:70:99:42:0,99,1485 +20 10030568 . C . . END=10031253 GT:DP:GQ:MIN_DP:PL 0/0:70:99:42:0,114,1710 20 10031254 . A AT, 1463.73 . AS_RAW_BaseQRankSum=|-0.1,1|NaN;AS_RAW_MQ=136800.00|168269.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=27,11|25,22|0,0;BaseQRankSum=-0.091;DP=87;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.017;RAW_MQ=309510.00;ReadPosRankSum=0.495 GT:AD:DP:GQ:PL:SB 0/1:38,47,0:85:99:1501,0,1159,1616,1300,2916:27,11,25,22 -20 10031255 . T . . END=10031255 GT:DP:GQ:MIN_DP:PL 0/0:88:0:88:0,0,0 -20 10031256 . G . . END=10031341 GT:DP:GQ:MIN_DP:PL 0/0:96:99:87:0,120,1800 +20 10031255 . T . . END=10031341 GT:DP:GQ:MIN_DP:PL 0/0:95:99:86:0,120,1800 20 10031342 . G A, 1834.77 . AS_RAW_BaseQRankSum=|1.8,1|NaN;AS_RAW_MQ=147600.00|184441.00|0.00;AS_RAW_MQRankSum=|-0.9,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=22,19|31,21|0,0;BaseQRankSum=1.833;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.866;RAW_MQ=332041.00;ReadPosRankSum=-0.012 GT:AD:DP:GQ:PL:SB 0/1:41,52,0:93:99:1863,0,1375,1986,1531,3517:22,19,31,21 20 10031343 . A . . END=10031797 GT:DP:GQ:MIN_DP:PL 0/0:91:99:66:0,120,1800 20 10031798 . G A, 4296.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|369410.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|57,47|0,0;DP=104;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=369410.00 GT:AD:DP:GQ:PL:SB 1/1:0,104,0:104:99:4325,313,0,4325,313,4325:0,0,57,47 @@ -886,11 +755,9 @@ 20 10032413 . T G, 869.77 . AS_RAW_BaseQRankSum=|-6.2,1|NaN;AS_RAW_MQ=123769.00|109369.00|0.00;AS_RAW_MQRankSum=|-0.1,1|NaN;AS_RAW_ReadPosRankSum=|-1.1,1|NaN;AS_SB_TABLE=15,20|20,11|0,0;BaseQRankSum=-6.142;DP=66;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.065;RAW_MQ=233138.00;ReadPosRankSum=-1.003 GT:AD:DP:GQ:PL:SB 0/1:35,31,0:66:99:898,0,1277,1003,1371,2374:15,20,20,11 20 10032414 . T . . END=10032881 GT:DP:GQ:MIN_DP:PL 0/0:70:99:55:0,120,1800 20 10032882 . A T, 1202.77 . AS_RAW_BaseQRankSum=|-3.7,1|NaN;AS_RAW_MQ=140400.00|126841.00|0.00;AS_RAW_MQRankSum=|-1.1,1|NaN;AS_RAW_ReadPosRankSum=|0.6,1|NaN;AS_SB_TABLE=28,11|22,14|0,0;BaseQRankSum=-3.697;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.014;RAW_MQ=267241.00;ReadPosRankSum=0.626 GT:AD:DP:GQ:PL:SB 0/1:39,36,0:75:99:1231,0,1406,1348,1514,2862:28,11,22,14 -20 10032883 . A . . END=10032966 GT:DP:GQ:MIN_DP:PL 0/0:67:99:61:0,99,1485 -20 10032967 . T . . END=10032971 GT:DP:GQ:MIN_DP:PL 0/0:68:90:67:0,90,1350 +20 10032883 . A . . END=10032971 GT:DP:GQ:MIN_DP:PL 0/0:67:99:61:0,120,1800 20 10032972 . C CAT, 1122.73 . AS_RAW_BaseQRankSum=|-0.4,1|NaN;AS_RAW_MQ=118800.00|105241.00|0.00;AS_RAW_MQRankSum=|-1.1,1|NaN;AS_RAW_ReadPosRankSum=|-1.3,1|NaN;AS_SB_TABLE=17,16|11,19|0,0;BaseQRankSum=-0.354;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.017;RAW_MQ=231241.00;ReadPosRankSum=-1.232 GT:AD:DP:GQ:PL:SB 0/1:33,30,0:63:99:1160,0,1477,1260,1568,2827:17,16,11,19 -20 10032973 . T . . END=10032973 GT:DP:GQ:MIN_DP:PL 0/0:65:0:65:0,0,104 -20 10032974 . G . . END=10033636 GT:DP:GQ:MIN_DP:PL 0/0:78:99:50:0,120,1800 +20 10032973 . T . . END=10033636 GT:DP:GQ:MIN_DP:PL 0/0:78:99:50:0,120,1800 20 10033637 . C . . END=10033637 GT:DP:GQ:MIN_DP:PL 0/0:58:97:58:0,97,2210 20 10033638 . C . . END=10034305 GT:DP:GQ:MIN_DP:PL 0/0:85:99:53:0,120,1800 20 10034306 . T C, 782.77 . AS_RAW_BaseQRankSum=|-3.7,1|NaN;AS_RAW_MQ=160610.00|104400.00|0.00;AS_RAW_MQRankSum=|1.1,1|NaN;AS_RAW_ReadPosRankSum=|0.5,1|NaN;AS_SB_TABLE=24,22|14,15|0,0;BaseQRankSum=-3.661;DP=76;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.150;RAW_MQ=268610.00;ReadPosRankSum=0.539 GT:AD:DP:GQ:PL:SB 0/1:46,29,0:75:99:811,0,1593,950,1680,2630:24,22,14,15 @@ -908,8 +775,7 @@ 20 10036161 . T . . END=10036161 GT:DP:GQ:MIN_DP:PL 0/0:42:82:42:0,82,1514 20 10036162 . G . . END=10036929 GT:DP:GQ:MIN_DP:PL 0/0:76:99:43:0,113,1513 20 10036930 . CGATAGCCCTAGCCCTAGATA C, 1036.73 . AS_RAW_BaseQRankSum=|0.2,1|NaN;AS_RAW_MQ=140400.00|58242.00|0.00;AS_RAW_MQRankSum=|-4.1,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=11,28|15,14|0,0;BaseQRankSum=0.200;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.048;RAW_MQ=274847.00;ReadPosRankSum=0.460 GT:AD:DP:GQ:PL:SB 0/1:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 -20 10036951 . G . . END=10036951 GT:DP:GQ:MIN_DP:PL 0/0:77:0:77:0,0,1197 -20 10036952 . A . . END=10036956 GT:DP:GQ:MIN_DP:PL 0/0:74:99:70:0,120,1800 +20 10036951 . G . . END=10036956 GT:DP:GQ:MIN_DP:PL 0/0:74:99:70:0,120,1800 20 10036957 . C . . END=10036957 GT:DP:GQ:MIN_DP:PL 0/0:70:37:70:0,37,2472 20 10036958 . C . . END=10036958 GT:DP:GQ:MIN_DP:PL 0/0:70:40:70:0,40,2490 20 10036959 . T . . END=10036959 GT:DP:GQ:MIN_DP:PL 0/0:70:99:70:0,120,1800 @@ -924,29 +790,11 @@ 20 10036968 . A . . END=10036968 GT:DP:GQ:MIN_DP:PL 0/0:74:64:74:0,64,2707 20 10036969 . T . . END=10037036 GT:DP:GQ:MIN_DP:PL 0/0:87:99:72:0,107,1800 20 10037037 . C T, 1436.77 . AS_RAW_BaseQRankSum=|3.5,1|NaN;AS_RAW_MQ=143521.00|149741.00|0.00;AS_RAW_MQRankSum=|-1.2,1|NaN;AS_RAW_ReadPosRankSum=|-1.7,1|NaN;AS_SB_TABLE=28,11|28,14|0,0;BaseQRankSum=3.504;DP=81;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.193;RAW_MQ=293262.00;ReadPosRankSum=-1.609 GT:AD:DP:GQ:PL:SB 0/1:39,42,0:81:99:1465,0,1124,1580,1251,2831:28,11,28,14 -20 10037038 . G . . END=10037097 GT:DP:GQ:MIN_DP:PL 0/0:92:99:80:0,111,1665 -20 10037098 . C . . END=10037098 GT:DP:GQ:MIN_DP:PL 0/0:86:9:86:0,9,2910 -20 10037099 . A . . END=10037100 GT:DP:GQ:MIN_DP:PL 0/0:89:90:88:0,90,1350 -20 10037101 . A . . END=10037101 GT:DP:GQ:MIN_DP:PL 0/0:87:81:87:0,81,1215 -20 10037102 . T . . END=10037102 GT:DP:GQ:MIN_DP:PL 0/0:90:72:90:0,72,1080 -20 10037103 . A . . END=10037103 GT:DP:GQ:MIN_DP:PL 0/0:90:66:90:0,66,990 -20 10037104 . T . . END=10037104 GT:DP:GQ:MIN_DP:PL 0/0:89:0:89:0,0,2830 -20 10037105 . A . . END=10037107 GT:DP:GQ:MIN_DP:PL 0/0:89:54:88:0,54,810 -20 10037108 . G . . END=10037108 GT:DP:GQ:MIN_DP:PL 0/0:85:21:85:0,21,315 -20 10037109 . A . . END=10037109 GT:DP:GQ:MIN_DP:PL 0/0:84:18:84:0,18,270 +20 10037038 . G . . END=10037109 GT:DP:GQ:MIN_DP:PL 0/0:88:99:75:0,120,1800 20 10037110 . T TGATA, 2780.73 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|193419.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|35,26|0,0;DP=74;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=240219.00 GT:AD:DP:GQ:PL:SB 1/1:0,61,0:61:99:2818,189,0,2819,190,2820:0,0,35,26 -20 10037111 . G . . END=10037111 GT:DP:GQ:MIN_DP:PL 0/0:84:0:84:0,0,0 -20 10037112 . A . . END=10037121 GT:DP:GQ:MIN_DP:PL 0/0:83:99:81:0,120,1800 -20 10037122 . A . . END=10037126 GT:DP:GQ:MIN_DP:PL 0/0:80:0:79:0,0,1989 -20 10037127 . A . . END=10037127 GT:DP:GQ:MIN_DP:PL 0/0:79:85:79:0,85,2945 -20 10037128 . T . . END=10037131 GT:DP:GQ:MIN_DP:PL 0/0:77:99:74:0,114,1710 -20 10037132 . T . . END=10037134 GT:DP:GQ:MIN_DP:PL 0/0:73:0:72:0,0,1990 -20 10037135 . A . . END=10037137 GT:DP:GQ:MIN_DP:PL 0/0:70:99:70:0,111,1665 -20 10037138 . G . . END=10037140 GT:DP:GQ:MIN_DP:PL 0/0:70:93:68:0,93,1395 -20 10037141 . A . . END=10037143 GT:DP:GQ:MIN_DP:PL 0/0:70:0:68:0,0,1786 +20 10037111 . G . . END=10037143 GT:DP:GQ:MIN_DP:PL 0/0:77:99:68:0,120,1800 20 10037144 . T TGATAGATA, 1823.73 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|57470.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|15,21|0,0;DP=70;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=187352.00 GT:AD:DP:GQ:PL:SB 1/1:0,36,0:36:99:1861,127,0,1864,129,1866:0,0,15,21 -20 10037145 . G . . END=10037145 GT:DP:GQ:MIN_DP:PL 0/0:75:0:75:0,0,8 -20 10037146 . A . . END=10037186 GT:DP:GQ:MIN_DP:PL 0/0:70:99:65:0,117,1755 +20 10037145 . G . . END=10037186 GT:DP:GQ:MIN_DP:PL 0/0:70:99:65:0,111,1665 20 10037187 . G . . END=10037187 GT:DP:GQ:MIN_DP:PL 0/0:68:0:68:0,0,2259 20 10037188 . A . . END=10037188 GT:DP:GQ:MIN_DP:PL 0/0:66:99:66:0,120,1800 20 10037189 . T . . END=10037189 GT:DP:GQ:MIN_DP:PL 0/0:67:50:67:0,50,2476 @@ -961,57 +809,24 @@ 20 10038583 . C . . END=10038583 GT:DP:GQ:MIN_DP:PL 0/0:55:91:55:0,91,1806 20 10038584 . A . . END=10039370 GT:DP:GQ:MIN_DP:PL 0/0:76:99:54:0,120,1800 20 10039371 . T G, 1324.77 . AS_RAW_BaseQRankSum=|-3.3,1|NaN;AS_RAW_MQ=122400.00|144000.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=15,19|24,16|0,0;BaseQRankSum=-3.260;DP=74;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=266400.00;ReadPosRankSum=0.391 GT:AD:DP:GQ:PL:SB 0/1:34,40,0:74:99:1353,0,1194,1455,1315,2770:15,19,24,16 -20 10039372 . T . . END=10040748 GT:DP:GQ:MIN_DP:PL 0/0:76:99:56:0,105,1575 -20 10040749 . T . . END=10040752 GT:DP:GQ:MIN_DP:PL 0/0:87:87:84:0,87,1305 -20 10040753 . C . . END=10040753 GT:DP:GQ:MIN_DP:PL 0/0:88:90:88:0,90,1350 -20 10040754 . T . . END=10040754 GT:DP:GQ:MIN_DP:PL 0/0:91:81:91:0,81,1215 -20 10040755 . G . . END=10040755 GT:DP:GQ:MIN_DP:PL 0/0:89:69:89:0,69,1035 -20 10040756 . T . . END=10040758 GT:DP:GQ:MIN_DP:PL 0/0:89:45:89:0,45,675 -20 10040759 . T . . END=10040759 GT:DP:GQ:MIN_DP:PL 0/0:89:48:89:0,48,720 -20 10040760 . T . . END=10040760 GT:DP:GQ:MIN_DP:PL 0/0:89:51:89:0,51,765 -20 10040761 . C . . END=10040761 GT:DP:GQ:MIN_DP:PL 0/0:88:48:88:0,48,720 -20 10040762 . T . . END=10040762 GT:DP:GQ:MIN_DP:PL 0/0:87:42:87:0,42,630 -20 10040763 . T . . END=10040763 GT:DP:GQ:MIN_DP:PL 0/0:87:30:87:0,30,450 -20 10040764 . T . . END=10040766 GT:DP:GQ:MIN_DP:PL 0/0:85:39:84:0,39,585 -20 10040767 . C . . END=10040767 GT:DP:GQ:MIN_DP:PL 0/0:83:36:83:0,36,540 -20 10040768 . T . . END=10040771 GT:DP:GQ:MIN_DP:PL 0/0:83:15:81:0,15,225 +20 10039372 . T . . END=10040770 GT:DP:GQ:MIN_DP:PL 0/0:76:99:56:0,120,1800 +20 10040771 . T . . END=10040771 GT:DP:GQ:MIN_DP:PL 0/0:81:60:81:0,60,2763 20 10040772 . C CT, 1995.73 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|178648.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|37,33|0,0;DP=79;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=211048.00 GT:AD:DP:GQ:PL:SB 1/1:0,70,0:70:99:2033,210,0,2034,210,2034:0,0,37,33 -20 10040773 . T . . END=10040773 GT:DP:GQ:MIN_DP:PL 0/0:81:0:81:0,0,0 -20 10040774 . T . . END=10040795 GT:DP:GQ:MIN_DP:PL 0/0:80:99:77:0,99,1485 -20 10040796 . T . . END=10040797 GT:DP:GQ:MIN_DP:PL 0/0:78:93:77:0,93,1395 -20 10040798 . C . . END=10040798 GT:DP:GQ:MIN_DP:PL 0/0:78:84:78:0,84,1260 -20 10040799 . T . . END=10040801 GT:DP:GQ:MIN_DP:PL 0/0:79:72:78:0,72,1080 -20 10040802 . G . . END=10040803 GT:DP:GQ:MIN_DP:PL 0/0:79:63:78:0,63,945 -20 10040804 . A . . END=10040805 GT:DP:GQ:MIN_DP:PL 0/0:78:57:77:0,57,855 -20 10040806 . T . . END=10040807 GT:DP:GQ:MIN_DP:PL 0/0:79:48:78:0,48,720 -20 10040808 . A . . END=10040809 GT:DP:GQ:MIN_DP:PL 0/0:80:42:79:0,42,630 -20 10040810 . C . . END=10040810 GT:DP:GQ:MIN_DP:PL 0/0:81:15:81:0,15,225 -20 10040811 . A . . END=10040811 GT:DP:GQ:MIN_DP:PL 0/0:80:3:80:0,3,45 +20 10040773 . T . . END=10040811 GT:DP:GQ:MIN_DP:PL 0/0:77:99:75:0,120,1800 20 10040812 . AT A, 2607.73 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|174499.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|36,35|0,0;DP=79;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=203299.00 GT:AD:DP:GQ:PL:SB 1/1:0,71,0:71:99:2645,214,0,2645,214,2645:0,0,36,35 -20 10040814 . T . . END=10040814 GT:DP:GQ:MIN_DP:PL 0/0:82:0:82:0,0,0 -20 10040815 . T . . END=10040819 GT:DP:GQ:MIN_DP:PL 0/0:79:99:78:0,109,1800 -20 10040820 . T . . END=10040820 GT:DP:GQ:MIN_DP:PL 0/0:77:75:77:0,75,2723 +20 10040814 . T . . END=10040820 GT:DP:GQ:MIN_DP:PL 0/0:78:99:77:0,120,1800 20 10040821 . T A, 1171.77 . AS_RAW_BaseQRankSum=|-0.1,1|NaN;AS_RAW_MQ=98015.00|101684.00|0.00;AS_RAW_MQRankSum=|-0.1,1|NaN;AS_RAW_ReadPosRankSum=|-1.4,1|NaN;AS_SB_TABLE=20,18|21,19|0,0;BaseQRankSum=-0.021;DP=78;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.097;RAW_MQ=199699.00;ReadPosRankSum=-1.385 GT:AD:DP:GQ:PL:SB 0/1:38,40,0:78:99:1200,0,1099,1314,1219,2533:20,18,21,19 20 10040822 . A . . END=10041303 GT:DP:GQ:MIN_DP:PL 0/0:71:99:54:0,119,1800 20 10041304 . C T, 2765.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|239810.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|34,34|0,0;DP=68;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=239810.00 GT:AD:DP:GQ:PL:SB 1/1:0,68,0:68:99:2794,204,0,2794,204,2794:0,0,34,34 -20 10041305 . G . . END=10041688 GT:DP:GQ:MIN_DP:PL 0/0:61:99:48:0,105,1575 -20 10041689 . T . . END=10041689 GT:DP:GQ:MIN_DP:PL 0/0:72:93:72:0,93,1395 -20 10041690 . C . . END=10041690 GT:DP:GQ:MIN_DP:PL 0/0:72:87:72:0,87,1305 -20 10041691 . A . . END=10041692 GT:DP:GQ:MIN_DP:PL 0/0:73:69:73:0,69,1035 -20 10041693 . T . . END=10041694 GT:DP:GQ:MIN_DP:PL 0/0:76:51:75:0,51,765 -20 10041695 . A . . END=10041695 GT:DP:GQ:MIN_DP:PL 0/0:75:48:75:0,48,720 -20 10041696 . A . . END=10041696 GT:DP:GQ:MIN_DP:PL 0/0:75:45:75:0,45,675 -20 10041697 . A . . END=10041697 GT:DP:GQ:MIN_DP:PL 0/0:75:12:75:0,12,180 +20 10041305 . G . . END=10041697 GT:DP:GQ:MIN_DP:PL 0/0:62:99:48:0,120,1800 20 10041698 . C CAT, 0.04 . AS_RAW_BaseQRankSum=|1.8,1|NaN;AS_RAW_MQ=151097.00|21600.00|0.00;AS_RAW_MQRankSum=|0.8,1|NaN;AS_RAW_ReadPosRankSum=|0.5,1|NaN;AS_SB_TABLE=21,27|2,4|0,0;BaseQRankSum=1.887;DP=74;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.844;RAW_MQ=265497.00;ReadPosRankSum=0.579 GT:AD:DP:GQ:PL:SB 0/1:48,6,0:54:17:17,0,1425,166,1446,1612:21,27,2,4 -20 10041699 . A . . END=10041699 GT:DP:GQ:MIN_DP:PL 0/0:77:5:77:0,5,2671 -20 10041700 . T . . END=10041700 GT:DP:GQ:MIN_DP:PL 0/0:77:27:77:0,27,405 +20 10041699 . A . . END=10041700 GT:DP:GQ:MIN_DP:PL 0/0:79:99:78:0,120,1800 20 10041701 . A ATG,ATATG, 1403.73 . AS_RAW_BaseQRankSum=|NaN|0.8,1|NaN;AS_RAW_MQ=23962.00|0.00|149018.00|0.00;AS_RAW_MQRankSum=|NaN|0.3,1|NaN;AS_RAW_ReadPosRankSum=|NaN|-0.3,1|NaN;AS_SB_TABLE=2,6|0,0|21,27|0,0;BaseQRankSum=0.848;DP=78;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=0.340;RAW_MQ=270590.00;ReadPosRankSum=-0.223 GT:AD:DP:GQ:PL:SB 0/2:8,0,48,0:56:58:1441,1582,2726,0,261,58,1575,2317,264,2201:2,6,21,27 -20 10041702 . T . . END=10041702 GT:DP:GQ:MIN_DP:PL 0/0:75:0:75:0,0,0 -20 10041703 . G . . END=10042318 GT:DP:GQ:MIN_DP:PL 0/0:64:99:49:0,117,1800 +20 10041702 . T . . END=10042318 GT:DP:GQ:MIN_DP:PL 0/0:64:99:49:0,117,1800 20 10042319 . C T, 2658.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|229851.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|38,28|0,0;DP=66;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=229851.00 GT:AD:DP:GQ:PL:SB 1/1:0,66,0:66:99:2687,199,0,2687,199,2687:0,0,38,28 20 10042320 . C . . END=10042760 GT:DP:GQ:MIN_DP:PL 0/0:74:99:60:0,120,1800 20 10042761 . A G, 3553.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|327600.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|58,33|0,0;DP=91;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=327600.00 GT:AD:DP:GQ:PL:SB 1/1:0,91,0:91:99:3582,272,0,3582,272,3582:0,0,58,33 -20 10042762 . G . . END=10042828 GT:DP:GQ:MIN_DP:PL 0/0:91:99:79:0,120,1800 +20 10042762 . G . . END=10042828 GT:DP:GQ:MIN_DP:PL 0/0:90:99:78:0,120,1800 20 10042829 . A G, 3055.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|278569.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|42,36|0,0;DP=78;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=278569.00 GT:AD:DP:GQ:PL:SB 1/1:0,78,0:78:99:3084,235,0,3084,235,3084:0,0,42,36 20 10042830 . C . . END=10043001 GT:DP:GQ:MIN_DP:PL 0/0:65:99:56:0,120,1800 20 10043002 . A T, 1287.77 . AS_RAW_BaseQRankSum=|3.9,1|NaN;AS_RAW_MQ=172800.00|136800.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=19,29|18,20|0,0;BaseQRankSum=3.986;DP=86;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=309600.00;ReadPosRankSum=-0.035 GT:AD:DP:GQ:PL:SB 0/1:48,38,0:86:99:1316,0,1659,1460,1773,3233:19,29,18,20 @@ -1021,18 +836,9 @@ 20 10045078 . G T, 3271.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|279389.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|37,44|0,0;DP=81;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=279389.00 GT:AD:DP:GQ:PL:SB 1/1:0,81,0:81:99:3300,244,0,3300,244,3300:0,0,37,44 20 10045079 . C . . END=10045641 GT:DP:GQ:MIN_DP:PL 0/0:71:99:60:0,120,1800 20 10045642 . G C, 3107.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|286610.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|38,43|0,0;DP=81;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=286610.00 GT:AD:DP:GQ:PL:SB 1/1:0,81,0:81:99:3136,243,0,3136,243,3136:0,0,38,43 -20 10045643 . A . . END=10046154 GT:DP:GQ:MIN_DP:PL 0/0:80:99:64:0,108,1620 -20 10046155 . G . . END=10046155 GT:DP:GQ:MIN_DP:PL 0/0:69:93:69:0,93,1395 -20 10046156 . G . . END=10046156 GT:DP:GQ:MIN_DP:PL 0/0:66:81:66:0,81,1215 -20 10046157 . G . . END=10046163 GT:DP:GQ:MIN_DP:PL 0/0:65:72:64:0,72,1080 -20 10046164 . A . . END=10046167 GT:DP:GQ:MIN_DP:PL 0/0:60:54:58:0,54,810 -20 10046168 . A . . END=10046170 GT:DP:GQ:MIN_DP:PL 0/0:61:51:59:0,51,765 -20 10046171 . A . . END=10046172 GT:DP:GQ:MIN_DP:PL 0/0:64:39:63:0,39,585 -20 10046173 . A . . END=10046176 GT:DP:GQ:MIN_DP:PL 0/0:63:21:62:0,21,315 -20 10046177 . A . . END=10046177 GT:DP:GQ:MIN_DP:PL 0/0:60:15:60:0,15,225 +20 10045643 . A . . END=10046177 GT:DP:GQ:MIN_DP:PL 0/0:79:99:58:0,120,1800 20 10046178 . AAGAAAGAAAG A, 2159.73 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|100945.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|23,27|0,0;DP=61;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=140545.00 GT:AD:DP:GQ:PL:SB 1/1:0,50,0:50:99:2197,152,0,2197,152,2197:0,0,23,27 -20 10046189 . A . . END=10046189 GT:DP:GQ:MIN_DP:PL 0/0:55:0:55:0,0,0 -20 10046190 . G . . END=10046435 GT:DP:GQ:MIN_DP:PL 0/0:67:99:52:0,108,1620 +20 10046189 . A . . END=10046435 GT:DP:GQ:MIN_DP:PL 0/0:67:99:52:0,108,1620 20 10046436 . A . . END=10046438 GT:DP:GQ:MIN_DP:PL 0/0:68:96:65:0,96,1440 20 10046439 . G . . END=10046439 GT:DP:GQ:MIN_DP:PL 0/0:66:99:66:0,99,1485 20 10046440 . G . . END=10046440 GT:DP:GQ:MIN_DP:PL 0/0:66:93:66:0,93,1395 @@ -1068,39 +874,25 @@ 20 10052688 . C A, 1062.77 . AS_RAW_BaseQRankSum=|0.1,1|NaN;AS_RAW_MQ=159769.00|115200.00|0.00;AS_RAW_MQRankSum=|0.8,1|NaN;AS_RAW_ReadPosRankSum=|1.4,1|NaN;AS_SB_TABLE=27,18|16,16|0,0;BaseQRankSum=0.180;DP=77;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.870;RAW_MQ=274969.00;ReadPosRankSum=1.443 GT:AD:DP:GQ:PL:SB 0/1:45,32,0:77:99:1091,0,1645,1226,1741,2967:27,18,16,16 20 10052689 . A . . END=10058021 GT:DP:GQ:MIN_DP:PL 0/0:74:99:36:0,99,1485 20 10058022 . T C, 975.77 . AS_RAW_BaseQRankSum=|-2.4,1|NaN;AS_RAW_MQ=125138.00|112441.00|0.00;AS_RAW_MQRankSum=|0.4,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=16,20|13,19|0,0;BaseQRankSum=-2.346;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.466;RAW_MQ=237579.00;ReadPosRankSum=0.018 GT:AD:DP:GQ:PL:SB 0/1:36,32,0:68:99:1004,0,1261,1112,1357,2469:16,20,13,19 -20 10058023 . A . . END=10062927 GT:DP:GQ:MIN_DP:PL 0/0:76:99:47:0,99,1485 -20 10062928 . T . . END=10062929 GT:DP:GQ:MIN_DP:PL 0/0:47:90:46:0,90,1350 -20 10062930 . T . . END=10062930 GT:DP:GQ:MIN_DP:PL 0/0:48:81:48:0,81,1215 -20 10062931 . G . . END=10062931 GT:DP:GQ:MIN_DP:PL 0/0:47:78:47:0,78,1170 -20 10062932 . T . . END=10062934 GT:DP:GQ:MIN_DP:PL 0/0:48:81:47:0,81,1215 +20 10058023 . A . . END=10062934 GT:DP:GQ:MIN_DP:PL 0/0:76:99:46:0,105,1575 20 10062935 . CAAA C,CA,CAA,CAAAA, 92.84 . AS_RAW_BaseQRankSum=|0.3,1|0.0,1|1.4,1|1.3,1|NaN;AS_RAW_MQ=18000.00|4441.00|7200.00|12169.00|24907.00|0.00;AS_RAW_MQRankSum=|-1.1,1|0.0,1|-0.8,1|-1.6,1|NaN;AS_RAW_ReadPosRankSum=|-1.1,1|-0.4,1|-0.3,1|-1.2,1|NaN;AS_SB_TABLE=2,3|1,1|1,1|3,1|4,6|0,0;BaseQRankSum=1.336;DP=79;ExcessHet=3.0103;MLEAC=0,0,0,1,0;MLEAF=0.00,0.00,0.00,0.500,0.00;MQRankSum=-1.405;RAW_MQ=232368.00;ReadPosRankSum=-0.986 GT:AD:DP:GQ:PL:SB 0/4:5,2,2,4,10,0:23:16:130,219,1823,163,1171,1044,115,628,576,505,0,158,82,16,101,243,986,887,608,171,888:2,3,9,9 20 10062939 . A . . END=10062955 GT:DP:GQ:MIN_DP:PL 0/0:82:99:74:0,120,1800 20 10062956 . T . . END=10062956 GT:DP:GQ:MIN_DP:PL 0/0:69:80:69:0,80,2241 20 10062957 . C . . END=10065775 GT:DP:GQ:MIN_DP:PL 0/0:70:99:42:0,105,1575 20 10065776 . C . . END=10065776 GT:DP:GQ:MIN_DP:PL 0/0:49:76:49:0,76,1707 20 10065777 . A . . END=10065777 GT:DP:GQ:MIN_DP:PL 0/0:48:94:48:0,94,1738 -20 10065778 . T . . END=10065778 GT:DP:GQ:MIN_DP:PL 0/0:48:99:48:0,111,1665 -20 10065779 . G . . END=10065779 GT:DP:GQ:MIN_DP:PL 0/0:52:0:52:0,0,1215 +20 10065778 . T . . END=10065778 GT:DP:GQ:MIN_DP:PL 0/0:48:99:48:0,120,1800 +20 10065779 . G . . END=10065779 GT:DP:GQ:MIN_DP:PL 0/0:52:0:52:0,0,1441 20 10065780 . T . . END=10065780 GT:DP:GQ:MIN_DP:PL 0/0:61:38:61:0,38,2046 20 10065781 . T . . END=10065781 GT:DP:GQ:MIN_DP:PL 0/0:71:75:71:0,75,1125 20 10065782 . T . . END=10065802 GT:DP:GQ:MIN_DP:PL 0/0:82:99:65:0,108,1620 20 10065803 . G . . END=10065803 GT:DP:GQ:MIN_DP:PL 0/0:59:81:59:0,81,2051 -20 10065804 . C . . END=10067041 GT:DP:GQ:MIN_DP:PL 0/0:72:99:48:0,103,1665 -20 10067042 . A . . END=10067043 GT:DP:GQ:MIN_DP:PL 0/0:52:90:52:0,90,1350 -20 10067044 . T . . END=10067045 GT:DP:GQ:MIN_DP:PL 0/0:52:84:52:0,84,1260 -20 10067046 . T . . END=10067046 GT:DP:GQ:MIN_DP:PL 0/0:52:75:52:0,75,1125 -20 10067047 . A . . END=10067048 GT:DP:GQ:MIN_DP:PL 0/0:51:66:50:0,66,990 +20 10065804 . C . . END=10067046 GT:DP:GQ:MIN_DP:PL 0/0:72:99:48:0,102,1530 +20 10067047 . A . . END=10067048 GT:DP:GQ:MIN_DP:PL 0/0:51:96:50:0,96,1440 20 10067049 . TAAAAAAAAA T,TA,TAA, 613.73 . AS_RAW_BaseQRankSum=|0.0,1|1.0,1|-0.5,1|NaN;AS_RAW_MQ=4441.00|8882.00|14164.00|13087.00|0.00;AS_RAW_MQRankSum=|0.0,1|-0.2,1|-0.7,1|NaN;AS_RAW_ReadPosRankSum=|-1.3,1|-0.7,1|-1.7,1|NaN;AS_SB_TABLE=1,1|3,1|5,2|4,5|0,0;BaseQRankSum=0.177;DP=69;ExcessHet=3.0103;MLEAC=0,1,1,0;MLEAF=0.00,0.500,0.500,0.00;MQRankSum=-0.342;RAW_MQ=204256.00;ReadPosRankSum=-1.322 GT:AD:DP:GQ:PL:SB 2/3:2,4,7,9,0:22:99:651,365,925,164,381,340,135,101,0,106,443,591,394,170,627:1,1,12,8 -20 10067059 . A . . END=10067060 GT:DP:GQ:MIN_DP:PL 0/0:57:87:56:0,87,1305 -20 10067061 . A . . END=10067061 GT:DP:GQ:MIN_DP:PL 0/0:59:90:59:0,90,1350 -20 10067062 . A . . END=10067066 GT:DP:GQ:MIN_DP:PL 0/0:61:99:56:0,99,1485 -20 10067067 . A . . END=10067067 GT:DP:GQ:MIN_DP:PL 0/0:52:19:52:0,19,1692 -20 10067068 . A . . END=10067068 GT:DP:GQ:MIN_DP:PL 0/0:47:0:47:0,0,1430 -20 10067069 . A . . END=10067069 GT:DP:GQ:MIN_DP:PL 0/0:42:26:42:0,26,1402 -20 10067070 . A . . END=10067070 GT:DP:GQ:MIN_DP:PL 0/0:40:84:40:0,84,1498 -20 10067071 . A . . END=10067075 GT:DP:GQ:MIN_DP:PL 0/0:41:99:39:0,105,1471 -20 10067076 . A . . END=10067076 GT:DP:GQ:MIN_DP:PL 0/0:44:97:44:0,97,1535 -20 10067077 . G . . END=10067089 GT:DP:GQ:MIN_DP:PL 0/0:48:99:45:0,110,1645 +20 10067059 . A . . END=10067067 GT:DP:GQ:MIN_DP:PL 0/0:57:99:50:0,99,1485 +20 10067068 . A . . END=10067070 GT:DP:GQ:MIN_DP:PL 0/0:44:96:44:0,96,1440 +20 10067071 . A . . END=10067089 GT:DP:GQ:MIN_DP:PL 0/0:48:99:46:0,102,1530 20 10067090 . C A, 2004.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|165948.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|27,28|0,0;DP=55;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=165948.00 GT:AD:DP:GQ:PL:SB 1/1:0,55,0:55:99:2033,164,0,2033,164,2033:0,0,27,28 20 10067091 . T . . END=10067263 GT:DP:GQ:MIN_DP:PL 0/0:76:99:50:0,120,1800 20 10067264 . G A, 2922.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|257282.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|38,35|0,0;DP=73;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=257282.00 GT:AD:DP:GQ:PL:SB 1/1:0,73,0:73:99:2951,219,0,2951,219,2951:0,0,38,35 @@ -1117,16 +909,15 @@ 20 10068034 . G . . END=10068040 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 20 10068041 . T . . END=10068043 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,1350 20 10068044 . T . . END=10068135 GT:DP:GQ:MIN_DP:PL 0/0:43:99:34:0,99,1485 -20 10068136 . A . . END=10068140 GT:DP:GQ:MIN_DP:PL 0/0:40:84:39:0,84,1260 -20 10068141 . T . . END=10068141 GT:DP:GQ:MIN_DP:PL 0/0:39:90:39:0,90,1350 -20 10068142 . C . . END=10068142 GT:DP:GQ:MIN_DP:PL 0/0:38:84:38:0,84,1260 -20 10068143 . T . . END=10068148 GT:DP:GQ:MIN_DP:PL 0/0:35:75:31:0,75,1125 -20 10068149 . T . . END=10068151 GT:DP:GQ:MIN_DP:PL 0/0:31:63:31:0,63,945 -20 10068152 . A . . END=10068155 GT:DP:GQ:MIN_DP:PL 0/0:29:57:28:0,57,855 -20 10068156 . A . . END=10068157 GT:DP:GQ:MIN_DP:PL 0/0:27:51:27:0,51,765 +20 10068136 . A . . END=10068138 GT:DP:GQ:MIN_DP:PL 0/0:40:87:40:0,87,1305 +20 10068139 . T . . END=10068141 GT:DP:GQ:MIN_DP:PL 0/0:39:90:39:0,90,1350 +20 10068142 . C . . END=10068148 GT:DP:GQ:MIN_DP:PL 0/0:35:81:31:0,81,1215 +20 10068149 . T . . END=10068150 GT:DP:GQ:MIN_DP:PL 0/0:31:75:31:0,75,1125 +20 10068151 . A . . END=10068155 GT:DP:GQ:MIN_DP:PL 0/0:29:63:28:0,63,945 +20 10068156 . A . . END=10068157 GT:DP:GQ:MIN_DP:PL 0/0:27:57:27:0,57,855 20 10068158 . GTGTATATATATA G, 66.73 . AS_RAW_BaseQRankSum=|-0.7,1|NaN;AS_RAW_MQ=5282.00|8882.00|0.00;AS_RAW_MQRankSum=|0.3,1|NaN;AS_RAW_ReadPosRankSum=|0.5,1|NaN;AS_SB_TABLE=0,3|2,2|0,0;BaseQRankSum=-0.652;DP=29;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.328;RAW_MQ=93364.00;ReadPosRankSum=0.524 GT:AD:DP:GQ:PL:SB 0/1:3,4,0:7:57:104,0,57,114,69,183:0,3,2,2 20 10068160 . GTATATATATATGTA G,*, 697.73 . AS_RAW_BaseQRankSum=|||;AS_RAW_MQ=0.00|1682.00|8882.00|0.00;AS_RAW_MQRankSum=|||;AS_RAW_ReadPosRankSum=|||;AS_SB_TABLE=0,0|0,2|2,2|0,0;DP=28;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;RAW_MQ=87005.00 GT:AD:DP:GQ:PL:SB 1/2:0,2,4,0:6:53:735,162,131,102,0,53,507,174,108,472:0,0,2,4 -20 10068175 . T . . END=10068175 GT:DP:GQ:MIN_DP:PL 0/0:20:17:20:0,17,729 +20 10068175 . T . . END=10068175 GT:DP:GQ:MIN_DP:PL 0/0:20:18:20:0,18,270 20 10068176 . A . . END=10068180 GT:DP:GQ:MIN_DP:PL 0/0:19:24:17:0,24,360 20 10068181 . T . . END=10068185 GT:DP:GQ:MIN_DP:PL 0/0:16:27:16:0,27,405 20 10068186 . A . . END=10068186 GT:DP:GQ:MIN_DP:PL 0/0:16:9:16:0,9,570 @@ -1140,16 +931,14 @@ 20 10068200 . A . . END=10068200 GT:DP:GQ:MIN_DP:PL 0/0:16:45:16:0,45,675 20 10068201 . T . . END=10068201 GT:DP:GQ:MIN_DP:PL 0/0:18:51:18:0,51,765 20 10068202 . A . . END=10068203 GT:DP:GQ:MIN_DP:PL 0/0:19:54:19:0,54,810 -20 10068204 . A . . END=10068206 GT:DP:GQ:MIN_DP:PL 0/0:21:57:20:0,57,855 -20 10068207 . C . . END=10068209 GT:DP:GQ:MIN_DP:PL 0/0:22:60:21:0,60,900 -20 10068210 . T . . END=10068215 GT:DP:GQ:MIN_DP:PL 0/0:26:75:26:0,75,960 -20 10068216 . C . . END=10068216 GT:DP:GQ:MIN_DP:PL 0/0:27:81:27:0,81,1065 -20 10068217 . C . . END=10068217 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20 10068218 . A . . END=10068223 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,1215 -20 10068224 . G . . END=10068225 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,1350 -20 10068226 . T . . END=10068227 GT:DP:GQ:MIN_DP:PL 0/0:32:87:31:0,87,1305 -20 10068228 . C . . END=10068228 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20 10068229 . T . . END=10068237 GT:DP:GQ:MIN_DP:PL 0/0:32:87:30:0,87,1305 +20 10068204 . A . . END=10068205 GT:DP:GQ:MIN_DP:PL 0/0:21:57:20:0,57,855 +20 10068206 . C . . END=10068206 GT:DP:GQ:MIN_DP:PL 0/0:21:54:21:0,54,810 +20 10068207 . C . . END=10068208 GT:DP:GQ:MIN_DP:PL 0/0:22:57:21:0,57,855 +20 10068209 . C . . END=10068209 GT:DP:GQ:MIN_DP:PL 0/0:23:63:23:0,63,945 +20 10068210 . T . . END=10068219 GT:DP:GQ:MIN_DP:PL 0/0:27:72:26:0,72,1080 +20 10068220 . C . . END=10068224 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 +20 10068225 . G . . END=10068225 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 +20 10068226 . T . . END=10068237 GT:DP:GQ:MIN_DP:PL 0/0:32:84:30:0,84,1260 20 10068238 . T . . END=10068247 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,1168 20 10068248 . T . . END=10068290 GT:DP:GQ:MIN_DP:PL 0/0:38:99:34:0,102,1384 20 10068291 . C . . END=10068299 GT:DP:GQ:MIN_DP:PL 0/0:40:90:36:0,90,1350 @@ -1175,20 +964,13 @@ 20 10068981 . G A, 2503.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|219600.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|27,34|0,0;DP=61;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=219600.00 GT:AD:DP:GQ:PL:SB 1/1:0,61,0:61:99:2532,184,0,2532,184,2532:0,0,27,34 20 10068982 . A . . END=10070601 GT:DP:GQ:MIN_DP:PL 0/0:74:99:46:0,120,1800 20 10070602 . T C, 2691.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|248164.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|37,35|0,0;DP=72;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=248164.00 GT:AD:DP:GQ:PL:SB 1/1:0,72,0:72:99:2720,216,0,2720,216,2720:0,0,37,35 -20 10070603 . A . . END=10070920 GT:DP:GQ:MIN_DP:PL 0/0:90:99:66:0,99,1485 -20 10070921 . C . . END=10070921 GT:DP:GQ:MIN_DP:PL 0/0:91:90:91:0,90,1350 -20 10070922 . A . . END=10070923 GT:DP:GQ:MIN_DP:PL 0/0:92:57:91:0,57,855 -20 10070924 . T . . END=10070924 GT:DP:GQ:MIN_DP:PL 0/0:89:18:89:0,18,270 -20 10070925 . C . . END=10070926 GT:DP:GQ:MIN_DP:PL 0/0:87:12:86:0,12,180 -20 10070927 . C . . END=10070928 GT:DP:GQ:MIN_DP:PL 0/0:84:3:83:0,3,45 -20 10070929 . A . . END=10070935 GT:DP:GQ:MIN_DP:PL 0/0:85:0:85:0,0,0 +20 10070603 . A . . END=10070935 GT:DP:GQ:MIN_DP:PL 0/0:90:99:66:0,120,1800 20 10070936 . T A, 3631.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|279633.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|44,37|0,0;DP=81;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=279633.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,81,0:81:99:0|1:10070936_T_A:3660,247,0,3660,247,3660:0,0,44,37 -20 10070937 . A . . END=10070937 GT:DP:GQ:MIN_DP:PL 0/0:84:3:84:0,3,45 +20 10070937 . A . . END=10070937 GT:DP:GQ:MIN_DP:PL 0/0:80:99:80:0,120,1800 20 10070938 . G GA, 3656.73 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|275964.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|43,36|0,0;DP=79;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=275964.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,79,0:79:99:0|1:10070936_T_A:3694,250,0,3694,250,3694:0,0,43,36 -20 10070939 . A . . END=10070939 GT:DP:GQ:MIN_DP:PL 0/0:83:0:83:0,0,0 -20 10070940 . G . . END=10071134 GT:DP:GQ:MIN_DP:PL 0/0:77:99:67:0,120,1800 +20 10070939 . A . . END=10071134 GT:DP:GQ:MIN_DP:PL 0/0:77:99:67:0,120,1800 20 10071135 . C T, 3257.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|276123.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|34,45|0,0;DP=79;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=276123.00 GT:AD:DP:GQ:PL:SB 1/1:0,79,0:79:99:3286,238,0,3286,238,3286:0,0,34,45 -20 10071136 . T . . END=10071186 GT:DP:GQ:MIN_DP:PL 0/0:83:99:78:0,120,1800 +20 10071136 . T . . END=10071186 GT:DP:GQ:MIN_DP:PL 0/0:83:99:77:0,120,1800 20 10071187 . G A, 3410.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|292441.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|30,52|0,0;DP=82;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=292441.00 GT:AD:DP:GQ:PL:SB 1/1:0,82,0:82:99:3439,246,0,3439,246,3439:0,0,30,52 20 10071188 . G . . END=10071889 GT:DP:GQ:MIN_DP:PL 0/0:61:99:44:0,111,1710 20 10071890 . T C, 1974.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|202969.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|28,29|0,0;DP=57;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=202969.00 GT:AD:DP:GQ:PL:SB 1/1:0,57,0:57:99:2003,171,0,2003,171,2003:0,0,28,29 @@ -1212,30 +994,19 @@ 20 10075142 . G . . END=10075142 GT:DP:GQ:MIN_DP:PL 0/0:65:91:65:0,91,2199 20 10075143 . A . . END=10075167 GT:DP:GQ:MIN_DP:PL 0/0:81:99:68:0,120,1800 20 10075168 . C T, 3612.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|309981.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|38,50|0,0;DP=88;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=309981.00 GT:AD:DP:GQ:PL:SB 1/1:0,88,0:88:99:3641,264,0,3641,264,3641:0,0,38,50 -20 10075169 . G . . END=10075488 GT:DP:GQ:MIN_DP:PL 0/0:67:99:49:0,99,1485 -20 10075489 . C . . END=10075490 GT:DP:GQ:MIN_DP:PL 0/0:70:90:70:0,90,1350 -20 10075491 . G . . END=10075492 GT:DP:GQ:MIN_DP:PL 0/0:71:75:70:0,75,1125 -20 10075493 . G . . END=10075495 GT:DP:GQ:MIN_DP:PL 0/0:72:63:71:0,63,945 -20 10075496 . G . . END=10075497 GT:DP:GQ:MIN_DP:PL 0/0:73:54:73:0,54,810 -20 10075498 . T . . END=10075498 GT:DP:GQ:MIN_DP:PL 0/0:72:42:72:0,42,630 -20 10075499 . G . . END=10075499 GT:DP:GQ:MIN_DP:PL 0/0:73:33:73:0,33,495 -20 10075500 . A . . END=10075500 GT:DP:GQ:MIN_DP:PL 0/0:73:27:73:0,27,405 -20 10075501 . T . . END=10075502 GT:DP:GQ:MIN_DP:PL 0/0:72:21:71:0,21,315 -20 10075503 . A . . END=10075506 GT:DP:GQ:MIN_DP:PL 0/0:75:3:72:0,3,45 -20 10075507 . A . . END=10075507 GT:DP:GQ:MIN_DP:PL 0/0:80:6:80:0,6,90 +20 10075169 . G . . END=10075507 GT:DP:GQ:MIN_DP:PL 0/0:68:99:49:0,119,1800 20 10075508 . GA G, 1928.73 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|262921.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|29,41|0,0;DP=77;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=288121.00 GT:AD:DP:GQ:PL:SB 1/1:0,70,0:70:99:1966,210,0,1966,210,1966:0,0,29,41 -20 10075510 . A . . END=10075510 GT:DP:GQ:MIN_DP:PL 0/0:80:0:80:0,0,0 -20 10075511 . A . . END=10076249 GT:DP:GQ:MIN_DP:PL 0/0:76:99:55:0,120,1800 +20 10075510 . A . . END=10076249 GT:DP:GQ:MIN_DP:PL 0/0:76:99:55:0,120,1800 20 10076250 . A G, 1107.77 . AS_RAW_BaseQRankSum=|-3.4,1|NaN;AS_RAW_MQ=144000.00|134666.00|0.00;AS_RAW_MQRankSum=|-1.5,1|NaN;AS_RAW_ReadPosRankSum=|0.2,1|NaN;AS_SB_TABLE=14,26|20,19|0,0;BaseQRankSum=-3.386;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.423;RAW_MQ=278666.00;ReadPosRankSum=0.270 GT:AD:DP:GQ:PL:SB 0/1:40,39,0:79:99:1136,0,1339,1257,1456,2712:14,26,20,19 20 10076251 . A . . END=10076338 GT:DP:GQ:MIN_DP:PL 0/0:70:99:62:0,120,1800 20 10076339 . A G, 1309.77 . AS_RAW_BaseQRankSum=|-0.1,1|NaN;AS_RAW_MQ=115200.00|141241.00|0.00;AS_RAW_MQRankSum=|-0.9,1|NaN;AS_RAW_ReadPosRankSum=|1.0,1|NaN;AS_SB_TABLE=12,20|18,22|0,0;BaseQRankSum=-0.069;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.866;RAW_MQ=256441.00;ReadPosRankSum=1.015 GT:AD:DP:GQ:PL:SB 0/1:32,40,0:72:99:1338,0,1035,1435,1156,2590:12,20,18,22 -20 10076340 . A . . END=10076398 GT:DP:GQ:MIN_DP:PL 0/0:88:99:72:0,120,1800 +20 10076340 . A . . END=10076398 GT:DP:GQ:MIN_DP:PL 0/0:88:99:71:0,120,1800 20 10076399 . G A, 1807.77 . AS_RAW_BaseQRankSum=|4.1,1|NaN;AS_RAW_MQ=158400.00|180000.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-1.1,1|NaN;AS_SB_TABLE=22,22|22,28|0,0;BaseQRankSum=4.154;DP=94;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=338400.00;ReadPosRankSum=-1.058 GT:AD:DP:GQ:PL:SB 0/1:44,50,0:94:99:1836,0,1544,1969,1694,3663:22,22,22,28 -20 10076400 . G . . END=10076988 GT:DP:GQ:MIN_DP:PL 0/0:73:99:51:0,102,1530 +20 10076400 . G . . END=10076988 GT:DP:GQ:MIN_DP:PL 0/0:73:99:51:0,120,1800 20 10076989 . CAA C,CA,CAAA, 214.73 . AS_RAW_BaseQRankSum=|-0.4,1|-1.0,1|0.1,1|NaN;AS_RAW_MQ=25200.00|10800.00|46800.00|22441.00|0.00;AS_RAW_MQRankSum=|0.0,1|0.0,1|-0.7,1|NaN;AS_RAW_ReadPosRankSum=|-1.3,1|-0.8,1|-0.4,1|NaN;AS_SB_TABLE=4,3|1,2|6,7|5,2|0,0;BaseQRankSum=-0.625;DP=75;ExcessHet=3.0103;MLEAC=0,1,1,0;MLEAF=0.00,0.500,0.500,0.00;MQRankSum=-0.473;RAW_MQ=253446.00;ReadPosRankSum=-0.918 GT:AD:DP:GQ:PL:SB 2/3:7,3,13,7,0:30:41:252,271,1146,41,448,376,147,276,0,361,322,712,423,318,705:4,3,12,11 -20 10076992 . A . . END=10077007 GT:DP:GQ:MIN_DP:PL 0/0:72:99:61:0,113,1800 +20 10076992 . A . . END=10077007 GT:DP:GQ:MIN_DP:PL 0/0:69:99:59:0,120,1800 20 10077008 . T A, 0 . AS_RAW_BaseQRankSum=|-1.9,1|NaN;AS_RAW_MQ=160082.00|11641.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|0.8,1|NaN;AS_SB_TABLE=18,28|4,0|0,0;BaseQRankSum=-1.806;DP=51;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.608;RAW_MQ=175323.00;ReadPosRankSum=0.805 GT:AD:DP:GQ:PGT:PID:PL:SB 0/0:46,4,0:50:42:0|1:10077008_T_A:0,42,2066,148,2078,2184:18,28,4,0 -20 10077009 . A . . END=10077009 GT:DP:GQ:MIN_DP:PL 0/0:54:99:54:0,120,1800 +20 10077009 . A . . END=10077009 GT:DP:GQ:MIN_DP:PL 0/0:52:99:52:0,120,1800 20 10077010 . G A, 0 . AS_RAW_BaseQRankSum=|-1.9,1|NaN;AS_RAW_MQ=167282.00|11641.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|0.9,1|NaN;AS_SB_TABLE=18,30|4,0|0,0;BaseQRankSum=-1.841;DP=53;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.658;RAW_MQ=182523.00;ReadPosRankSum=0.911 GT:AD:DP:GQ:PGT:PID:PL:SB 0/0:48,4,0:52:42:0|1:10077008_T_A:0,42,2066,148,2078,2184:18,30,4,0 20 10077011 . A . . END=10077751 GT:DP:GQ:MIN_DP:PL 0/0:69:99:44:0,102,1654 20 10077752 . T C, 1345.77 . AS_RAW_BaseQRankSum=|-6.6,1|NaN;AS_RAW_MQ=122400.00|162000.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.4,1|NaN;AS_SB_TABLE=16,18|16,29|0,0;BaseQRankSum=-6.503;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=284400.00;ReadPosRankSum=-0.352 GT:AD:DP:GQ:PL:SB 0/1:34,45,0:79:99:1374,0,1187,1477,1322,2799:16,18,16,29 @@ -1280,25 +1051,27 @@ 20 10087394 . T G, 1688.77 . AS_RAW_BaseQRankSum=|-2.4,1|NaN;AS_RAW_MQ=123241.00|176400.00|0.00;AS_RAW_MQRankSum=|1.2,1|NaN;AS_RAW_ReadPosRankSum=|0.8,1|NaN;AS_SB_TABLE=21,14|24,25|0,0;BaseQRankSum=-2.340;DP=84;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.207;RAW_MQ=299641.00;ReadPosRankSum=0.885 GT:AD:DP:GQ:PL:SB 0/1:35,49,0:84:99:1717,0,1186,1823,1334,3156:21,14,24,25 20 10087395 . T . . END=10087753 GT:DP:GQ:MIN_DP:PL 0/0:83:99:61:0,120,1800 20 10087754 . T G, 1347.77 . AS_RAW_BaseQRankSum=|0.3,1|NaN;AS_RAW_MQ=133200.00|154100.00|0.00;AS_RAW_MQRankSum=|2.1,1|NaN;AS_RAW_ReadPosRankSum=|-0.6,1|NaN;AS_SB_TABLE=23,14|24,17|0,0;BaseQRankSum=0.355;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.193;RAW_MQ=288141.00;ReadPosRankSum=-0.551 GT:AD:DP:GQ:PL:SB 0/1:37,41,0:78:99:1376,0,1239,1488,1362,2849:23,14,24,17 -20 10087755 . G . . END=10087803 GT:DP:GQ:MIN_DP:PL 0/0:102:99:83:0,120,1800 +20 10087755 . G . . END=10087803 GT:DP:GQ:MIN_DP:PL 0/0:100:99:81:0,120,1800 20 10087804 . C T, 1619.77 . AS_RAW_BaseQRankSum=|1.9,1|NaN;AS_RAW_MQ=178541.00|190769.00|0.00;AS_RAW_MQRankSum=|2.6,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=33,17|28,22|0,0;BaseQRankSum=1.940;DP=100;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.618;RAW_MQ=369310.00;ReadPosRankSum=0.341 GT:AD:DP:GQ:PL:SB 0/1:50,50,0:100:99:1648,0,1511,1797,1661,3458:33,17,28,22 -20 10087805 . G . . END=10087819 GT:DP:GQ:MIN_DP:PL 0/0:101:99:97:0,120,1800 +20 10087805 . G . . END=10087819 GT:DP:GQ:MIN_DP:PL 0/0:101:99:96:0,120,1800 20 10087820 . CAG C,CAGAG, 428.73 . AS_RAW_BaseQRankSum=|NaN|-2.0,1|NaN;AS_RAW_MQ=123769.00|0.00|63869.00|0.00;AS_RAW_MQRankSum=|NaN|0.4,1|NaN;AS_RAW_ReadPosRankSum=|NaN|-0.4,1|NaN;AS_SB_TABLE=17,18|0,0|8,10|0,0;BaseQRankSum=-1.974;DP=99;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=0.422;RAW_MQ=362700.00;ReadPosRankSum=-0.357 GT:AD:DP:GQ:PL:SB 0/2:35,0,18,0:53:99:466,669,2577,0,1197,1168,661,2237,1238,2189:17,18,8,10 -20 10087823 . A . . END=10087841 GT:DP:GQ:MIN_DP:PL 0/0:87:99:83:0,120,1800 -20 10087842 . A . . END=10087842 GT:DP:GQ:MIN_DP:PL 0/0:82:64:82:0,64,2763 -20 10087843 . A . . END=10088062 GT:DP:GQ:MIN_DP:PL 0/0:95:99:71:0,120,1800 +20 10087823 . A . . END=10087841 GT:DP:GQ:MIN_DP:PL 0/0:86:99:83:0,120,1800 +20 10087842 . A . . END=10087842 GT:DP:GQ:MIN_DP:PL 0/0:82:0:82:0,0,2206 +20 10087843 . A . . END=10087843 GT:DP:GQ:MIN_DP:PL 0/0:82:73:82:0,73,2973 +20 10087844 . G . . END=10087844 GT:DP:GQ:MIN_DP:PL 0/0:80:0:80:0,0,2190 +20 10087845 . A . . END=10088062 GT:DP:GQ:MIN_DP:PL 0/0:95:99:71:0,120,1800 20 10088063 . C T, 1417.77 . AS_RAW_BaseQRankSum=|3.4,1|NaN;AS_RAW_MQ=171410.00|156169.00|0.00;AS_RAW_MQRankSum=|0.5,1|NaN;AS_RAW_ReadPosRankSum=|0.2,1|NaN;AS_SB_TABLE=24,25|18,26|0,0;BaseQRankSum=3.405;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.515;RAW_MQ=327579.00;ReadPosRankSum=0.285 GT:AD:DP:GQ:PL:SB 0/1:49,44,0:93:99:1446,0,1403,1592,1535,3128:24,25,18,26 20 10088064 . G . . END=10088698 GT:DP:GQ:MIN_DP:PL 0/0:87:99:60:0,120,1800 20 10088699 . C T, 776.77 . AS_RAW_BaseQRankSum=|3.8,1|NaN;AS_RAW_MQ=127369.00|71528.00|0.00;AS_RAW_MQRankSum=|-3.2,1|NaN;AS_RAW_ReadPosRankSum=|-1.5,1|NaN;AS_SB_TABLE=15,21|19,7|0,0;BaseQRankSum=3.803;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.140;RAW_MQ=199738.00;ReadPosRankSum=-1.456 GT:AD:DP:GQ:PL:SB 0/1:36,26,0:62:99:805,0,1088,913,1166,2079:15,21,19,7 -20 10088700 . G . . END=10088729 GT:DP:GQ:MIN_DP:PL 0/0:54:99:52:0,120,1800 +20 10088700 . G . . END=10088729 GT:DP:GQ:MIN_DP:PL 0/0:53:99:51:0,120,1800 20 10088730 . G A, 972.77 . AS_RAW_BaseQRankSum=|0.2,1|NaN;AS_RAW_MQ=104400.00|43958.00|0.00;AS_RAW_MQRankSum=|-4.9,1|NaN;AS_RAW_ReadPosRankSum=|0.5,1|NaN;AS_SB_TABLE=11,18|16,7|0,0;BaseQRankSum=0.224;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.839;RAW_MQ=148358.00;ReadPosRankSum=0.581 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:29,23,0:52:99:0|1:10088730_G_A:1001,0,1152,1092,1231,2322:11,18,16,7 -20 10088731 . G . . END=10088735 GT:DP:GQ:MIN_DP:PL 0/0:56:99:56:0,120,1800 +20 10088731 . G . . END=10088735 GT:DP:GQ:MIN_DP:PL 0/0:55:99:55:0,120,1800 20 10088736 . A C, 1081.77 . AS_RAW_BaseQRankSum=|0.2,1|NaN;AS_RAW_MQ=100800.00|48882.00|0.00;AS_RAW_MQRankSum=|-5.2,1|NaN;AS_RAW_ReadPosRankSum=|0.5,1|NaN;AS_SB_TABLE=10,18|16,11|0,0;BaseQRankSum=0.282;DP=55;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.169;RAW_MQ=149682.00;ReadPosRankSum=0.573 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:28,27,0:55:99:0|1:10088730_G_A:1110,0,1194,1203,1281,2484:10,18,16,11 -20 10088737 . C . . END=10088746 GT:DP:GQ:MIN_DP:PL 0/0:57:99:53:0,120,1800 +20 10088737 . C . . END=10088746 GT:DP:GQ:MIN_DP:PL 0/0:56:99:53:0,120,1800 20 10088747 . A G, 1111.77 . AS_RAW_BaseQRankSum=|-3.9,1|NaN;AS_RAW_MQ=90000.00|55398.00|0.00;AS_RAW_MQRankSum=|-5.0,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=10,15|18,11|0,0;BaseQRankSum=-3.877;DP=55;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.907;RAW_MQ=146239.00;ReadPosRankSum=0.009 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:25,29,0:54:99:0|1:10088730_G_A:1140,0,995,1219,1085,2304:10,15,18,11 -20 10088748 . G . . END=10088798 GT:DP:GQ:MIN_DP:PL 0/0:50:99:46:0,109,1710 +20 10088748 . G . . END=10088798 GT:DP:GQ:MIN_DP:PL 0/0:49:99:46:0,114,1710 20 10088799 . G A, 1018.77 . AS_RAW_BaseQRankSum=|5.5,1|NaN;AS_RAW_MQ=74903.00|75137.00|0.00;AS_RAW_MQRankSum=|-2.5,1|NaN;AS_RAW_ReadPosRankSum=|1.0,1|NaN;AS_SB_TABLE=14,8|12,19|0,0;BaseQRankSum=5.503;DP=53;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.498;RAW_MQ=150040.00;ReadPosRankSum=1.075 GT:AD:DP:GQ:PL:SB 0/1:22,31,0:53:99:1047,0,617,1114,711,1824:14,8,12,19 -20 10088800 . T . . END=10088831 GT:DP:GQ:MIN_DP:PL 0/0:54:99:50:0,108,1800 +20 10088800 . T . . END=10088831 GT:DP:GQ:MIN_DP:PL 0/0:54:99:50:0,113,1800 20 10088832 . G . . END=10088842 GT:DP:GQ:MIN_DP:PL 0/0:53:63:36:0,63,945 20 10088843 . C . . END=10088843 GT:DP:GQ:MIN_DP:PL 0/0:25:16:25:0,16,759 20 10088844 . A . . END=10088844 GT:DP:GQ:MIN_DP:PL 0/0:25:37:25:0,37,718 @@ -1317,17 +1090,11 @@ 20 10088867 . A . . END=10088870 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 20 10088871 . T . . END=10088894 GT:DP:GQ:MIN_DP:PL 0/0:39:99:33:0,99,1294 20 10088895 . C T, 532.77 . AS_RAW_BaseQRankSum=|2.4,1|NaN;AS_RAW_MQ=74073.00|60377.00|0.00;AS_RAW_MQRankSum=|0.5,1|NaN;AS_RAW_ReadPosRankSum=|1.3,1|NaN;AS_SB_TABLE=10,13|8,10|0,0;BaseQRankSum=2.462;DP=41;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.577;RAW_MQ=134450.00;ReadPosRankSum=1.301 GT:AD:DP:GQ:PL:SB 0/1:23,18,0:41:99:561,0,673,630,726,1356:10,13,8,10 -20 10088896 . G . . END=10088963 GT:DP:GQ:MIN_DP:PL 0/0:50:99:42:0,99,1485 -20 10088964 . G . . END=10088964 GT:DP:GQ:MIN_DP:PL 0/0:68:61:68:0,61,1979 -20 10088965 . T . . END=10088965 GT:DP:GQ:MIN_DP:PL 0/0:68:55:68:0,55,2178 -20 10088966 . C . . END=10088967 GT:DP:GQ:MIN_DP:PL 0/0:71:0:70:0,0,2081 +20 10088896 . G . . END=10088967 GT:DP:GQ:MIN_DP:PL 0/0:49:99:42:0,110,1709 20 10088968 . C CAAA, 1175.73 . AS_RAW_BaseQRankSum=|0.5,1|NaN;AS_RAW_MQ=105241.00|42471.00|0.00;AS_RAW_MQRankSum=|-4.8,1|NaN;AS_RAW_ReadPosRankSum=|2.4,1|NaN;AS_SB_TABLE=16,14|14,9|0,0;BaseQRankSum=0.552;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.750;RAW_MQ=177808.00;ReadPosRankSum=2.416 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:30,23,0:53:99:0|1:10088968_C_CAAA:1213,0,1367,1310,1463,2773:16,14,14,9 -20 10088969 . A . . END=10088969 GT:DP:GQ:MIN_DP:PL 0/0:72:0:72:0,0,1374 -20 10088970 . A . . END=10088978 GT:DP:GQ:MIN_DP:PL 0/0:76:99:75:0,120,1800 -20 10088979 . A . . END=10088979 GT:DP:GQ:MIN_DP:PL 0/0:78:57:78:0,57,2694 +20 10088969 . A . . END=10088979 GT:DP:GQ:MIN_DP:PL 0/0:71:99:70:0,120,1800 20 10088980 . T C, 1247.77 . AS_RAW_BaseQRankSum=|-1.6,1|NaN;AS_RAW_MQ=124923.00|51430.00|0.00;AS_RAW_MQRankSum=|-5.3,1|NaN;AS_RAW_ReadPosRankSum=|1.2,1|NaN;AS_SB_TABLE=19,18|15,16|0,0;BaseQRankSum=-1.585;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.232;RAW_MQ=176353.00;ReadPosRankSum=1.288 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:37,31,0:68:99:0|1:10088968_C_CAAA:1276,0,1627,1394,1729,3123:19,18,15,16 -20 10088981 . A . . END=10088981 GT:DP:GQ:MIN_DP:PL 0/0:78:40:78:0,40,2558 -20 10088982 . A . . END=10088984 GT:DP:GQ:MIN_DP:PL 0/0:78:99:77:0,120,1800 +20 10088981 . A . . END=10088984 GT:DP:GQ:MIN_DP:PL 0/0:71:99:69:0,120,1800 20 10088985 . T C, 1178.77 . AS_RAW_BaseQRankSum=|-0.2,1|NaN;AS_RAW_MQ=138965.00|52799.00|0.00;AS_RAW_MQRankSum=|-5.3,1|NaN;AS_RAW_ReadPosRankSum=|1.2,1|NaN;AS_SB_TABLE=22,20|15,17|0,0;BaseQRankSum=-0.192;DP=74;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.248;RAW_MQ=191764.00;ReadPosRankSum=1.228 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:42,32,0:74:99:0|1:10088968_C_CAAA:1207,0,1729,1333,1826,3159:22,20,15,17 20 10088986 . A . . END=10088989 GT:DP:GQ:MIN_DP:PL 0/0:82:99:81:0,120,1800 20 10088990 . A . . END=10088990 GT:DP:GQ:MIN_DP:PL 0/0:84:7:84:0,7,2771 @@ -1343,15 +1110,11 @@ 20 10089043 . T . . END=10089043 GT:DP:GQ:MIN_DP:PL 0/0:76:79:76:0,79,2231 20 10089044 . G . . END=10089440 GT:DP:GQ:MIN_DP:PL 0/0:82:99:74:0,120,1800 20 10089441 . A G, 1179.77 . AS_RAW_BaseQRankSum=|-4.9,1|NaN;AS_RAW_MQ=133200.00|137641.00|0.00;AS_RAW_MQRankSum=|-1.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.2,1|NaN;AS_SB_TABLE=19,18|14,25|0,0;BaseQRankSum=-4.885;DP=76;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.948;RAW_MQ=270841.00;ReadPosRankSum=-0.156 GT:AD:DP:GQ:PL:SB 0/1:37,39,0:76:99:1208,0,1313,1319,1430,2749:19,18,14,25 -20 10089442 . G . . END=10089524 GT:DP:GQ:MIN_DP:PL 0/0:82:99:74:0,120,1800 +20 10089442 . G . . END=10089524 GT:DP:GQ:MIN_DP:PL 0/0:81:99:74:0,120,1800 20 10089525 . C T, 1548.77 . AS_RAW_BaseQRankSum=|5.8,1|NaN;AS_RAW_MQ=131810.00|154800.00|0.00;AS_RAW_MQRankSum=|1.5,1|NaN;AS_RAW_ReadPosRankSum=|0.8,1|NaN;AS_SB_TABLE=22,16|20,23|0,0;BaseQRankSum=5.859;DP=81;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.531;RAW_MQ=286610.00;ReadPosRankSum=0.862 GT:AD:DP:GQ:PL:SB 0/1:38,43,0:81:99:1577,0,1088,1691,1217,2908:22,16,20,23 -20 10089526 . G . . END=10090283 GT:DP:GQ:MIN_DP:PL 0/0:73:99:55:0,108,1620 -20 10090284 . A . . END=10090284 GT:DP:GQ:MIN_DP:PL 0/0:69:87:69:0,87,1305 -20 10090285 . A . . END=10090287 GT:DP:GQ:MIN_DP:PL 0/0:70:90:70:0,90,1350 -20 10090288 . C . . END=10090288 GT:DP:GQ:MIN_DP:PL 0/0:70:78:70:0,78,1170 +20 10089526 . G . . END=10090288 GT:DP:GQ:MIN_DP:PL 0/0:72:99:55:0,111,1800 20 10090289 . CAA C,CA, 384.73 . AS_RAW_BaseQRankSum=|0.6,1|0.3,1|NaN;AS_RAW_MQ=50400.00|14400.00|75900.00|0.00;AS_RAW_MQRankSum=|0.0,1|1.5,1|NaN;AS_RAW_ReadPosRankSum=|-1.5,1|0.5,1|NaN;AS_SB_TABLE=7,7|3,1|8,12|0,0;BaseQRankSum=0.441;DP=80;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=1.393;RAW_MQ=287682.00;ReadPosRankSum=0.048 GT:AD:DP:GQ:PL:SB 0/2:14,4,20,0:38:99:422,360,986,0,261,230,477,867,348,928:7,7,11,13 -20 10090292 . A . . END=10090292 GT:DP:GQ:MIN_DP:PL 0/0:79:38:79:0,38,2756 -20 10090293 . A . . END=10090763 GT:DP:GQ:MIN_DP:PL 0/0:75:99:61:0,120,1800 +20 10090292 . A . . END=10090763 GT:DP:GQ:MIN_DP:PL 0/0:75:99:61:0,120,1800 20 10090764 . A G, 840.77 . AS_RAW_BaseQRankSum=|-2.7,1|NaN;AS_RAW_MQ=122400.00|104400.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|1.2,1|NaN;AS_SB_TABLE=12,22|14,15|0,0;BaseQRankSum=-2.659;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=226800.00;ReadPosRankSum=1.207 GT:AD:DP:GQ:PL:SB 0/1:34,29,0:63:99:869,0,1207,972,1294,2265:12,22,14,15 20 10090765 . A . . END=10090969 GT:DP:GQ:MIN_DP:PL 0/0:75:99:65:0,120,1800 20 10090970 . T C, 1257.77 . AS_RAW_BaseQRankSum=|-0.5,1|NaN;AS_RAW_MQ=114338.00|129600.00|0.00;AS_RAW_MQRankSum=|1.5,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=20,13|20,16|0,0;BaseQRankSum=-0.484;DP=69;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.509;RAW_MQ=243938.00;ReadPosRankSum=-0.072 GT:AD:DP:GQ:PL:SB 0/1:33,36,0:69:99:1286,0,1092,1384,1201,2585:20,13,20,16 @@ -1361,13 +1124,9 @@ 20 10092415 . A G, 1635.77 . AS_RAW_BaseQRankSum=|-6.8,1|NaN;AS_RAW_MQ=187200.00|176400.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=27,25|24,25|0,0;BaseQRankSum=-6.731;DP=101;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=363600.00;ReadPosRankSum=0.082 GT:AD:DP:GQ:PL:SB 0/1:52,49,0:101:99:1664,0,1902,1820,2049,3870:27,25,24,25 20 10092416 . G . . END=10092926 GT:DP:GQ:MIN_DP:PL 0/0:80:99:60:0,120,1800 20 10092927 . G T, 106.77 . AS_RAW_BaseQRankSum=|-2.6,1|NaN;AS_RAW_MQ=212400.00|41282.00|0.00;AS_RAW_MQRankSum=|-3.1,1|NaN;AS_RAW_ReadPosRankSum=|-0.3,1|NaN;AS_SB_TABLE=43,16|0,13|0,0;BaseQRankSum=-2.507;DP=73;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.009;RAW_MQ=257282.00;ReadPosRankSum=-0.220 GT:AD:DP:GQ:PL:SB 0/1:59,13,0:72:99:135,0,1864,310,1901,2211:43,16,0,13 -20 10092928 . T . . END=10093558 GT:DP:GQ:MIN_DP:PL 0/0:79:99:57:0,111,1665 -20 10093559 . T . . END=10093562 GT:DP:GQ:MIN_DP:PL 0/0:62:90:60:0,90,1350 -20 10093563 . G . . END=10093566 GT:DP:GQ:MIN_DP:PL 0/0:61:84:60:0,84,1260 -20 10093567 . G . . END=10093567 GT:DP:GQ:MIN_DP:PL 0/0:59:75:59:0,75,1125 +20 10092928 . T . . END=10093567 GT:DP:GQ:MIN_DP:PL 0/0:79:99:57:0,120,1800 20 10093568 . GTT G,GT,GTTT, 326.73 . AS_RAW_BaseQRankSum=|-1.7,1|1.1,1|0.2,1|NaN;AS_RAW_MQ=61200.00|11641.00|62869.00|14400.00|0.00;AS_RAW_MQRankSum=|-2.0,1|1.0,1|0.0,1|NaN;AS_RAW_ReadPosRankSum=|1.6,1|0.6,1|1.1,1|NaN;AS_SB_TABLE=7,10|2,2|7,10|1,3|0,0;BaseQRankSum=0.426;DP=59;ExcessHet=3.0103;MLEAC=0,1,0,0;MLEAF=0.00,0.500,0.00,0.00;MQRankSum=0.410;RAW_MQ=203561.00;ReadPosRankSum=1.257 GT:AD:DP:GQ:PL:SB 0/2:17,4,17,4,0:42:99:364,329,1122,0,430,386,377,710,293,909,431,838,449,780,885:7,10,10,15 -20 10093571 . T . . END=10093571 GT:DP:GQ:MIN_DP:PL 0/0:57:59:57:0,59,2043 -20 10093572 . T . . END=10093922 GT:DP:GQ:MIN_DP:PL 0/0:62:99:51:0,99,1485 +20 10093571 . T . . END=10093922 GT:DP:GQ:MIN_DP:PL 0/0:62:99:51:0,99,1485 20 10093923 . T A, 1075.77 . AS_RAW_BaseQRankSum=|-0.7,1|NaN;AS_RAW_MQ=122419.00|112285.00|0.00;AS_RAW_MQRankSum=|0.3,1|NaN;AS_RAW_ReadPosRankSum=|-1.6,1|NaN;AS_SB_TABLE=18,17|15,17|0,0;BaseQRankSum=-0.667;DP=67;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.358;RAW_MQ=234704.00;ReadPosRankSum=-1.583 GT:AD:DP:GQ:PL:SB 0/1:35,32,0:67:99:1104,0,1257,1209,1353,2563:18,17,15,17 20 10093924 . G . . END=10094250 GT:DP:GQ:MIN_DP:PL 0/0:66:99:53:0,120,1800 20 10094251 . T A, 1270.77 . AS_RAW_BaseQRankSum=|0.2,1|NaN;AS_RAW_MQ=93600.00|129600.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|1.8,1|NaN;AS_SB_TABLE=10,16|23,13|0,0;BaseQRankSum=0.251;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=223200.00;ReadPosRankSum=1.806 GT:AD:DP:GQ:PL:SB 0/1:26,36,0:62:99:1299,0,781,1376,889,2265:10,16,23,13 @@ -1377,8 +1136,7 @@ 20 10094774 . C T, 1036.77 . AS_RAW_BaseQRankSum=|-0.8,1|NaN;AS_RAW_MQ=141241.00|126000.00|0.00;AS_RAW_MQRankSum=|0.9,1|NaN;AS_RAW_ReadPosRankSum=|0.1,1|NaN;AS_SB_TABLE=24,16|21,14|0,0;BaseQRankSum=-0.784;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.962;RAW_MQ=267241.00;ReadPosRankSum=0.197 GT:AD:DP:GQ:PL:SB 0/1:40,35,0:75:99:1065,0,1282,1185,1385,2570:24,16,21,14 20 10094775 . A . . END=10095431 GT:DP:GQ:MIN_DP:PL 0/0:77:99:63:0,120,1800 20 10095432 . GTGATGATGA G, 839.73 . AS_RAW_BaseQRankSum=|1.2,1|NaN;AS_RAW_MQ=97200.00|35579.00|0.00;AS_RAW_MQRankSum=|-4.5,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=16,11|12,11|0,0;BaseQRankSum=1.265;DP=77;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.431;RAW_MQ=227748.00;ReadPosRankSum=0.396 GT:AD:DP:GQ:PL:SB 0/1:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11 -20 10095442 . T . . END=10095442 GT:DP:GQ:MIN_DP:PL 0/0:71:0:71:0,0,1080 -20 10095443 . G . . END=10095740 GT:DP:GQ:MIN_DP:PL 0/0:81:99:64:0,120,1800 +20 10095442 . T . . END=10095740 GT:DP:GQ:MIN_DP:PL 0/0:80:99:64:0,120,1800 20 10095741 . A G, 1075.77 . AS_RAW_BaseQRankSum=|-0.6,1|NaN;AS_RAW_MQ=126841.00|103087.00|0.00;AS_RAW_MQRankSum=|-2.4,1|NaN;AS_RAW_ReadPosRankSum=|-0.5,1|NaN;AS_SB_TABLE=14,22|18,16|0,0;BaseQRankSum=-0.534;DP=71;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.313;RAW_MQ=233528.00;ReadPosRankSum=-0.500 GT:AD:DP:GQ:PL:SB 0/1:36,34,0:70:99:1104,0,1233,1213,1335,2547:14,22,18,16 20 10095742 . G . . END=10096292 GT:DP:GQ:MIN_DP:PL 0/0:73:99:63:0,120,1800 20 10096293 . C T, 1355.77 . AS_RAW_BaseQRankSum=|4.6,1|NaN;AS_RAW_MQ=123220.00|134041.00|0.00;AS_RAW_MQRankSum=|1.3,1|NaN;AS_RAW_ReadPosRankSum=|-1.2,1|NaN;AS_SB_TABLE=21,16|21,17|0,0;BaseQRankSum=4.664;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.397;RAW_MQ=257261.00;ReadPosRankSum=-1.135 GT:AD:DP:GQ:PL:SB 0/1:37,38,0:75:99:1384,0,1258,1495,1372,2867:21,16,21,17 @@ -1386,32 +1144,22 @@ 20 10096596 . C T, 1562.77 . AS_RAW_BaseQRankSum=|2.7,1|NaN;AS_RAW_MQ=136779.00|163682.00|0.00;AS_RAW_MQRankSum=|0.6,1|NaN;AS_RAW_ReadPosRankSum=|-0.2,1|NaN;AS_SB_TABLE=19,21|23,24|0,0;BaseQRankSum=2.728;DP=87;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.612;RAW_MQ=300461.00;ReadPosRankSum=-0.170 GT:AD:DP:GQ:PL:SB 0/1:40,47,0:87:99:1591,0,1273,1711,1414,3125:19,21,23,24 20 10096597 . T . . END=10096767 GT:DP:GQ:MIN_DP:PL 0/0:90:99:75:0,120,1800 20 10096768 . A C, 1682.77 . AS_RAW_BaseQRankSum=|-2.8,1|NaN;AS_RAW_MQ=151200.00|168123.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|0.6,1|NaN;AS_SB_TABLE=25,17|24,25|0,0;BaseQRankSum=-2.764;DP=91;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.609;RAW_MQ=319323.00;ReadPosRankSum=0.613 GT:AD:DP:GQ:PL:SB 0/1:42,49,0:91:99:1711,0,1452,1838,1600,3437:25,17,24,25 -20 10096769 . A . . END=10096898 GT:DP:GQ:MIN_DP:PL 0/0:78:99:65:0,99,1485 +20 10096769 . A . . END=10096898 GT:DP:GQ:MIN_DP:PL 0/0:78:99:65:0,120,1800 20 10096899 . G T, 1614.77 . AS_RAW_BaseQRankSum=|2.7,1|NaN;AS_RAW_MQ=140400.00|139538.00|0.00;AS_RAW_MQRankSum=|-1.4,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=19,20|12,28|0,0;BaseQRankSum=2.755;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.387;RAW_MQ=279938.00;ReadPosRankSum=0.422 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:39,40,0:79:99:0|1:10096899_G_T:1643,0,1520,1764,1649,3413:19,20,12,28 -20 10096900 . G . . END=10096904 GT:DP:GQ:MIN_DP:PL 0/0:83:99:79:0,108,1620 +20 10096900 . G . . END=10096904 GT:DP:GQ:MIN_DP:PL 0/0:82:99:78:0,120,1800 20 10096905 . TA T, 1600.73 . AS_RAW_BaseQRankSum=|-0.8,1|NaN;AS_RAW_MQ=144000.00|147579.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=20,20|13,30|0,0;BaseQRankSum=-0.755;DP=83;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.677;RAW_MQ=291579.00;ReadPosRankSum=0.461 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:40,43,0:83:99:0|1:10096899_G_T:1638,0,1623,1768,1752,3520:20,20,13,30 -20 10096907 . A . . END=10096907 GT:DP:GQ:MIN_DP:PL 0/0:83:0:83:0,0,0 -20 10096908 . T . . END=10096932 GT:DP:GQ:MIN_DP:PL 0/0:85:99:83:0,120,1800 +20 10096907 . A . . END=10096932 GT:DP:GQ:MIN_DP:PL 0/0:84:99:82:0,120,1800 20 10096933 . G C, 1511.77 . AS_RAW_BaseQRankSum=|-2.0,1|NaN;AS_RAW_MQ=158400.00|140379.00|0.00;AS_RAW_MQRankSum=|-1.9,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=28,16|13,28|0,0;BaseQRankSum=-1.914;DP=85;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.802;RAW_MQ=298779.00;ReadPosRankSum=0.334 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:44,41,0:85:99:0|1:10096933_G_C:1540,0,1770,1684,1896,3580:28,16,13,28 -20 10096934 . T . . END=10096957 GT:DP:GQ:MIN_DP:PL 0/0:91:99:87:0,120,1800 +20 10096934 . T . . END=10096957 GT:DP:GQ:MIN_DP:PL 0/0:90:99:86:0,120,1800 20 10096958 . G A, 1766.77 . AS_RAW_BaseQRankSum=|2.8,1|NaN;AS_RAW_MQ=162000.00|161979.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|-1.9,1|NaN;AS_SB_TABLE=27,18|16,31|0,0;BaseQRankSum=2.839;DP=92;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.701;RAW_MQ=323979.00;ReadPosRankSum=-1.833 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:45,47,0:92:99:0|1:10096933_G_C:1795,0,1629,1929,1773,3702:27,18,16,31 20 10096959 . G . . END=10097074 GT:DP:GQ:MIN_DP:PL 0/0:92:99:84:0,120,1800 20 10097075 . T G, 1445.77 . AS_RAW_BaseQRankSum=|-2.6,1|NaN;AS_RAW_MQ=159700.00|155928.00|0.00;AS_RAW_MQRankSum=|-1.4,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=18,26|26,22|0,0;BaseQRankSum=-2.533;DP=92;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.389;RAW_MQ=315628.00;ReadPosRankSum=0.082 GT:AD:DP:GQ:PL:SB 0/1:44,48,0:92:99:1474,0,1482,1606,1626,3232:18,26,26,22 -20 10097076 . A . . END=10097100 GT:DP:GQ:MIN_DP:PL 0/0:92:99:79:0,99,1485 +20 10097076 . A . . END=10097100 GT:DP:GQ:MIN_DP:PL 0/0:91:99:77:0,120,1800 20 10097101 . C CTTT,CTTTT, 1091.73 . AS_RAW_BaseQRankSum=|-0.9,1|-1.2,1|NaN;AS_RAW_MQ=121504.00|76887.00|6803.00|0.00;AS_RAW_MQRankSum=|-1.8,1|-4.5,1|NaN;AS_RAW_ReadPosRankSum=|2.7,1|-1.4,1|NaN;AS_SB_TABLE=22,12|12,14|3,1|0,0;BaseQRankSum=-1.134;DP=76;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=-2.428;RAW_MQ=252294.00;ReadPosRankSum=2.086 GT:AD:DP:GQ:PL:SB 0/1:34,26,4,0:64:99:1129,0,1306,558,1324,2012,982,1430,2052,2377:22,12,15,15 -20 10097102 . T . . END=10097102 GT:DP:GQ:MIN_DP:PL 0/0:77:0:77:0,0,200 -20 10097103 . T . . END=10097435 GT:DP:GQ:MIN_DP:PL 0/0:70:99:60:0,99,1485 +20 10097102 . T . . END=10097435 GT:DP:GQ:MIN_DP:PL 0/0:70:99:60:0,120,1800 20 10097436 . CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT C, 1054.73 . AS_RAW_BaseQRankSum=|1.8,1|NaN;AS_RAW_MQ=204882.00|57261.00|0.00;AS_RAW_MQRankSum=|-6.5,1|NaN;AS_RAW_ReadPosRankSum=|-3.1,1|NaN;AS_SB_TABLE=23,34|11,21|0,0;BaseQRankSum=1.820;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-6.464;RAW_MQ=262143.00;ReadPosRankSum=-3.097 GT:AD:DP:GQ:PL:SB 0/1:57,32,0:89:99:1092,0,2241,1263,2338,3601:23,34,11,21 20 10097437 . TTTTC *,T, 2089.73 . AS_RAW_BaseQRankSum=|||;AS_RAW_MQ=0.00|57261.00|84469.00|0.00;AS_RAW_MQRankSum=|||;AS_RAW_ReadPosRankSum=|||;AS_SB_TABLE=0,0|11,21|5,18|0,0;DP=76;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;RAW_MQ=217330.00 GT:AD:DP:GQ:PL:SB 1/2:0,32,23,0:55:99:2127,940,1799,1195,0,1125,2201,1453,1262,2642:0,0,16,39 -20 10097442 . T . . END=10097442 GT:DP:GQ:MIN_DP:PL 0/0:63:0:63:0,0,698 -20 10097443 . T . . END=10097445 GT:DP:GQ:MIN_DP:PL 0/0:63:75:63:0,75,1125 -20 10097446 . T . . END=10097450 GT:DP:GQ:MIN_DP:PL 0/0:64:81:63:0,81,1215 -20 10097451 . T . . END=10097452 GT:DP:GQ:MIN_DP:PL 0/0:63:90:61:0,90,1350 -20 10097453 . C . . END=10097455 GT:DP:GQ:MIN_DP:PL 0/0:63:71:62:0,71,2168 -20 10097456 . T . . END=10097458 GT:DP:GQ:MIN_DP:PL 0/0:64:0:61:0,0,1556 -20 10097459 . T . . END=10097459 GT:DP:GQ:MIN_DP:PL 0/0:60:21:60:0,21,2116 -20 10097460 . T . . END=10097460 GT:DP:GQ:MIN_DP:PL 0/0:61:24:61:0,24,2071 -20 10097461 . C . . END=10097475 GT:DP:GQ:MIN_DP:PL 0/0:61:0:58:0,0,1102 +20 10097442 . T . . END=10097475 GT:DP:GQ:MIN_DP:PL 0/0:78:0:63:0,0,557 20 10097476 . T . . END=10097476 GT:DP:GQ:MIN_DP:PL 0/0:66:11:66:0,11,2255 20 10097477 . C . . END=10097625 GT:DP:GQ:MIN_DP:PL 0/0:69:99:45:0,109,1710 20 10097626 . C A, 626.77 . AS_RAW_BaseQRankSum=|1.0,1|NaN;AS_RAW_MQ=98041.00|64779.00|0.00;AS_RAW_MQRankSum=|-1.4,1|NaN;AS_RAW_ReadPosRankSum=|1.0,1|NaN;AS_SB_TABLE=8,20|8,12|0,0;BaseQRankSum=1.085;DP=48;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.331;RAW_MQ=162820.00;ReadPosRankSum=1.015 GT:AD:DP:GQ:PL:SB 0/1:28,20,0:48:99:655,0,957,739,1017,1757:8,20,8,12 @@ -1464,34 +1212,24 @@ 20 10098149 . T . . END=10098150 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 20 10098151 . A . . END=10098160 GT:DP:GQ:MIN_DP:PL 0/0:33:83:31:0,83,1260 20 10098161 . A . . END=10098176 GT:DP:GQ:MIN_DP:PL 0/0:33:90:31:0,90,1350 -20 10098177 . C . . END=10098185 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,1215 -20 10098186 . A . . END=10098199 GT:DP:GQ:MIN_DP:PL 0/0:29:72:27:0,72,1080 -20 10098200 . C . . END=10098203 GT:DP:GQ:MIN_DP:PL 0/0:28:60:28:0,60,900 -20 10098204 . G . . END=10098204 GT:DP:GQ:MIN_DP:PL 0/0:28:48:28:0,48,720 -20 10098205 . T . . END=10098206 GT:DP:GQ:MIN_DP:PL 0/0:28:45:28:0,45,675 -20 10098207 . T . . END=10098208 GT:DP:GQ:MIN_DP:PL 0/0:28:42:27:0,42,630 -20 10098209 . T . . END=10098214 GT:DP:GQ:MIN_DP:PL 0/0:24:36:24:0,36,540 -20 10098215 . T . . END=10098216 GT:DP:GQ:MIN_DP:PL 0/0:22:33:21:0,33,495 -20 10098217 . T . . END=10098217 GT:DP:GQ:MIN_DP:PL 0/0:21:27:21:0,27,405 -20 10098218 . G . . END=10098218 GT:DP:GQ:MIN_DP:PL 0/0:21:22:21:0,22,768 +20 10098177 . C . . END=10098197 GT:DP:GQ:MIN_DP:PL 0/0:30:81:27:0,81,1116 +20 10098198 . A . . END=10098203 GT:DP:GQ:MIN_DP:PL 0/0:28:72:27:0,72,1080 +20 10098204 . G . . END=10098216 GT:DP:GQ:MIN_DP:PL 0/0:24:60:21:0,60,900 +20 10098217 . T . . END=10098218 GT:DP:GQ:MIN_DP:PL 0/0:21:54:21:0,54,810 20 10098219 . TATATATA T, 295.73 . AS_RAW_BaseQRankSum=|3.1,1|NaN;AS_RAW_MQ=40441.00|25264.00|0.00;AS_RAW_MQRankSum=|-0.3,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=0,12|0,9|0,0;BaseQRankSum=3.147;DP=21;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.205;RAW_MQ=65705.00;ReadPosRankSum=0.427 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:12,9,0:21:99:0|1:10098219_TATATATA_T:333,0,461,369,488,858:0,12,0,9 -20 10098227 . T . . END=10098227 GT:DP:GQ:MIN_DP:PL 0/0:18:0:18:0,0,86 -20 10098228 . T . . END=10098228 GT:DP:GQ:MIN_DP:PL 0/0:18:14:18:0,14,662 -20 10098229 . A . . END=10098229 GT:DP:GQ:MIN_DP:PL 0/0:18:21:18:0,21,315 -20 10098230 . T . . END=10098230 GT:DP:GQ:MIN_DP:PL 0/0:18:16:18:0,16,657 -20 10098231 . A . . END=10098231 GT:DP:GQ:MIN_DP:PL 0/0:18:19:18:0,19,656 -20 10098232 . T . . END=10098232 GT:DP:GQ:MIN_DP:PL 0/0:17:11:17:0,11,615 -20 10098233 . A . . END=10098236 GT:DP:GQ:MIN_DP:PL 0/0:15:21:12:0,21,315 +20 10098227 . T . . END=10098228 GT:DP:GQ:MIN_DP:PL 0/0:18:30:18:0,30,450 +20 10098229 . A . . END=10098236 GT:DP:GQ:MIN_DP:PL 0/0:17:21:13:0,21,315 20 10098237 . A T, 244.77 . AS_RAW_BaseQRankSum=|0.0,1|NaN;AS_RAW_MQ=21600.00|15464.00|0.00;AS_RAW_MQRankSum=|-1.8,1|NaN;AS_RAW_ReadPosRankSum=|0.2,1|NaN;AS_SB_TABLE=0,6|0,7|0,0;BaseQRankSum=0.006;DP=13;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.742;RAW_MQ=37064.00;ReadPosRankSum=0.277 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:6,7,0:13:99:0|1:10098219_TATATATA_T:273,0,273,294,294,588:0,6,0,7 -20 10098238 . A . . END=10098244 GT:DP:GQ:MIN_DP:PL 0/0:10:21:8:0,21,315 -20 10098245 . T . . END=10098248 GT:DP:GQ:MIN_DP:PL 0/0:9:24:9:0,24,360 -20 10098249 . A . . END=10098255 GT:DP:GQ:MIN_DP:PL 0/0:8:18:8:0,18,270 +20 10098238 . A . . END=10098244 GT:DP:GQ:MIN_DP:PL 0/0:10:21:9:0,21,315 +20 10098245 . T . . END=10098248 GT:DP:GQ:MIN_DP:PL 0/0:10:24:10:0,24,360 +20 10098249 . A . . END=10098250 GT:DP:GQ:MIN_DP:PL 0/0:10:18:9:0,18,270 +20 10098251 . A . . END=10098255 GT:DP:GQ:MIN_DP:PL 0/0:8:15:8:0,15,225 20 10098256 . T . . END=10098264 GT:DP:GQ:MIN_DP:PL 0/0:8:9:6:0,9,135 20 10098265 . T C, 133.77 . AS_RAW_BaseQRankSum=|1.8,1|NaN;AS_RAW_MQ=7200.00|3364.00|0.00;AS_RAW_MQRankSum=|-1.9,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=0,2|0,4|0,0;BaseQRankSum=1.834;DP=6;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.834;RAW_MQ=10564.00;ReadPosRankSum=0.000 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:2,4,0:6:59:0|1:10098219_TATATATA_T:162,0,59,168,71,239:0,2,0,4 -20 10098266 . A . . END=10098276 GT:DP:GQ:MIN_DP:PL 0/0:4:9:3:0,9,121 -20 10098277 . T . . END=10098279 GT:DP:GQ:MIN_DP:PL 0/0:3:6:3:0,6,90 -20 10098280 . A . . END=10098296 GT:DP:GQ:MIN_DP:PL 0/0:4:9:3:0,9,114 -20 10098297 . A . . END=10098307 GT:DP:GQ:MIN_DP:PL 0/0:3:6:2:0,6,86 +20 10098266 . A . . END=10098272 GT:DP:GQ:MIN_DP:PL 0/0:4:9:4:0,9,135 +20 10098273 . A . . END=10098279 GT:DP:GQ:MIN_DP:PL 0/0:3:6:3:0,6,90 +20 10098280 . A . . END=10098290 GT:DP:GQ:MIN_DP:PL 0/0:4:9:3:0,9,126 +20 10098291 . A . . END=10098307 GT:DP:GQ:MIN_DP:PL 0/0:3:6:2:0,6,86 20 10098308 . AAT A, 0 . AS_RAW_BaseQRankSum=|NaN|NaN;AS_RAW_MQ=7200.00|0.00|0.00;AS_RAW_MQRankSum=|NaN|NaN;AS_RAW_ReadPosRankSum=|NaN|NaN;AS_SB_TABLE=0,0|0,0|0,0;DP=2;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;RAW_MQ=7200.00 GT:AD:DP:GQ:PL:SB 0/0:2,0,0:2:6:0,6,81,6,81,81:0,2,0,0 20 10098311 . A . . END=10098321 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,80 20 10098322 . A . . END=10098327 GT:DP:GQ:MIN_DP:PL 0/0:3:9:3:0,9,121 @@ -1499,9 +1237,8 @@ 20 10098330 . A . . END=10098343 GT:DP:GQ:MIN_DP:PL 0/0:4:9:4:0,9,135 20 10098344 . A . . END=10098344 GT:DP:GQ:MIN_DP:PL 0/0:4:0:4:0,0,1 20 10098345 . T . . END=10098350 GT:DP:GQ:MIN_DP:PL 0/0:3:9:3:0,9,125 -20 10098351 . T . . END=10098357 GT:DP:GQ:MIN_DP:PL 0/0:3:6:3:0,6,90 -20 10098358 . T . . END=10098359 GT:DP:GQ:MIN_DP:PL 0/0:3:3:3:0,3,45 -20 10098360 . A . . END=10098380 GT:DP:GQ:MIN_DP:PL 0/0:1:0:1:0,0,0 +20 10098351 . T . . END=10098360 GT:DP:GQ:MIN_DP:PL 0/0:3:3:3:0,3,45 +20 10098361 . T . . END=10098380 GT:DP:GQ:MIN_DP:PL 0/0:1:0:1:0,0,0 20 10098381 . T . . END=10098454 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,37 20 10098455 . A . . END=10098551 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0 20 10098552 . T . . END=10098637 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,40 @@ -1550,24 +1287,21 @@ 20 10098821 . T . . END=10098823 GT:DP:GQ:MIN_DP:PL 0/0:17:51:17:0,51,677 20 10098824 . A . . END=10098826 GT:DP:GQ:MIN_DP:PL 0/0:18:54:18:0,54,705 20 10098827 . T . . END=10098827 GT:DP:GQ:MIN_DP:PL 0/0:19:57:19:0,57,752 -20 10098828 . T . . END=10098857 GT:DP:GQ:MIN_DP:PL 0/0:25:60:20:0,60,799 -20 10098858 . G . . END=10098858 GT:DP:GQ:MIN_DP:PL 0/0:24:57:24:0,57,855 +20 10098828 . T . . END=10098835 GT:DP:GQ:MIN_DP:PL 0/0:21:60:20:0,60,799 +20 10098836 . G . . END=10098841 GT:DP:GQ:MIN_DP:PL 0/0:24:72:24:0,72,906 +20 10098842 . C . . END=10098842 GT:DP:GQ:MIN_DP:PL 0/0:24:69:24:0,69,1035 +20 10098843 . A . . END=10098858 GT:DP:GQ:MIN_DP:PL 0/0:26:72:24:0,72,990 20 10098859 . G . . END=10098859 GT:DP:GQ:MIN_DP:PL 0/0:24:29:24:0,29,851 -20 10098860 . T . . END=10098861 GT:DP:GQ:MIN_DP:PL 0/0:24:57:23:0,57,855 -20 10098862 . T . . END=10098862 GT:DP:GQ:MIN_DP:PL 0/0:25:60:25:0,60,900 -20 10098863 . G . . END=10098867 GT:DP:GQ:MIN_DP:PL 0/0:25:57:25:0,57,855 -20 10098868 . C . . END=10098868 GT:DP:GQ:MIN_DP:PL 0/0:25:54:25:0,54,810 -20 10098869 . G . . END=10098870 GT:DP:GQ:MIN_DP:PL 0/0:27:60:27:0,60,900 -20 10098871 . C . . END=10098873 GT:DP:GQ:MIN_DP:PL 0/0:29:57:28:0,57,855 -20 10098874 . A . . END=10098874 GT:DP:GQ:MIN_DP:PL 0/0:30:54:30:0,54,810 -20 10098875 . C . . END=10098876 GT:DP:GQ:MIN_DP:PL 0/0:30:48:30:0,48,720 -20 10098877 . G . . END=10098880 GT:DP:GQ:MIN_DP:PL 0/0:31:45:30:0,45,675 -20 10098881 . C . . END=10098881 GT:DP:GQ:MIN_DP:PL 0/0:31:48:31:0,48,720 -20 10098882 . C . . END=10098883 GT:DP:GQ:MIN_DP:PL 0/0:32:51:32:0,51,765 -20 10098884 . C . . END=10098884 GT:DP:GQ:MIN_DP:PL 0/0:32:48:32:0,48,720 +20 10098860 . T . . END=10098860 GT:DP:GQ:MIN_DP:PL 0/0:23:69:23:0,69,881 +20 10098861 . G . . END=10098868 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,960 +20 10098869 . G . . END=10098877 GT:DP:GQ:MIN_DP:PL 0/0:29:81:27:0,81,902 +20 10098878 . C . . END=10098878 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,1170 +20 10098879 . A . . END=10098881 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,1215 +20 10098882 . C . . END=10098882 GT:DP:GQ:MIN_DP:PL 0/0:32:60:32:0,60,1207 +20 10098883 . T . . END=10098883 GT:DP:GQ:MIN_DP:PL 0/0:32:56:32:0,56,1237 +20 10098884 . C . . END=10098884 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,1260 20 10098885 . C CA, 433.73 . AS_RAW_BaseQRankSum=|0.1,1|NaN;AS_RAW_MQ=58969.00|18188.00|0.00;AS_RAW_MQRankSum=|-4.5,1|NaN;AS_RAW_ReadPosRankSum=|-1.1,1|NaN;AS_SB_TABLE=16,1|13,1|0,0;BaseQRankSum=0.165;DP=31;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.449;RAW_MQ=77157.00;ReadPosRankSum=-1.073 GT:AD:DP:GQ:PL:SB 0/1:17,14,0:31:99:471,0,572,523,614,1137:16,1,13,1 -20 10098886 . C . . END=10098886 GT:DP:GQ:MIN_DP:PL 0/0:31:0:31:0,0,240 -20 10098887 . C . . END=10098890 GT:DP:GQ:MIN_DP:PL 0/0:31:84:29:0,84,1260 +20 10098886 . C . . END=10098890 GT:DP:GQ:MIN_DP:PL 0/0:31:84:29:0,84,1260 20 10098891 . C . . END=10098891 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 20 10098892 . G . . END=10098900 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 20 10098901 . T . . END=10098907 GT:DP:GQ:MIN_DP:PL 0/0:29:72:28:0,72,1080 @@ -1610,28 +1344,28 @@ 20 10099044 . A C, 334.77 . AS_RAW_BaseQRankSum=|-1.2,1|NaN;AS_RAW_MQ=51769.00|8082.00|0.00;AS_RAW_MQRankSum=|-4.5,1|NaN;AS_RAW_ReadPosRankSum=|-2.3,1|NaN;AS_SB_TABLE=12,3|7,2|0,0;BaseQRankSum=-1.148;DP=24;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.418;RAW_MQ=59851.00;ReadPosRankSum=-2.207 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:15,9,0:24:99:0|1:10099029_T_C:363,0,768,420,798,1218:12,3,7,2 20 10099045 . C . . END=10099045 GT:DP:GQ:MIN_DP:PL 0/0:24:60:24:0,60,900 20 10099046 . T C, 304.77 . AS_RAW_BaseQRankSum=|-2.2,1|NaN;AS_RAW_MQ=51769.00|8082.00|0.00;AS_RAW_MQRankSum=|-4.5,1|NaN;AS_RAW_ReadPosRankSum=|-2.3,1|NaN;AS_SB_TABLE=12,3|7,2|0,0;BaseQRankSum=-2.165;DP=24;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.418;RAW_MQ=59851.00;ReadPosRankSum=-2.297 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:15,9,0:24:99:0|1:10099029_T_C:333,0,603,378,630,1008:12,3,7,2 -20 10099047 . G . . END=10099054 GT:DP:GQ:MIN_DP:PL 0/0:26:63:25:0,63,945 +20 10099047 . G . . END=10099052 GT:DP:GQ:MIN_DP:PL 0/0:24:57:23:0,57,855 +20 10099053 . G . . END=10099054 GT:DP:GQ:MIN_DP:PL 0/0:23:54:23:0,54,810 20 10099055 . T C, 256.77 . AS_RAW_BaseQRankSum=|-1.6,1|NaN;AS_RAW_MQ=51769.00|6786.00|0.00;AS_RAW_MQRankSum=|-4.4,1|NaN;AS_RAW_ReadPosRankSum=|-2.0,1|NaN;AS_SB_TABLE=11,4|6,2|0,0;BaseQRankSum=-1.554;DP=23;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.316;RAW_MQ=58555.00;ReadPosRankSum=-1.970 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:15,8,0:23:99:0|1:10099029_T_C:285,0,673,336,697,1033:11,4,6,2 -20 10099056 . T . . END=10099059 GT:DP:GQ:MIN_DP:PL 0/0:29:75:28:0,75,1125 -20 10099060 . A . . END=10099065 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1118 -20 10099066 . C . . END=10099068 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,1172 -20 10099069 . A . . END=10099069 GT:DP:GQ:MIN_DP:PL 0/0:32:82:32:0,82,1208 -20 10099070 . G . . END=10099078 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 +20 10099056 . T . . END=10099061 GT:DP:GQ:MIN_DP:PL 0/0:24:60:23:0,60,900 +20 10099062 . A . . END=10099067 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,921 +20 10099068 . G . . END=10099072 GT:DP:GQ:MIN_DP:PL 0/0:27:81:27:0,81,1042 +20 10099073 . T . . END=10099077 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 +20 10099078 . G . . END=10099078 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 20 10099079 . C T, 116.77 . AS_RAW_BaseQRankSum=|1.4,1|NaN;AS_RAW_MQ=70213.00|8485.00|0.00;AS_RAW_MQRankSum=|-2.9,1|NaN;AS_RAW_ReadPosRankSum=|0.9,1|NaN;AS_SB_TABLE=11,12|4,2|0,0;BaseQRankSum=1.434;DP=29;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.821;RAW_MQ=78698.00;ReadPosRankSum=0.969 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:23,6,0:29:99:0|1:10099029_T_C:145,0,886,217,904,1120:11,12,4,2 -20 10099080 . G . . END=10099087 GT:DP:GQ:MIN_DP:PL 0/0:36:90:35:0,90,1350 -20 10099088 . C . . END=10099090 GT:DP:GQ:MIN_DP:PL 0/0:37:87:37:0,87,1305 -20 10099091 . C . . END=10099091 GT:DP:GQ:MIN_DP:PL 0/0:39:90:39:0,90,1350 -20 10099092 . A . . END=10099098 GT:DP:GQ:MIN_DP:PL 0/0:40:81:39:0,81,1215 -20 10099099 . C . . END=10099105 GT:DP:GQ:MIN_DP:PL 0/0:42:72:41:0,72,1080 -20 10099106 . T . . END=10099108 GT:DP:GQ:MIN_DP:PL 0/0:45:66:42:0,66,990 -20 10099109 . T . . END=10099110 GT:DP:GQ:MIN_DP:PL 0/0:48:72:47:0,72,1080 +20 10099080 . G . . END=10099089 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 +20 10099090 . A . . END=10099095 GT:DP:GQ:MIN_DP:PL 0/0:34:90:31:0,90,1350 +20 10099096 . A . . END=10099096 GT:DP:GQ:MIN_DP:PL 0/0:35:74:35:0,74,1310 +20 10099097 . G . . END=10099100 GT:DP:GQ:MIN_DP:PL 0/0:35:93:34:0,93,1395 +20 10099101 . G . . END=10099105 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1485 +20 10099106 . T . . END=10099106 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1440 +20 10099107 . T . . END=10099110 GT:DP:GQ:MIN_DP:PL 0/0:41:99:39:0,99,1485 20 10099111 . T TTTTGTTTG, 656.73 . AS_RAW_BaseQRankSum=|-1.3,1|NaN;AS_RAW_MQ=68844.00|15693.00|0.00;AS_RAW_MQRankSum=|-4.1,1|NaN;AS_RAW_ReadPosRankSum=|-0.3,1|NaN;AS_SB_TABLE=13,9|7,6|0,0;BaseQRankSum=-1.207;DP=42;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.071;RAW_MQ=109737.00;ReadPosRankSum=-0.273 GT:AD:DP:GQ:PL:SB 0/1:22,13,0:35:99:694,0,802,763,859,1622:13,9,7,6 -20 10099112 . T . . END=10099112 GT:DP:GQ:MIN_DP:PL 0/0:55:0:55:0,0,194 -20 10099113 . T . . END=10099139 GT:DP:GQ:MIN_DP:PL 0/0:63:99:57:0,120,1800 +20 10099112 . T . . END=10099139 GT:DP:GQ:MIN_DP:PL 0/0:57:99:49:0,114,1710 20 10099140 . G T, 1005.77 . AS_RAW_BaseQRankSum=|-0.2,1|NaN;AS_RAW_MQ=108000.00|84512.00|0.00;AS_RAW_MQRankSum=|-2.5,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=18,12|22,10|0,0;BaseQRankSum=-0.114;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.469;RAW_MQ=192512.00;ReadPosRankSum=0.338 GT:AD:DP:GQ:PL:SB 0/1:30,32,0:62:99:1034,0,931,1122,1028,2150:18,12,22,10 20 10099141 . G . . END=10099189 GT:DP:GQ:MIN_DP:PL 0/0:67:99:64:0,120,1800 20 10099190 . G T, 1034.77 . AS_RAW_BaseQRankSum=|-0.1,1|NaN;AS_RAW_MQ=118800.00|96551.00|0.00;AS_RAW_MQRankSum=|-1.8,1|NaN;AS_RAW_ReadPosRankSum=|-1.3,1|NaN;AS_SB_TABLE=21,12|21,11|0,0;BaseQRankSum=-0.034;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.711;RAW_MQ=215351.00;ReadPosRankSum=-1.260 GT:AD:DP:GQ:PL:SB 0/1:33,32,0:65:99:1063,0,1154,1162,1251,2413:21,12,21,11 -20 10099191 . C . . END=10099219 GT:DP:GQ:MIN_DP:PL 0/0:59:99:46:0,111,1665 +20 10099191 . C . . END=10099219 GT:DP:GQ:MIN_DP:PL 0/0:58:99:46:0,111,1665 20 10099220 . A G, 577.77 . AS_RAW_BaseQRankSum=|-1.7,1|NaN;AS_RAW_MQ=90000.00|59477.00|0.00;AS_RAW_MQRankSum=|-2.6,1|NaN;AS_RAW_ReadPosRankSum=|0.6,1|NaN;AS_SB_TABLE=15,10|11,9|0,0;BaseQRankSum=-1.664;DP=45;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.596;RAW_MQ=149477.00;ReadPosRankSum=0.629 GT:AD:DP:GQ:PL:SB 0/1:25,20,0:45:99:606,0,873,681,933,1614:15,10,11,9 20 10099221 . T . . END=10099229 GT:DP:GQ:MIN_DP:PL 0/0:44:99:42:0,102,1530 20 10099230 . T . . END=10099233 GT:DP:GQ:MIN_DP:PL 0/0:41:90:41:0,90,1350 @@ -1650,6 +1384,6 @@ 20 10099565 . C T, 1346.77 . AS_RAW_BaseQRankSum=|4.5,1|NaN;AS_RAW_MQ=111600.00|131810.00|0.00;AS_RAW_MQRankSum=|-1.3,1|NaN;AS_RAW_ReadPosRankSum=|1.2,1|NaN;AS_SB_TABLE=23,8|21,17|0,0;BaseQRankSum=4.595;DP=69;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.266;RAW_MQ=243410.00;ReadPosRankSum=1.225 GT:AD:DP:GQ:PL:SB 0/1:31,38,0:69:99:1375,0,994,1468,1108,2576:23,8,21,17 20 10099566 . T . . END=10099754 GT:DP:GQ:MIN_DP:PL 0/0:77:99:66:0,120,1800 20 10099755 . C T, 1098.77 . AS_RAW_BaseQRankSum=|1.5,1|NaN;AS_RAW_MQ=116569.00|112441.00|0.00;AS_RAW_MQRankSum=|-0.1,1|NaN;AS_RAW_ReadPosRankSum=|-0.3,1|NaN;AS_SB_TABLE=20,13|17,15|0,0;BaseQRankSum=1.550;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.022;RAW_MQ=229010.00;ReadPosRankSum=-0.230 GT:AD:DP:GQ:PL:SB 0/1:33,32,0:65:99:1127,0,1148,1226,1245,2470:20,13,17,15 -20 10099756 . C . . END=10099831 GT:DP:GQ:MIN_DP:PL 0/0:64:99:59:0,120,1800 +20 10099756 . C . . END=10099831 GT:DP:GQ:MIN_DP:PL 0/0:63:99:58:0,120,1800 20 10099832 . A G, 1073.77 . AS_RAW_BaseQRankSum=|-4.6,1|NaN;AS_RAW_MQ=133707.00|116569.00|0.00;AS_RAW_MQRankSum=|0.8,1|NaN;AS_RAW_ReadPosRankSum=|-1.1,1|NaN;AS_SB_TABLE=22,17|14,19|0,0;BaseQRankSum=-4.563;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.869;RAW_MQ=250276.00;ReadPosRankSum=-1.023 GT:AD:DP:GQ:PL:SB 0/1:39,33,0:72:99:1102,0,1430,1220,1530,2749:22,17,14,19 20 10099833 . T . . END=10100000 GT:DP:GQ:MIN_DP:PL 0/0:85:99:73:0,120,1800 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf index 23ab0e767e8..897c5701ec0 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf @@ -96,7 +96,7 @@ 20 10000211 . C T, 941.77 . BaseQRankSum=1.867;DP=53;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.057;RAW_MQ=188569.00;ReadPosRankSum=0.703 GT:AD:DP:GQ:PL:SB 0/1:26,27,0:53:99:970,0,906,1049,988,2036:15,11,11,16 20 10000212 . A . . END=10000438 GT:DP:GQ:MIN_DP:PL 0/0:79:99:55:0,120,1800 20 10000439 . T G, 2804.77 . DP=80;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=279076.00 GT:AD:DP:GQ:PL:SB 1/1:0,80,0:80:99:2833,240,0,2833,240,2833:0,0,49,31 -20 10000440 . T . . END=10000585 GT:DP:GQ:MIN_DP:PL 0/0:55:99:41:0,100,1530 +20 10000440 . T . . END=10000585 GT:DP:GQ:MIN_DP:PL 0/0:55:99:41:0,102,1530 20 10000586 . C . . END=10000586 GT:DP:GQ:MIN_DP:PL 0/0:44:93:44:0,93,1503 20 10000587 . G . . END=10000597 GT:DP:GQ:MIN_DP:PL 0/0:46:99:42:0,108,1620 20 10000598 . T A, 1941.77 . DP=49;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=149628.00 GT:AD:DP:GQ:PL:SB 1/1:0,49,0:49:99:1970,147,0,1970,147,1970:0,0,19,30 @@ -108,40 +108,28 @@ 20 10001019 . T G, 650.77 . BaseQRankSum=-2.541;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-7.498;RAW_MQ=159195.00;ReadPosRankSum=-0.925 GT:AD:DP:GQ:PL:SB 0/1:39,26,0:65:99:679,0,1426,796,1504,2300:17,22,14,12 20 10001020 . C . . END=10001297 GT:DP:GQ:MIN_DP:PL 0/0:68:99:46:0,117,1755 20 10001298 . T A, 2917.77 . DP=74;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=218493.00 GT:AD:DP:GQ:PL:SB 1/1:0,73,0:73:99:2946,220,0,2946,220,2946:0,0,41,32 -20 10001299 . C . . END=10001402 GT:DP:GQ:MIN_DP:PL 0/0:71:99:51:0,99,1485 -20 10001403 . A . . END=10001403 GT:DP:GQ:MIN_DP:PL 0/0:50:93:50:0,93,1395 -20 10001404 . A . . END=10001406 GT:DP:GQ:MIN_DP:PL 0/0:50:81:50:0,81,1215 -20 10001407 . T . . END=10001407 GT:DP:GQ:MIN_DP:PL 0/0:50:78:50:0,78,1170 -20 10001408 . C . . END=10001410 GT:DP:GQ:MIN_DP:PL 0/0:50:63:49:0,63,945 -20 10001411 . T . . END=10001411 GT:DP:GQ:MIN_DP:PL 0/0:50:54:50:0,54,810 -20 10001412 . A . . END=10001412 GT:DP:GQ:MIN_DP:PL 0/0:50:48:50:0,48,720 -20 10001413 . T . . END=10001414 GT:DP:GQ:MIN_DP:PL 0/0:51:42:51:0,42,630 -20 10001415 . T . . END=10001415 GT:DP:GQ:MIN_DP:PL 0/0:50:39:50:0,39,585 -20 10001416 . A . . END=10001420 GT:DP:GQ:MIN_DP:PL 0/0:50:33:49:0,33,495 -20 10001421 . G . . END=10001422 GT:DP:GQ:MIN_DP:PL 0/0:50:30:49:0,30,450 -20 10001423 . T . . END=10001426 GT:DP:GQ:MIN_DP:PL 0/0:50:24:49:0,24,360 +20 10001299 . C . . END=10001426 GT:DP:GQ:MIN_DP:PL 0/0:63:99:49:0,111,1800 20 10001427 . T . . END=10001427 GT:DP:GQ:MIN_DP:PL 0/0:53:5:53:0,5,1899 -20 10001428 . T . . END=10001429 GT:DP:GQ:MIN_DP:PL 0/0:54:21:53:0,21,315 +20 10001428 . T . . END=10001429 GT:DP:GQ:MIN_DP:PL 0/0:54:99:53:0,120,1800 20 10001430 . G . . END=10001431 GT:DP:GQ:MIN_DP:PL 0/0:56:0:56:0,0,1743 -20 10001432 . A . . END=10001432 GT:DP:GQ:MIN_DP:PL 0/0:56:18:56:0,18,270 +20 10001432 . A . . END=10001432 GT:DP:GQ:MIN_DP:PL 0/0:56:99:56:0,120,1800 20 10001433 . T . . END=10001433 GT:DP:GQ:MIN_DP:PL 0/0:56:0:56:0,0,1779 -20 10001434 . G . . END=10001434 GT:DP:GQ:MIN_DP:PL 0/0:56:18:56:0,18,270 +20 10001434 . G . . END=10001434 GT:DP:GQ:MIN_DP:PL 0/0:56:99:56:0,120,1800 20 10001435 . A . . END=10001435 GT:DP:GQ:MIN_DP:PL 0/0:55:0:55:0,0,1790 20 10001436 . A AAGGCT, 2301.73 . DP=55;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=92755.00 GT:AD:DP:GQ:PL:SB 1/1:0,50,0:50:99:2339,156,0,2340,157,2340:0,0,43,7 -20 10001437 . A . . END=10001437 GT:DP:GQ:MIN_DP:PL 0/0:57:0:57:0,0,0 -20 10001438 . G . . END=10001473 GT:DP:GQ:MIN_DP:PL 0/0:62:99:51:0,118,1800 +20 10001437 . A . . END=10001473 GT:DP:GQ:MIN_DP:PL 0/0:61:99:51:0,120,1800 20 10001474 . C T, 2640.77 . DP=73;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=140615.00 GT:AD:DP:GQ:PL:SB 1/1:0,73,0:73:99:2669,219,0,2669,219,2669:0,0,48,25 20 10001475 . G . . END=10001616 GT:DP:GQ:MIN_DP:PL 0/0:95:99:72:0,120,1800 20 10001617 . C A, 1731.77 . BaseQRankSum=1.261;DP=103;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.373;RAW_MQ=358589.00;ReadPosRankSum=-0.280 GT:AD:DP:GQ:PL:SB 0/1:52,51,0:103:99:1760,0,1781,1916,1935,3851:23,29,33,18 -20 10001618 . T . . END=10001627 GT:DP:GQ:MIN_DP:PL 0/0:101:99:95:0,120,1800 +20 10001618 . T . . END=10001627 GT:DP:GQ:MIN_DP:PL 0/0:100:99:94:0,120,1800 20 10001628 . G A, 3898.77 . DP=95;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=332548.00 GT:AD:DP:GQ:PL:SB 1/1:0,95,0:95:99:3927,285,0,3927,285,3927:0,0,55,40 -20 10001629 . G . . END=10001660 GT:DP:GQ:MIN_DP:PL 0/0:82:99:76:0,120,1800 +20 10001629 . G . . END=10001660 GT:DP:GQ:MIN_DP:PL 0/0:81:99:76:0,120,1800 20 10001661 . T C, 3606.77 . DP=81;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=275574.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,81,0:81:99:0|1:10001661_T_C:3635,249,0,3635,249,3635:0,0,49,32 -20 10001662 . T . . END=10001669 GT:DP:GQ:MIN_DP:PL 0/0:83:99:82:0,120,1800 +20 10001662 . T . . END=10001669 GT:DP:GQ:MIN_DP:PL 0/0:82:99:81:0,120,1800 20 10001670 . T G, 3673.77 . DP=81;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=267297.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,81,0:81:99:0|1:10001661_T_C:3702,253,0,3702,253,3702:0,0,46,35 20 10001671 . G . . END=10002057 GT:DP:GQ:MIN_DP:PL 0/0:76:99:57:0,120,1800 20 10002058 . T G, 2963.77 . BaseQRankSum=1.931;DP=75;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=3.068;RAW_MQ=250206.00;ReadPosRankSum=0.624 GT:AD:DP:GQ:PL:SB 1/1:1,74,0:75:99:2992,216,0,2994,223,3001:1,0,51,23 -20 10002059 . A . . END=10002098 GT:DP:GQ:MIN_DP:PL 0/0:78:99:65:0,120,1800 +20 10002059 . A . . END=10002098 GT:DP:GQ:MIN_DP:PL 0/0:77:99:65:0,120,1800 20 10002099 . C T, 1194.77 . BaseQRankSum=-0.282;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.850;RAW_MQ=205929.00;ReadPosRankSum=0.173 GT:AD:DP:GQ:PL:SB 0/1:27,38,0:65:99:1223,0,844,1304,958,2262:19,8,23,15 20 10002100 . T . . END=10002137 GT:DP:GQ:MIN_DP:PL 0/0:59:99:49:0,120,1800 20 10002138 . C G, 2443.77 . DP=53;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=168463.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,53,0:53:99:0|1:10002138_C_G:2472,169,0,2472,169,2472:0,0,27,26 @@ -151,16 +139,16 @@ 20 10002202 . G . . END=10002203 GT:DP:GQ:MIN_DP:PL 0/0:49:96:47:0,96,1440 20 10002204 . G . . END=10002212 GT:DP:GQ:MIN_DP:PL 0/0:46:99:45:0,99,1485 20 10002213 . T . . END=10002213 GT:DP:GQ:MIN_DP:PL 0/0:45:65:45:0,65,1504 -20 10002214 . G . . END=10002448 GT:DP:GQ:MIN_DP:PL 0/0:74:99:44:0,102,1530 -20 10002449 . T . . END=10002450 GT:DP:GQ:MIN_DP:PL 0/0:52:90:51:0,90,1350 -20 10002451 . T . . END=10002454 GT:DP:GQ:MIN_DP:PL 0/0:50:81:48:0,81,1215 -20 10002455 . A . . END=10002455 GT:DP:GQ:MIN_DP:PL 0/0:50:72:50:0,72,1080 -20 10002456 . T . . END=10002456 GT:DP:GQ:MIN_DP:PL 0/0:52:48:52:0,48,720 +20 10002214 . G . . END=10002454 GT:DP:GQ:MIN_DP:PL 0/0:74:99:44:0,102,1530 +20 10002455 . A . . END=10002455 GT:DP:GQ:MIN_DP:PL 0/0:50:93:50:0,93,1395 +20 10002456 . T . . END=10002456 GT:DP:GQ:MIN_DP:PL 0/0:52:78:52:0,78,1170 20 10002457 . A . . END=10002457 GT:DP:GQ:MIN_DP:PL 0/0:52:0:52:0,0,1572 20 10002458 . G GT,GTTT,GTTTTT, 2135.73 . DP=47;ExcessHet=3.0103;MLEAC=1,1,0,0;MLEAF=0.500,0.500,0.00,0.00;RAW_MQ=127415.00 GT:AD:DP:GQ:PL:SB 1/2:0,6,6,4,0:16:9:2172,654,493,249,0,82,353,33,9,214,876,512,168,254,730:0,0,12,4 -20 10002459 . T . . END=10002459 GT:DP:GQ:MIN_DP:PL 0/0:59:0:59:0,0,1511 -20 10002460 . T . . END=10002466 GT:DP:GQ:MIN_DP:PL 0/0:62:72:61:0,72,1080 -20 10002467 . T . . END=10002469 GT:DP:GQ:MIN_DP:PL 0/0:64:81:63:0,81,1215 +20 10002459 . T . . END=10002459 GT:DP:GQ:MIN_DP:PL 0/0:58:78:58:0,78,1170 +20 10002460 . T . . END=10002460 GT:DP:GQ:MIN_DP:PL 0/0:60:87:60:0,87,1305 +20 10002461 . T . . END=10002467 GT:DP:GQ:MIN_DP:PL 0/0:62:90:60:0,90,1350 +20 10002468 . T . . END=10002468 GT:DP:GQ:MIN_DP:PL 0/0:64:99:64:0,99,1485 +20 10002469 . T . . END=10002469 GT:DP:GQ:MIN_DP:PL 0/0:62:81:62:0,81,1215 20 10002470 . C T, 2522.77 . DP=61;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=144226.00 GT:AD:DP:GQ:PL:SB 1/1:0,61,0:61:99:2551,189,0,2551,189,2551:0,0,34,27 20 10002471 . T . . END=10002471 GT:DP:GQ:MIN_DP:PL 0/0:63:84:63:0,84,1260 20 10002472 . T . . END=10002474 GT:DP:GQ:MIN_DP:PL 0/0:63:90:63:0,90,1350 @@ -209,18 +197,15 @@ 20 10003832 . G A, 2705.77 . DP=66;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=215436.00 GT:AD:DP:GQ:PL:SB 1/1:0,66,0:66:99:2734,199,0,2734,199,2734:0,0,23,43 20 10003833 . T . . END=10004093 GT:DP:GQ:MIN_DP:PL 0/0:69:99:43:0,108,1620 20 10004094 . A C, 1825.77 . DP=53;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=147492.00 GT:AD:DP:GQ:PL:SB 1/1:0,53,0:53:99:1854,157,0,1854,157,1854:0,0,35,18 -20 10004095 . C . . END=10004146 GT:DP:GQ:MIN_DP:PL 0/0:52:99:45:0,109,1596 +20 10004095 . C . . END=10004146 GT:DP:GQ:MIN_DP:PL 0/0:51:99:45:0,109,1596 20 10004147 . A G, 1837.77 . DP=52;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=157262.00 GT:AD:DP:GQ:PL:SB 1/1:0,52,0:52:99:1866,156,0,1866,156,1866:0,0,21,31 -20 10004148 . G . . END=10004192 GT:DP:GQ:MIN_DP:PL 0/0:51:99:47:0,112,1687 +20 10004148 . G . . END=10004192 GT:DP:GQ:MIN_DP:PL 0/0:49:99:45:0,106,1637 20 10004193 . G T, 918.77 . BaseQRankSum=-0.504;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.421;RAW_MQ=182869.00;ReadPosRankSum=1.512 GT:AD:DP:GQ:PL:SB 0/1:23,29,0:52:99:947,0,775,1016,860,1876:12,11,12,17 -20 10004194 . C . . END=10004214 GT:DP:GQ:MIN_DP:PL 0/0:53:99:49:0,102,1530 -20 10004215 . C . . END=10004215 GT:DP:GQ:MIN_DP:PL 0/0:53:96:53:0,96,1440 -20 10004216 . T . . END=10004218 GT:DP:GQ:MIN_DP:PL 0/0:53:84:53:0,84,1260 -20 10004219 . C . . END=10004221 GT:DP:GQ:MIN_DP:PL 0/0:52:72:51:0,72,1080 +20 10004194 . C . . END=10004221 GT:DP:GQ:MIN_DP:PL 0/0:50:99:46:0,105,1575 20 10004222 . C CA, 12.96 . BaseQRankSum=0.335;DP=54;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.042;RAW_MQ=194729.00;ReadPosRankSum=1.271 GT:AD:DP:GQ:PL:SB 0/1:31,8,0:39:50:50,0,923,153,952,1105:18,13,4,4 20 10004223 . A AG, 47.73 . BaseQRankSum=-0.480;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.886;RAW_MQ=210769.00;ReadPosRankSum=0.339 GT:AD:DP:GQ:PL:SB 0/1:36,11,0:47:85:85,0,982,193,1017,1210:16,20,5,6 -20 10004224 . A . . END=10004224 GT:DP:GQ:MIN_DP:PL 0/0:70:0:70:0,0,450 -20 10004225 . A . . END=10004240 GT:DP:GQ:MIN_DP:PL 0/0:70:99:65:0,114,1710 +20 10004224 . A . . END=10004224 GT:DP:GQ:MIN_DP:PL 0/0:66:0:66:0,0,1403 +20 10004225 . A . . END=10004240 GT:DP:GQ:MIN_DP:PL 0/0:70:99:65:0,117,1755 20 10004241 . G . . END=10004241 GT:DP:GQ:MIN_DP:PL 0/0:66:0:66:0,0,1965 20 10004242 . A . . END=10004350 GT:DP:GQ:MIN_DP:PL 0/0:73:99:58:0,120,1800 20 10004351 . C G, 2755.77 . DP=70;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=243987.00 GT:AD:DP:GQ:PL:SB 1/1:0,70,0:70:99:2784,211,0,2784,211,2784:0,0,38,32 @@ -230,10 +215,9 @@ 20 10004610 . A C, 3625.77 . DP=89;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=306605.00 GT:AD:DP:GQ:PL:SB 1/1:0,89,0:89:99:3654,267,0,3654,267,3654:0,0,46,43 20 10004611 . C . . END=10004724 GT:DP:GQ:MIN_DP:PL 0/0:75:99:64:0,120,1800 20 10004725 . A G, 951.77 . BaseQRankSum=-2.154;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.008;RAW_MQ=198562.00;ReadPosRankSum=2.087 GT:AD:DP:GQ:PL:SB 0/1:35,30,0:65:99:980,0,1168,1085,1258,2343:10,25,17,13 -20 10004726 . T . . END=10004768 GT:DP:GQ:MIN_DP:PL 0/0:67:99:63:0,105,1575 +20 10004726 . T . . END=10004768 GT:DP:GQ:MIN_DP:PL 0/0:66:99:62:0,120,1800 20 10004769 . TAAAACTATGC T, 981.73 . BaseQRankSum=1.603;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-6.625;RAW_MQ=216626.00;ReadPosRankSum=1.879 GT:AD:DP:GQ:PL:SB 0/1:37,27,0:64:99:1019,0,1471,1130,1554,2684:14,23,7,20 -20 10004780 . A . . END=10004780 GT:DP:GQ:MIN_DP:PL 0/0:70:0:70:0,0,795 -20 10004781 . A . . END=10004873 GT:DP:GQ:MIN_DP:PL 0/0:77:99:69:0,120,1800 +20 10004780 . A . . END=10004873 GT:DP:GQ:MIN_DP:PL 0/0:77:99:69:0,120,1800 20 10004874 . A C, 3602.77 . DP=87;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=306223.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,87,0:87:99:0|1:10004874_A_C:3631,261,0,3631,261,3631:0,0,54,33 20 10004875 . T . . END=10004886 GT:DP:GQ:MIN_DP:PL 0/0:86:99:85:0,120,1800 20 10004887 . A G, 1323.77 . BaseQRankSum=0.356;DP=85;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.067;RAW_MQ=300482.00;ReadPosRankSum=-1.114 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:45,40,0:85:99:0|1:10004874_A_C:1352,0,1542,1487,1662,3149:24,21,24,16 @@ -241,7 +225,7 @@ 20 10005010 . C T, 2934.77 . DP=72;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=256441.00 GT:AD:DP:GQ:PL:SB 1/1:0,72,0:72:99:2963,217,0,2963,217,2963:0,0,44,28 20 10005011 . G . . END=10005426 GT:DP:GQ:MIN_DP:PL 0/0:72:99:51:0,120,1800 20 10005427 . C T, 2214.77 . DP=55;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=195241.00 GT:AD:DP:GQ:PL:SB 1/1:0,55,0:55:99:2243,165,0,2243,165,2243:0,0,27,28 -20 10005428 . A . . END=10005498 GT:DP:GQ:MIN_DP:PL 0/0:71:99:58:0,120,1800 +20 10005428 . A . . END=10005498 GT:DP:GQ:MIN_DP:PL 0/0:71:99:57:0,120,1800 20 10005499 . A G, 3053.77 . DP=76;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=273600.00 GT:AD:DP:GQ:PL:SB 1/1:0,76,0:76:99:3082,229,0,3082,229,3082:0,0,45,31 20 10005500 . T . . END=10005586 GT:DP:GQ:MIN_DP:PL 0/0:71:99:66:0,120,1800 20 10005587 . A G, 1229.77 . BaseQRankSum=-0.834;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.972;RAW_MQ=256969.00;ReadPosRankSum=0.248 GT:AD:DP:GQ:PL:SB 0/1:36,36,0:72:99:1258,0,1236,1366,1345,2710:19,17,16,20 @@ -253,17 +237,9 @@ 20 10006404 . A C, 2928.77 . DP=77;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=269451.00 GT:AD:DP:GQ:PL:SB 1/1:0,76,0:76:99:2957,228,0,2957,228,2957:0,0,27,49 20 10006405 . C . . END=10006681 GT:DP:GQ:MIN_DP:PL 0/0:78:99:65:0,120,1800 20 10006682 . T A, 2874.77 . DP=73;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=257810.00 GT:AD:DP:GQ:PL:SB 1/1:0,73,0:73:99:2903,219,0,2903,219,2903:0,0,44,29 -20 10006683 . A . . END=10006807 GT:DP:GQ:MIN_DP:PL 0/0:65:99:61:0,99,1485 -20 10006808 . C . . END=10006808 GT:DP:GQ:MIN_DP:PL 0/0:75:78:75:0,78,1170 -20 10006809 . C . . END=10006813 GT:DP:GQ:MIN_DP:PL 0/0:76:60:75:0,60,900 -20 10006814 . T . . END=10006814 GT:DP:GQ:MIN_DP:PL 0/0:79:57:79:0,57,855 -20 10006815 . C . . END=10006815 GT:DP:GQ:MIN_DP:PL 0/0:80:51:80:0,51,765 -20 10006816 . T . . END=10006816 GT:DP:GQ:MIN_DP:PL 0/0:80:45:80:0,45,675 -20 10006817 . A . . END=10006817 GT:DP:GQ:MIN_DP:PL 0/0:80:33:80:0,33,495 -20 10006818 . A . . END=10006818 GT:DP:GQ:MIN_DP:PL 0/0:77:30:77:0,30,450 +20 10006683 . A . . END=10006818 GT:DP:GQ:MIN_DP:PL 0/0:65:99:61:0,120,1800 20 10006819 . AAAAC A, 2531.73 . DP=76;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=284000.00 GT:AD:DP:GQ:PL:SB 1/1:0,58,0:58:99:2569,176,0,2569,176,2569:0,0,30,28 -20 10006824 . A . . END=10006824 GT:DP:GQ:MIN_DP:PL 0/0:75:0:75:0,0,0 -20 10006825 . A . . END=10007149 GT:DP:GQ:MIN_DP:PL 0/0:77:99:59:0,120,1800 +20 10006824 . A . . END=10007149 GT:DP:GQ:MIN_DP:PL 0/0:77:99:59:0,120,1800 20 10007150 . G C, 669.77 . BaseQRankSum=-4.476;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=226800.00;ReadPosRankSum=-0.077 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:38,25,0:63:99:0|1:10007150_G_C:698,0,1479,813,1554,2366:16,22,14,11 20 10007151 . G . . END=10007174 GT:DP:GQ:MIN_DP:PL 0/0:57:99:56:0,120,1800 20 10007175 . C T, 1350.77 . BaseQRankSum=2.249;DP=61;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.319;RAW_MQ=216841.00;ReadPosRankSum=-1.213 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:23,38,0:61:99:1|0:10007150_G_C:1379,0,780,1448,894,2343:9,14,18,20 @@ -273,72 +249,34 @@ 20 10007531 . A G, 2920.77 . DP=72;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=256969.00 GT:AD:DP:GQ:PL:SB 1/1:0,72,0:72:99:2949,217,0,2949,217,2949:0,0,48,24 20 10007532 . G . . END=10007979 GT:DP:GQ:MIN_DP:PL 0/0:80:99:65:0,120,1800 20 10007980 . A C, 3524.77 . DP=90;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=331800.00 GT:AD:DP:GQ:PL:SB 1/1:0,90,0:90:99:3553,270,0,3553,270,3553:0,0,39,51 -20 10007981 . A . . END=10008013 GT:DP:GQ:MIN_DP:PL 0/0:85:99:81:0,99,1485 -20 10008014 . C . . END=10008014 GT:DP:GQ:MIN_DP:PL 0/0:85:90:85:0,90,1350 -20 10008015 . C . . END=10008015 GT:DP:GQ:MIN_DP:PL 0/0:88:87:88:0,87,1305 -20 10008016 . A . . END=10008020 GT:DP:GQ:MIN_DP:PL 0/0:90:72:89:0,72,1080 -20 10008021 . G . . END=10008021 GT:DP:GQ:MIN_DP:PL 0/0:86:54:86:0,54,810 -20 10008022 . A . . END=10008023 GT:DP:GQ:MIN_DP:PL 0/0:85:33:85:0,33,495 -20 10008024 . A . . END=10008028 GT:DP:GQ:MIN_DP:PL 0/0:87:9:86:0,9,135 +20 10007981 . A . . END=10008028 GT:DP:GQ:MIN_DP:PL 0/0:86:99:80:0,120,1800 20 10008029 . T TA, 1986.73 . BaseQRankSum=0.409;DP=88;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=0.576;RAW_MQ=327251.00;ReadPosRankSum=-1.326 GT:AD:DP:GQ:PL:SB 1/1:3,72,0:75:99:2024,145,0,2033,222,2110:1,2,27,45 -20 10008030 . A . . END=10008030 GT:DP:GQ:MIN_DP:PL 0/0:91:0:91:0,0,0 -20 10008031 . A . . END=10008127 GT:DP:GQ:MIN_DP:PL 0/0:82:99:77:0,105,1575 -20 10008128 . T . . END=10008129 GT:DP:GQ:MIN_DP:PL 0/0:79:93:78:0,93,1395 -20 10008130 . T . . END=10008131 GT:DP:GQ:MIN_DP:PL 0/0:78:78:77:0,78,1170 -20 10008132 . C . . END=10008133 GT:DP:GQ:MIN_DP:PL 0/0:77:60:76:0,60,900 -20 10008134 . A . . END=10008134 GT:DP:GQ:MIN_DP:PL 0/0:79:54:79:0,54,810 -20 10008135 . G . . END=10008135 GT:DP:GQ:MIN_DP:PL 0/0:79:48:79:0,48,720 -20 10008136 . A . . END=10008136 GT:DP:GQ:MIN_DP:PL 0/0:78:24:78:0,24,360 -20 10008137 . T . . END=10008139 GT:DP:GQ:MIN_DP:PL 0/0:77:21:76:0,21,315 -20 10008140 . T . . END=10008140 GT:DP:GQ:MIN_DP:PL 0/0:78:18:78:0,18,270 -20 10008141 . C . . END=10008141 GT:DP:GQ:MIN_DP:PL 0/0:79:9:79:0,9,135 -20 10008142 . T . . END=10008142 GT:DP:GQ:MIN_DP:PL 0/0:77:6:77:0,6,90 -20 10008143 . C . . END=10008145 GT:DP:GQ:MIN_DP:PL 0/0:77:3:76:0,3,45 +20 10008030 . A . . END=10008145 GT:DP:GQ:MIN_DP:PL 0/0:82:99:76:0,120,1800 20 10008146 . TA T, 2141.73 . DP=73;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=268000.00 GT:AD:DP:GQ:PL:SB 1/1:0,70,0:70:99:2179,211,0,2179,211,2179:0,0,38,32 -20 10008148 . A . . END=10008148 GT:DP:GQ:MIN_DP:PL 0/0:74:0:74:0,0,0 -20 10008149 . A . . END=10008220 GT:DP:GQ:MIN_DP:PL 0/0:81:99:74:0,120,1800 +20 10008148 . A . . END=10008220 GT:DP:GQ:MIN_DP:PL 0/0:80:99:72:0,120,1800 20 10008221 . T C, 3224.77 . DP=80;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=289669.00 GT:AD:DP:GQ:PL:SB 1/1:0,80,0:80:99:3253,240,0,3253,240,3253:0,0,43,37 20 10008222 . T . . END=10008457 GT:DP:GQ:MIN_DP:PL 0/0:64:99:45:0,108,1620 20 10008458 . T G, 2654.77 . DP=69;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=191842.00 GT:AD:DP:GQ:PL:SB 1/1:0,69,0:69:99:2683,207,0,2683,207,2683:0,0,30,39 20 10008459 . A . . END=10008732 GT:DP:GQ:MIN_DP:PL 0/0:70:99:40:0,105,1575 -20 10008733 . T . . END=10008737 GT:DP:GQ:MIN_DP:PL 0/0:47:90:47:0,90,1350 -20 10008738 . C . . END=10008740 GT:DP:GQ:MIN_DP:PL 0/0:50:81:49:0,81,1215 -20 10008741 . C . . END=10008741 GT:DP:GQ:MIN_DP:PL 0/0:52:78:52:0,78,1170 +20 10008733 . T . . END=10008733 GT:DP:GQ:MIN_DP:PL 0/0:47:94:47:0,94,1689 +20 10008734 . G . . END=10008741 GT:DP:GQ:MIN_DP:PL 0/0:48:99:47:0,120,1800 20 10008742 . G T, 715.77 . BaseQRankSum=3.893;DP=49;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.502;RAW_MQ=67874.00;ReadPosRankSum=0.190 GT:AD:DP:GQ:PL:SB 0/1:23,26,0:49:99:744,0,580,813,658,1471:10,13,11,15 -20 10008743 . T . . END=10008744 GT:DP:GQ:MIN_DP:PL 0/0:52:72:52:0,72,1080 -20 10008745 . T . . END=10008746 GT:DP:GQ:MIN_DP:PL 0/0:52:63:52:0,63,945 -20 10008747 . T . . END=10008749 GT:DP:GQ:MIN_DP:PL 0/0:49:57:48:0,57,855 -20 10008750 . T . . END=10008750 GT:DP:GQ:MIN_DP:PL 0/0:47:51:47:0,51,765 -20 10008751 . A . . END=10008751 GT:DP:GQ:MIN_DP:PL 0/0:49:30:49:0,30,450 -20 10008752 . A . . END=10008754 GT:DP:GQ:MIN_DP:PL 0/0:51:33:51:0,33,495 -20 10008755 . A . . END=10008755 GT:DP:GQ:MIN_DP:PL 0/0:51:36:51:0,36,540 -20 10008756 . T . . END=10008756 GT:DP:GQ:MIN_DP:PL 0/0:45:33:45:0,33,495 -20 10008757 . A . . END=10008757 GT:DP:GQ:MIN_DP:PL 0/0:48:24:48:0,24,360 +20 10008743 . T . . END=10008757 GT:DP:GQ:MIN_DP:PL 0/0:46:99:42:0,99,1485 20 10008758 . C CA, 684.14 . BaseQRankSum=0.130;DP=44;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=-1.168;RAW_MQ=54656.00;ReadPosRankSum=-0.052 GT:AD:DP:GQ:PL:SB 1/1:4,31,0:35:10:721,10,0,733,102,825:3,1,16,15 -20 10008759 . A . . END=10008759 GT:DP:GQ:MIN_DP:PL 0/0:55:0:55:0,0,0 -20 10008760 . A . . END=10008772 GT:DP:GQ:MIN_DP:PL 0/0:55:99:53:0,120,1800 +20 10008759 . A . . END=10008772 GT:DP:GQ:MIN_DP:PL 0/0:55:99:53:0,120,1800 20 10008773 . T . . END=10008773 GT:DP:GQ:MIN_DP:PL 0/0:54:0:54:0,0,1660 20 10008774 . T . . END=10008774 GT:DP:GQ:MIN_DP:PL 0/0:55:99:55:0,117,1755 20 10008775 . A . . END=10008775 GT:DP:GQ:MIN_DP:PL 0/0:55:60:55:0,60,1923 -20 10008776 . G . . END=10008910 GT:DP:GQ:MIN_DP:PL 0/0:55:99:45:0,100,1530 -20 10008911 . G . . END=10008911 GT:DP:GQ:MIN_DP:PL 0/0:45:93:45:0,93,1395 -20 10008912 . A . . END=10008916 GT:DP:GQ:MIN_DP:PL 0/0:46:84:45:0,84,1260 -20 10008917 . G . . END=10008917 GT:DP:GQ:MIN_DP:PL 0/0:46:78:46:0,78,1170 -20 10008918 . T . . END=10008920 GT:DP:GQ:MIN_DP:PL 0/0:50:66:48:0,66,990 +20 10008776 . G . . END=10008920 GT:DP:GQ:MIN_DP:PL 0/0:54:99:45:0,99,1480 20 10008921 . C CA, 253.73 . BaseQRankSum=0.610;DP=49;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.906;RAW_MQ=155512.00;ReadPosRankSum=0.173 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:18,16,0:34:99:0|1:10008921_C_CA:291,0,366,345,415,761:10,8,8,8 -20 10008922 . A . . END=10008922 GT:DP:GQ:MIN_DP:PL 0/0:51:0:51:0,0,714 -20 10008923 . A . . END=10008934 GT:DP:GQ:MIN_DP:PL 0/0:58:99:55:0,117,1755 -20 10008935 . T . . END=10008936 GT:DP:GQ:MIN_DP:PL 0/0:54:73:52:0,73,1586 -20 10008937 . A . . END=10008938 GT:DP:GQ:MIN_DP:PL 0/0:55:99:54:0,111,1665 -20 10008939 . T . . END=10008940 GT:DP:GQ:MIN_DP:PL 0/0:52:93:51:0,93,1395 -20 10008941 . A . . END=10008942 GT:DP:GQ:MIN_DP:PL 0/0:50:84:49:0,84,1260 -20 10008943 . A . . END=10008946 GT:DP:GQ:MIN_DP:PL 0/0:49:72:49:0,72,1080 -20 10008947 . T . . END=10008947 GT:DP:GQ:MIN_DP:PL 0/0:48:66:48:0,66,990 +20 10008922 . A . . END=10008942 GT:DP:GQ:MIN_DP:PL 0/0:53:99:47:0,114,1710 +20 10008943 . A . . END=10008944 GT:DP:GQ:MIN_DP:PL 0/0:47:78:47:0,78,1170 +20 10008945 . A . . END=10008947 GT:DP:GQ:MIN_DP:PL 0/0:47:81:46:0,81,1215 20 10008948 . TA T, 2057.73 . BaseQRankSum=0.994;DP=52;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=2.047;RAW_MQ=138622.00;ReadPosRankSum=0.884 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:1,50,0:51:99:0|1:10008921_C_CA:2095,107,0,2098,159,2150:1,0,35,15 -20 10008950 . A . . END=10008951 GT:DP:GQ:MIN_DP:PL 0/0:48:0:48:0,0,0 +20 10008950 . A . . END=10008950 GT:DP:GQ:MIN_DP:PL 0/0:52:99:52:0,99,1485 +20 10008951 . A . . END=10008951 GT:DP:GQ:MIN_DP:PL 0/0:51:93:51:0,93,1395 20 10008952 . CACACACACACACA C,CCA,CCACACACACA,CCACACACACACA, 1666.73 . BaseQRankSum=0.941;DP=59;ExcessHet=3.0103;MLEAC=0,1,0,1,0;MLEAF=0.00,0.500,0.00,0.500,0.00;MQRankSum=1.844;RAW_MQ=154068.00;ReadPosRankSum=0.716 GT:AD:DP:GQ:PL:SB 2/4:1,3,14,5,11,0:34:99:1704,876,1258,525,811,845,726,514,173,703,582,342,0,443,530,1135,1092,744,779,607,1321:1,0,25,8 -20 10008966 . C . . END=10008966 GT:DP:GQ:MIN_DP:PL 0/0:56:95:56:0,95,1995 -20 10008967 . A . . END=10008986 GT:DP:GQ:MIN_DP:PL 0/0:58:99:56:0,120,1800 +20 10008966 . C . . END=10008986 GT:DP:GQ:MIN_DP:PL 0/0:58:99:56:0,120,1800 20 10008987 . A . . END=10008989 GT:DP:GQ:MIN_DP:PL 0/0:59:94:59:0,94,2181 20 10008990 . C . . END=10009226 GT:DP:GQ:MIN_DP:PL 0/0:61:99:38:0,102,1530 20 10009227 . A G, 1369.77 . BaseQRankSum=-2.220;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.428;RAW_MQ=202588.00;ReadPosRankSum=-1.159 GT:AD:DP:GQ:PL:SB 0/1:23,39,0:62:99:1398,0,740,1468,857,2325:16,7,19,20 @@ -352,42 +290,30 @@ 20 10009719 . A G, 1895.77 . DP=59;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=207410.00 GT:AD:DP:GQ:PL:SB 1/1:0,59,0:59:99:1924,175,0,1924,175,1924:0,0,26,33 20 10009720 . T . . END=10009794 GT:DP:GQ:MIN_DP:PL 0/0:54:99:47:0,120,1800 20 10009795 . A G, 1880.77 . DP=47;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=166969.00 GT:AD:DP:GQ:PL:SB 1/1:0,47,0:47:99:1909,141,0,1909,141,1909:0,0,16,31 -20 10009796 . C . . END=10009828 GT:DP:GQ:MIN_DP:PL 0/0:48:99:44:0,120,1800 -20 10009829 . A . . END=10009829 GT:DP:GQ:MIN_DP:PL 0/0:54:69:54:0,69,1035 -20 10009830 . G . . END=10009830 GT:DP:GQ:MIN_DP:PL 0/0:54:72:54:0,72,1080 -20 10009831 . A . . END=10009832 GT:DP:GQ:MIN_DP:PL 0/0:54:63:53:0,63,945 -20 10009833 . A . . END=10009833 GT:DP:GQ:MIN_DP:PL 0/0:53:27:53:0,27,405 -20 10009834 . G . . END=10009834 GT:DP:GQ:MIN_DP:PL 0/0:53:30:53:0,30,450 -20 10009835 . A . . END=10009838 GT:DP:GQ:MIN_DP:PL 0/0:55:33:54:0,33,495 -20 10009839 . A . . END=10009839 GT:DP:GQ:MIN_DP:PL 0/0:54:30:54:0,30,450 -20 10009840 . A . . END=10009840 GT:DP:GQ:MIN_DP:PL 0/0:54:33:54:0,33,495 -20 10009841 . A . . END=10009841 GT:DP:GQ:MIN_DP:PL 0/0:55:27:55:0,27,405 +20 10009796 . C . . END=10009832 GT:DP:GQ:MIN_DP:PL 0/0:49:99:44:0,99,1485 +20 10009833 . A . . END=10009840 GT:DP:GQ:MIN_DP:PL 0/0:53:66:51:0,66,990 +20 10009841 . A . . END=10009841 GT:DP:GQ:MIN_DP:PL 0/0:51:39:51:0,39,585 20 10009842 . G GAA, 532.73 . BaseQRankSum=0.872;DP=51;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.603;RAW_MQ=150092.00;ReadPosRankSum=1.720 GT:AD:DP:GQ:PL:SB 0/1:19,15,0:34:99:570,0,690,629,738,1367:9,10,8,7 -20 10009843 . A . . END=10009843 GT:DP:GQ:MIN_DP:PL 0/0:56:27:56:0,27,405 +20 10009843 . A . . END=10009843 GT:DP:GQ:MIN_DP:PL 0/0:51:36:51:0,36,540 20 10009844 . G A, 661.77 . BaseQRankSum=1.048;DP=51;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.975;RAW_MQ=147168.00;ReadPosRankSum=-1.555 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:16,19,0:35:99:0|1:10009844_G_A:690,0,586,739,644,1382:8,8,9,10 -20 10009845 . A . . END=10009847 GT:DP:GQ:MIN_DP:PL 0/0:55:30:55:0,30,450 -20 10009848 . G . . END=10009848 GT:DP:GQ:MIN_DP:PL 0/0:58:39:58:0,39,585 -20 10009849 . A . . END=10009850 GT:DP:GQ:MIN_DP:PL 0/0:59:45:58:0,45,675 -20 10009851 . A . . END=10009851 GT:DP:GQ:MIN_DP:PL 0/0:60:51:60:0,51,765 -20 10009852 . G . . END=10009852 GT:DP:GQ:MIN_DP:PL 0/0:60:54:60:0,54,810 -20 10009853 . A . . END=10009853 GT:DP:GQ:MIN_DP:PL 0/0:61:57:61:0,57,855 -20 10009854 . G . . END=10009860 GT:DP:GQ:MIN_DP:PL 0/0:61:60:60:0,60,900 -20 10009861 . A . . END=10009867 GT:DP:GQ:MIN_DP:PL 0/0:58:72:56:0,72,1080 -20 10009868 . G . . END=10009870 GT:DP:GQ:MIN_DP:PL 0/0:57:81:56:0,81,1215 +20 10009845 . A . . END=10009847 GT:DP:GQ:MIN_DP:PL 0/0:51:42:51:0,42,630 +20 10009848 . G . . END=10009848 GT:DP:GQ:MIN_DP:PL 0/0:54:51:54:0,51,765 +20 10009849 . A . . END=10009850 GT:DP:GQ:MIN_DP:PL 0/0:55:57:54:0,57,855 +20 10009851 . A . . END=10009853 GT:DP:GQ:MIN_DP:PL 0/0:56:63:56:0,63,945 +20 10009854 . G . . END=10009860 GT:DP:GQ:MIN_DP:PL 0/0:57:72:56:0,72,1080 +20 10009861 . A . . END=10009864 GT:DP:GQ:MIN_DP:PL 0/0:58:84:56:0,84,1260 +20 10009865 . A . . END=10009869 GT:DP:GQ:MIN_DP:PL 0/0:57:90:56:0,90,1350 +20 10009870 . G . . END=10009870 GT:DP:GQ:MIN_DP:PL 0/0:57:99:57:0,99,1485 20 10009871 . A G, 658.77 . BaseQRankSum=-0.803;DP=60;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.495;RAW_MQ=154737.00;ReadPosRankSum=1.539 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:17,19,0:36:99:0|1:10009844_G_A:687,0,594,739,652,1391:10,7,9,10 -20 10009872 . G . . END=10009873 GT:DP:GQ:MIN_DP:PL 0/0:57:96:55:0,96,1440 -20 10009874 . G . . END=10009874 GT:DP:GQ:MIN_DP:PL 0/0:58:99:58:0,102,1530 +20 10009872 . G . . END=10009874 GT:DP:GQ:MIN_DP:PL 0/0:57:99:55:0,108,1620 20 10009875 . A G,AGGGAGG, 2369.73 . BaseQRankSum=0.378;DP=57;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;MQRankSum=1.361;RAW_MQ=143937.00;ReadPosRankSum=1.040 GT:AD:DP:GQ:PL:SB 1/2:2,15,13,0:30:99:2407,645,533,697,0,574,1881,655,700,1805:2,0,12,16 -20 10009876 . G . . END=10009876 GT:DP:GQ:MIN_DP:PL 0/0:57:99:57:0,108,2100 -20 10009877 . A . . END=10009877 GT:DP:GQ:MIN_DP:PL 0/0:55:85:55:0,85,1858 -20 10009878 . G . . END=10009878 GT:DP:GQ:MIN_DP:PL 0/0:55:99:55:0,108,1620 +20 10009876 . G . . END=10009878 GT:DP:GQ:MIN_DP:PL 0/0:52:99:51:0,114,1710 20 10009879 . A G, 2244.77 . BaseQRankSum=1.534;DP=49;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=1.570;RAW_MQ=120661.00;ReadPosRankSum=1.113 GT:AD:DP:GQ:PL:SB 1/1:2,47,0:49:99:2273,150,0,2276,154,2279:2,0,15,32 -20 10009880 . G . . END=10009880 GT:DP:GQ:MIN_DP:PL 0/0:52:80:52:0,80,1858 -20 10009881 . A . . END=10009882 GT:DP:GQ:MIN_DP:PL 0/0:51:99:50:0,108,1755 +20 10009880 . G . . END=10009882 GT:DP:GQ:MIN_DP:PL 0/0:49:99:48:0,120,1800 20 10009883 . A G, 2151.77 . DP=49;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=129338.00 GT:AD:DP:GQ:PL:SB 1/1:0,47,0:47:99:2180,147,0,2180,147,2181:0,0,15,32 20 10009884 . G . . END=10009884 GT:DP:GQ:MIN_DP:PL 0/0:53:99:53:0,120,1800 -20 10009885 . A . . END=10009885 GT:DP:GQ:MIN_DP:PL 0/0:52:58:52:0,58,1739 -20 10009886 . A . . END=10009886 GT:DP:GQ:MIN_DP:PL 0/0:53:0:53:0,0,1490 +20 10009885 . A . . END=10009885 GT:DP:GQ:MIN_DP:PL 0/0:52:96:52:0,96,1815 +20 10009886 . A . . END=10009886 GT:DP:GQ:MIN_DP:PL 0/0:53:0:53:0,0,1567 20 10009887 . G . . END=10009887 GT:DP:GQ:MIN_DP:PL 0/0:50:99:50:0,109,1906 20 10009888 . A . . END=10009888 GT:DP:GQ:MIN_DP:PL 0/0:51:0:51:0,0,1610 20 10009889 . A . . END=10009891 GT:DP:GQ:MIN_DP:PL 0/0:49:99:49:0,106,1800 @@ -396,20 +322,9 @@ 20 10009894 . G . . END=10009894 GT:DP:GQ:MIN_DP:PL 0/0:53:48:53:0,48,1842 20 10009895 . G . . END=10010392 GT:DP:GQ:MIN_DP:PL 0/0:70:99:45:0,111,1665 20 10010393 . T G, 1464.77 . BaseQRankSum=-3.351;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.284;RAW_MQ=278882.00;ReadPosRankSum=-1.738 GT:AD:DP:GQ:PL:SB 0/1:36,43,0:79:99:1493,0,1230,1601,1359,2961:24,12,19,24 -20 10010394 . T . . END=10010518 GT:DP:GQ:MIN_DP:PL 0/0:82:99:67:0,102,1530 -20 10010519 . T . . END=10010522 GT:DP:GQ:MIN_DP:PL 0/0:90:81:89:0,81,1215 -20 10010523 . G . . END=10010526 GT:DP:GQ:MIN_DP:PL 0/0:92:63:90:0,63,945 -20 10010527 . A . . END=10010527 GT:DP:GQ:MIN_DP:PL 0/0:88:54:88:0,54,810 -20 10010528 . T . . END=10010528 GT:DP:GQ:MIN_DP:PL 0/0:88:51:88:0,51,765 -20 10010529 . T . . END=10010529 GT:DP:GQ:MIN_DP:PL 0/0:88:48:88:0,48,720 -20 10010530 . T . . END=10010531 GT:DP:GQ:MIN_DP:PL 0/0:87:45:86:0,45,675 -20 10010532 . A . . END=10010532 GT:DP:GQ:MIN_DP:PL 0/0:84:39:84:0,39,585 -20 10010533 . G . . END=10010533 GT:DP:GQ:MIN_DP:PL 0/0:83:33:83:0,33,495 -20 10010534 . A . . END=10010534 GT:DP:GQ:MIN_DP:PL 0/0:84:24:84:0,24,360 -20 10010535 . A . . END=10010535 GT:DP:GQ:MIN_DP:PL 0/0:85:12:85:0,12,180 +20 10010394 . T . . END=10010535 GT:DP:GQ:MIN_DP:PL 0/0:83:99:67:0,120,1800 20 10010536 . G GA, 2462.73 . DP=85;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=322900.00 GT:AD:DP:GQ:PL:SB 1/1:0,79,0:79:99:2500,243,0,2500,244,2500:0,0,36,43 -20 10010537 . A . . END=10010537 GT:DP:GQ:MIN_DP:PL 0/0:88:0:88:0,0,0 -20 10010538 . A . . END=10010765 GT:DP:GQ:MIN_DP:PL 0/0:79:99:68:0,120,1800 +20 10010537 . A . . END=10010765 GT:DP:GQ:MIN_DP:PL 0/0:79:99:68:0,120,1800 20 10010766 . T G, 2411.77 . DP=67;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=241200.00 GT:AD:DP:GQ:PL:SB 1/1:0,66,0:66:99:2440,199,0,2440,199,2440:0,0,35,31 20 10010767 . G . . END=10010831 GT:DP:GQ:MIN_DP:PL 0/0:74:99:61:0,120,1800 20 10010832 . T C, 2951.77 . DP=75;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=265538.00 GT:AD:DP:GQ:PL:SB 1/1:0,75,0:75:99:2980,226,0,2980,226,2980:0,0,31,44 @@ -423,45 +338,25 @@ 20 10011666 . C T, 2961.77 . DP=73;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=254523.00 GT:AD:DP:GQ:PL:SB 1/1:0,73,0:73:99:2990,220,0,2990,220,2990:0,0,43,30 20 10011667 . A . . END=10011938 GT:DP:GQ:MIN_DP:PL 0/0:87:99:64:0,111,1665 20 10011939 . C T, 2469.77 . DP=61;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=193043.00 GT:AD:DP:GQ:PL:SB 1/1:0,61,0:61:99:2498,184,0,2498,184,2498:0,0,23,38 -20 10011940 . G . . END=10011944 GT:DP:GQ:MIN_DP:PL 0/0:62:99:54:0,114,1710 -20 10011945 . G . . END=10011945 GT:DP:GQ:MIN_DP:PL 0/0:50:84:50:0,84,1730 -20 10011946 . T . . END=10011992 GT:DP:GQ:MIN_DP:PL 0/0:53:99:44:0,102,1530 -20 10011993 . C . . END=10011996 GT:DP:GQ:MIN_DP:PL 0/0:59:90:57:0,90,1350 -20 10011997 . A . . END=10011998 GT:DP:GQ:MIN_DP:PL 0/0:59:75:59:0,75,1125 -20 10011999 . T . . END=10012000 GT:DP:GQ:MIN_DP:PL 0/0:60:63:59:0,63,945 -20 10012001 . A . . END=10012001 GT:DP:GQ:MIN_DP:PL 0/0:60:57:60:0,57,855 -20 10012002 . C . . END=10012002 GT:DP:GQ:MIN_DP:PL 0/0:61:51:61:0,51,765 -20 10012003 . T . . END=10012005 GT:DP:GQ:MIN_DP:PL 0/0:61:48:61:0,48,720 -20 10012006 . T . . END=10012006 GT:DP:GQ:MIN_DP:PL 0/0:63:39:63:0,39,585 -20 10012007 . A . . END=10012007 GT:DP:GQ:MIN_DP:PL 0/0:64:36:64:0,36,540 -20 10012008 . G . . END=10012010 GT:DP:GQ:MIN_DP:PL 0/0:64:33:63:0,33,495 -20 10012011 . T . . END=10012011 GT:DP:GQ:MIN_DP:PL 0/0:65:24:65:0,24,360 -20 10012012 . C . . END=10012012 GT:DP:GQ:MIN_DP:PL 0/0:65:21:65:0,21,315 -20 10012013 . C . . END=10012013 GT:DP:GQ:MIN_DP:PL 0/0:66:18:66:0,18,270 -20 10012014 . A . . END=10012015 GT:DP:GQ:MIN_DP:PL 0/0:66:9:66:0,9,135 -20 10012016 . T . . END=10012016 GT:DP:GQ:MIN_DP:PL 0/0:68:3:68:0,3,45 -20 10012017 . A . . END=10012020 GT:DP:GQ:MIN_DP:PL 0/0:68:0:68:0,0,0 +20 10011940 . G . . END=10012020 GT:DP:GQ:MIN_DP:PL 0/0:56:99:42:0,101,1575 20 10012021 . CA C, 1975.73 . DP=70;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=228076.00 GT:AD:DP:GQ:PL:SB 1/1:0,66,0:66:99:2013,198,0,2013,198,2013:0,0,26,40 -20 10012023 . A . . END=10012023 GT:DP:GQ:MIN_DP:PL 0/0:69:0:69:0,0,0 -20 10012024 . A . . END=10012147 GT:DP:GQ:MIN_DP:PL 0/0:70:99:38:0,99,1485 +20 10012023 . A . . END=10012147 GT:DP:GQ:MIN_DP:PL 0/0:70:99:38:0,99,1485 20 10012148 . G . . END=10012157 GT:DP:GQ:MIN_DP:PL 0/0:38:90:37:0,90,1350 20 10012158 . A . . END=10012159 GT:DP:GQ:MIN_DP:PL 0/0:35:84:34:0,84,1260 20 10012160 . C . . END=10012162 GT:DP:GQ:MIN_DP:PL 0/0:34:78:34:0,78,1170 20 10012163 . G . . END=10012167 GT:DP:GQ:MIN_DP:PL 0/0:34:81:33:0,81,1215 20 10012168 . C . . END=10012170 GT:DP:GQ:MIN_DP:PL 0/0:31:78:29:0,78,1170 -20 10012171 . T . . END=10012174 GT:DP:GQ:MIN_DP:PL 0/0:29:61:29:0,61,1035 -20 10012175 . C . . END=10012175 GT:DP:GQ:MIN_DP:PL 0/0:30:72:30:0,72,1080 -20 10012176 . A . . END=10012176 GT:DP:GQ:MIN_DP:PL 0/0:29:69:29:0,69,1035 -20 10012177 . C . . END=10012179 GT:DP:GQ:MIN_DP:PL 0/0:31:72:30:0,72,1080 -20 10012180 . C . . END=10012181 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20 10012182 . C . . END=10012183 GT:DP:GQ:MIN_DP:PL 0/0:30:78:29:0,78,1170 -20 10012184 . C . . END=10012196 GT:DP:GQ:MIN_DP:PL 0/0:32:81:30:0,81,1215 -20 10012197 . C . . END=10012197 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20 10012198 . G . . END=10012200 GT:DP:GQ:MIN_DP:PL 0/0:33:84:32:0,84,1260 -20 10012201 . T . . END=10012201 GT:DP:GQ:MIN_DP:PL 0/0:30:53:30:0,53,1087 +20 10012171 . T . . END=10012171 GT:DP:GQ:MIN_DP:PL 0/0:29:61:29:0,61,1086 +20 10012172 . C . . END=10012178 GT:DP:GQ:MIN_DP:PL 0/0:29:72:29:0,72,1080 +20 10012179 . G . . END=10012188 GT:DP:GQ:MIN_DP:PL 0/0:31:81:29:0,81,1157 +20 10012189 . G . . END=10012189 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 +20 10012190 . C . . END=10012196 GT:DP:GQ:MIN_DP:PL 0/0:32:87:30:0,87,1305 +20 10012197 . C . . END=10012197 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 +20 10012198 . G . . END=10012198 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 +20 10012199 . C . . END=10012200 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 +20 10012201 . T . . END=10012201 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 20 10012202 . C . . END=10012202 GT:DP:GQ:MIN_DP:PL 0/0:32:62:32:0,62,1157 -20 10012203 . C . . END=10012203 GT:DP:GQ:MIN_DP:PL 0/0:32:53:32:0,53,1153 -20 10012204 . T . . END=10012211 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,1350 +20 10012203 . C . . END=10012211 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,1350 20 10012212 . G . . END=10012215 GT:DP:GQ:MIN_DP:PL 0/0:31:84:30:0,84,1260 20 10012216 . C . . END=10012221 GT:DP:GQ:MIN_DP:PL 0/0:33:72:32:0,72,1080 20 10012222 . T . . END=10012224 GT:DP:GQ:MIN_DP:PL 0/0:32:69:32:0,69,1035 @@ -513,10 +408,7 @@ 20 10012399 . G . . END=10012402 GT:DP:GQ:MIN_DP:PL 0/0:16:45:15:0,45,561 20 10012403 . T . . END=10012403 GT:DP:GQ:MIN_DP:PL 0/0:15:17:15:0,17,521 20 10012404 . G . . END=10012404 GT:DP:GQ:MIN_DP:PL 0/0:14:42:14:0,42,564 -20 10012405 . G . . END=10012405 GT:DP:GQ:MIN_DP:PL 0/0:15:39:15:0,39,585 -20 10012406 . C . . END=10012406 GT:DP:GQ:MIN_DP:PL 0/0:15:3:15:0,3,396 -20 10012407 . G . . END=10012407 GT:DP:GQ:MIN_DP:PL 0/0:15:2:15:0,2,481 -20 10012408 . G . . END=10012409 GT:DP:GQ:MIN_DP:PL 0/0:15:39:15:0,39,585 +20 10012405 . G . . END=10012409 GT:DP:GQ:MIN_DP:PL 0/0:15:39:15:0,39,585 20 10012410 . C . . END=10012410 GT:DP:GQ:MIN_DP:PL 0/0:15:33:15:0,33,495 20 10012411 . C . . END=10012412 GT:DP:GQ:MIN_DP:PL 0/0:15:30:14:0,30,450 20 10012413 . C . . END=10012416 GT:DP:GQ:MIN_DP:PL 0/0:16:33:14:0,33,495 @@ -551,63 +443,56 @@ 20 10012475 . C . . END=10012476 GT:DP:GQ:MIN_DP:PL 0/0:20:36:19:0,36,540 20 10012477 . G . . END=10012478 GT:DP:GQ:MIN_DP:PL 0/0:18:33:17:0,33,495 20 10012479 . A G, 592.77 . DP=17;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=45990.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,17,0:17:50:0|1:10012479_A_G:621,50,0,621,50,621:0,0,9,8 -20 10012480 . G . . END=10012482 GT:DP:GQ:MIN_DP:PL 0/0:17:24:16:0,24,360 +20 10012480 . G . . END=10012482 GT:DP:GQ:MIN_DP:PL 0/0:16:24:15:0,24,360 20 10012483 . G . . END=10012489 GT:DP:GQ:MIN_DP:PL 0/0:13:27:12:0,27,405 20 10012490 . G . . END=10012490 GT:DP:GQ:MIN_DP:PL 0/0:11:22:11:0,22,359 20 10012491 . T . . END=10012491 GT:DP:GQ:MIN_DP:PL 0/0:8:24:8:0,24,269 -20 10012492 . G . . END=10012494 GT:DP:GQ:MIN_DP:PL 0/0:9:27:9:0,27,304 -20 10012495 . C . . END=10012497 GT:DP:GQ:MIN_DP:PL 0/0:11:30:11:0,30,450 +20 10012492 . G . . END=10012497 GT:DP:GQ:MIN_DP:PL 0/0:10:27:9:0,27,304 20 10012498 . C G, 466.77 . DP=11;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=22302.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,11,0:11:33:0|1:10012479_A_G:495,33,0,495,33,495:0,0,4,7 -20 10012499 . G . . END=10012501 GT:DP:GQ:MIN_DP:PL 0/0:12:30:10:0,30,350 -20 10012502 . C . . END=10012503 GT:DP:GQ:MIN_DP:PL 0/0:12:27:12:0,27,405 -20 10012504 . C . . END=10012508 GT:DP:GQ:MIN_DP:PL 0/0:11:24:10:0,24,360 -20 10012509 . A . . END=10012513 GT:DP:GQ:MIN_DP:PL 0/0:12:30:11:0,30,450 -20 10012514 . C . . END=10012514 GT:DP:GQ:MIN_DP:PL 0/0:11:24:11:0,24,360 -20 10012515 . A . . END=10012515 GT:DP:GQ:MIN_DP:PL 0/0:12:27:12:0,27,405 -20 10012516 . G . . END=10012517 GT:DP:GQ:MIN_DP:PL 0/0:12:24:11:0,24,360 +20 10012499 . G . . END=10012501 GT:DP:GQ:MIN_DP:PL 0/0:11:27:9:0,27,334 +20 10012502 . C . . END=10012503 GT:DP:GQ:MIN_DP:PL 0/0:11:24:11:0,24,360 +20 10012504 . C . . END=10012508 GT:DP:GQ:MIN_DP:PL 0/0:10:21:10:0,21,315 +20 10012509 . A . . END=10012513 GT:DP:GQ:MIN_DP:PL 0/0:11:27:10:0,27,405 +20 10012514 . C . . END=10012515 GT:DP:GQ:MIN_DP:PL 0/0:10:21:10:0,21,315 +20 10012516 . G . . END=10012517 GT:DP:GQ:MIN_DP:PL 0/0:10:18:9:0,18,270 20 10012518 . T C, 406.77 . DP=9;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=15102.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,9,0:9:30:0|1:10012479_A_G:435,30,0,435,30,435:0,0,4,5 -20 10012519 . C . . END=10012519 GT:DP:GQ:MIN_DP:PL 0/0:12:27:12:0,27,405 -20 10012520 . A . . END=10012520 GT:DP:GQ:MIN_DP:PL 0/0:12:24:12:0,24,400 +20 10012519 . C . . END=10012520 GT:DP:GQ:MIN_DP:PL 0/0:10:21:10:0,21,315 20 10012521 . C T, 46.77 . BaseQRankSum=2.362;DP=11;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.038;RAW_MQ=19192.00;ReadPosRankSum=1.973 GT:AD:DP:GQ:PL:SB 0/1:8,3,0:11:75:75,0,224,99,233,332:4,4,2,1 -20 10012522 . A . . END=10012525 GT:DP:GQ:MIN_DP:PL 0/0:12:30:11:0,30,450 -20 10012526 . G . . END=10012526 GT:DP:GQ:MIN_DP:PL 0/0:10:27:10:0,27,405 -20 10012527 . C . . END=10012527 GT:DP:GQ:MIN_DP:PL 0/0:10:24:10:0,24,360 -20 10012528 . T . . END=10012536 GT:DP:GQ:MIN_DP:PL 0/0:10:21:9:0,21,315 -20 10012537 . T . . END=10012541 GT:DP:GQ:MIN_DP:PL 0/0:8:18:8:0,18,270 -20 10012542 . C . . END=10012544 GT:DP:GQ:MIN_DP:PL 0/0:8:15:8:0,15,225 -20 10012545 . C . . END=10012546 GT:DP:GQ:MIN_DP:PL 0/0:7:12:6:0,12,180 -20 10012547 . G . . END=10012547 GT:DP:GQ:MIN_DP:PL 0/0:8:7:8:0,7,219 -20 10012548 . G . . END=10012548 GT:DP:GQ:MIN_DP:PL 0/0:8:12:8:0,12,180 -20 10012549 . C . . END=10012549 GT:DP:GQ:MIN_DP:PL 0/0:8:7:8:0,7,255 -20 10012550 . C . . END=10012552 GT:DP:GQ:MIN_DP:PL 0/0:10:12:10:0,12,180 -20 10012553 . A . . END=10012555 GT:DP:GQ:MIN_DP:PL 0/0:10:9:10:0,9,135 -20 10012556 . T . . END=10012557 GT:DP:GQ:MIN_DP:PL 0/0:9:6:9:0,6,90 -20 10012558 . C . . END=10012558 GT:DP:GQ:MIN_DP:PL 0/0:9:3:9:0,3,45 -20 10012559 . C . . END=10012569 GT:DP:GQ:MIN_DP:PL 0/0:9:0:8:0,0,0 +20 10012522 . A . . END=10012525 GT:DP:GQ:MIN_DP:PL 0/0:11:24:9:0,24,360 +20 10012526 . G . . END=10012526 GT:DP:GQ:MIN_DP:PL 0/0:8:21:8:0,21,315 +20 10012527 . C . . END=10012545 GT:DP:GQ:MIN_DP:PL 0/0:7:18:6:0,18,188 +20 10012546 . G . . END=10012546 GT:DP:GQ:MIN_DP:PL 0/0:5:15:5:0,15,174 +20 10012547 . G . . END=10012548 GT:DP:GQ:MIN_DP:PL 0/0:6:18:6:0,18,207 +20 10012549 . C . . END=10012549 GT:DP:GQ:MIN_DP:PL 0/0:6:1:6:0,1,186 +20 10012550 . C . . END=10012562 GT:DP:GQ:MIN_DP:PL 0/0:8:24:8:0,24,296 +20 10012563 . G . . END=10012564 GT:DP:GQ:MIN_DP:PL 0/0:8:21:8:0,21,315 +20 10012565 . G . . END=10012567 GT:DP:GQ:MIN_DP:PL 0/0:9:24:8:0,24,261 +20 10012568 . G . . END=10012569 GT:DP:GQ:MIN_DP:PL 0/0:9:21:8:0,21,315 20 10012570 . G GCA, 457.73 . DP=9;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=12736.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,9,0:9:33:0|1:10012570_G_GCA:495,33,0,495,33,495:0,0,8,1 -20 10012571 . G . . END=10012571 GT:DP:GQ:MIN_DP:PL 0/0:11:0:11:0,0,0 +20 10012571 . G . . END=10012571 GT:DP:GQ:MIN_DP:PL 0/0:11:27:11:0,27,405 20 10012572 . GT G, 457.73 . DP=11;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=17177.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,11,0:11:33:0|1:10012570_G_GCA:495,33,0,495,33,495:0,0,10,1 -20 10012574 . G . . END=10012575 GT:DP:GQ:MIN_DP:PL 0/0:12:0:12:0,0,0 -20 10012576 . T . . END=10012576 GT:DP:GQ:MIN_DP:PL 0/0:12:4:12:0,4,413 -20 10012577 . C . . END=10012577 GT:DP:GQ:MIN_DP:PL 0/0:12:9:12:0,9,419 -20 10012578 . G . . END=10012578 GT:DP:GQ:MIN_DP:PL 0/0:12:2:12:0,2,328 +20 10012574 . G . . END=10012575 GT:DP:GQ:MIN_DP:PL 0/0:12:30:11:0,30,450 +20 10012576 . T . . END=10012577 GT:DP:GQ:MIN_DP:PL 0/0:12:33:12:0,33,495 +20 10012578 . G . . END=10012578 GT:DP:GQ:MIN_DP:PL 0/0:11:30:11:0,30,450 20 10012579 . G . . END=10012581 GT:DP:GQ:MIN_DP:PL 0/0:12:33:12:0,33,495 20 10012582 . C . . END=10012587 GT:DP:GQ:MIN_DP:PL 0/0:13:36:13:0,36,540 -20 10012588 . G . . END=10012589 GT:DP:GQ:MIN_DP:PL 0/0:13:33:12:0,33,495 -20 10012590 . C . . END=10012591 GT:DP:GQ:MIN_DP:PL 0/0:14:36:14:0,36,540 +20 10012588 . G . . END=10012588 GT:DP:GQ:MIN_DP:PL 0/0:12:33:12:0,33,495 +20 10012589 . C . . END=10012589 GT:DP:GQ:MIN_DP:PL 0/0:13:36:13:0,36,540 +20 10012590 . C . . END=10012591 GT:DP:GQ:MIN_DP:PL 0/0:14:39:14:0,39,585 20 10012592 . G . . END=10012592 GT:DP:GQ:MIN_DP:PL 0/0:14:14:14:0,14,377 -20 10012593 . C . . END=10012595 GT:DP:GQ:MIN_DP:PL 0/0:14:36:14:0,36,540 -20 10012596 . T . . END=10012597 GT:DP:GQ:MIN_DP:PL 0/0:14:33:14:0,33,495 -20 10012598 . C . . END=10012600 GT:DP:GQ:MIN_DP:PL 0/0:14:30:14:0,30,450 -20 10012601 . G . . END=10012605 GT:DP:GQ:MIN_DP:PL 0/0:15:33:15:0,33,495 -20 10012606 . C . . END=10012606 GT:DP:GQ:MIN_DP:PL 0/0:15:30:15:0,30,450 -20 10012607 . C . . END=10012609 GT:DP:GQ:MIN_DP:PL 0/0:15:27:14:0,27,405 -20 10012610 . C . . END=10012618 GT:DP:GQ:MIN_DP:PL 0/0:17:30:17:0,30,450 -20 10012619 . T . . END=10012624 GT:DP:GQ:MIN_DP:PL 0/0:19:21:17:0,21,315 -20 10012625 . C . . END=10012630 GT:DP:GQ:MIN_DP:PL 0/0:21:24:20:0,24,360 +20 10012593 . C . . END=10012600 GT:DP:GQ:MIN_DP:PL 0/0:14:39:14:0,39,585 +20 10012601 . G . . END=10012606 GT:DP:GQ:MIN_DP:PL 0/0:15:42:15:0,42,630 +20 10012607 . C . . END=10012607 GT:DP:GQ:MIN_DP:PL 0/0:15:39:15:0,39,585 +20 10012608 . C . . END=10012609 GT:DP:GQ:MIN_DP:PL 0/0:15:42:14:0,42,545 +20 10012610 . C . . END=10012618 GT:DP:GQ:MIN_DP:PL 0/0:17:48:17:0,48,720 +20 10012619 . T . . END=10012620 GT:DP:GQ:MIN_DP:PL 0/0:17:51:17:0,51,653 +20 10012621 . G . . END=10012621 GT:DP:GQ:MIN_DP:PL 0/0:19:57:19:0,57,672 +20 10012622 . G . . END=10012624 GT:DP:GQ:MIN_DP:PL 0/0:19:54:19:0,54,810 +20 10012625 . C . . END=10012625 GT:DP:GQ:MIN_DP:PL 0/0:20:57:20:0,57,855 +20 10012626 . C . . END=10012630 GT:DP:GQ:MIN_DP:PL 0/0:21:60:21:0,60,900 20 10012631 . C CG, 484.73 . BaseQRankSum=-1.030;DP=21;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.670;RAW_MQ=49065.00;ReadPosRankSum=-1.813 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:8,13,0:21:99:0|1:10012631_C_CG:522,0,297,546,336,882:8,0,9,4 -20 10012632 . G . . END=10012632 GT:DP:GQ:MIN_DP:PL 0/0:21:0:21:0,0,0 -20 10012633 . C . . END=10012633 GT:DP:GQ:MIN_DP:PL 0/0:20:35:20:0,35,707 +20 10012632 . G . . END=10012632 GT:DP:GQ:MIN_DP:PL 0/0:21:54:21:0,54,810 +20 10012633 . C . . END=10012633 GT:DP:GQ:MIN_DP:PL 0/0:20:51:20:0,51,765 20 10012634 . C . . END=10012635 GT:DP:GQ:MIN_DP:PL 0/0:22:54:22:0,54,810 20 10012636 . G C, 527.77 . BaseQRankSum=2.711;DP=22;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.513;RAW_MQ=52665.00;ReadPosRankSum=-1.915 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:8,14,0:22:99:0|1:10012631_C_CG:556,0,294,580,336,916:8,0,10,4 20 10012637 . A . . END=10012639 GT:DP:GQ:MIN_DP:PL 0/0:20:54:20:0,54,810 @@ -638,7 +523,9 @@ 20 10012733 . G . . END=10012736 GT:DP:GQ:MIN_DP:PL 0/0:31:72:27:0,72,1080 20 10012737 . G . . END=10012739 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 20 10012740 . C . . END=10012742 GT:DP:GQ:MIN_DP:PL 0/0:29:75:29:0,75,1125 -20 10012743 . C . . END=10012750 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 +20 10012743 . C . . END=10012746 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 +20 10012747 . C . . END=10012747 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,1170 +20 10012748 . A . . END=10012750 GT:DP:GQ:MIN_DP:PL 0/0:31:81:29:0,81,1215 20 10012751 . T C, 937.77 . DP=30;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=78546.00 GT:AD:DP:GQ:PL:SB 1/1:0,30,0:30:89:966,89,0,966,89,966:0,0,17,13 20 10012752 . C . . END=10012752 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 20 10012753 . T . . END=10012753 GT:DP:GQ:MIN_DP:PL 0/0:29:74:29:0,74,1014 @@ -683,8 +570,7 @@ 20 10014590 . A . . END=10014590 GT:DP:GQ:MIN_DP:PL 0/0:44:93:44:0,93,1625 20 10014591 . T . . END=10014989 GT:DP:GQ:MIN_DP:PL 0/0:72:99:42:0,116,1732 20 10014990 . C CAT, 1237.73 . BaseQRankSum=1.930;DP=87;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.107;RAW_MQ=321369.00;ReadPosRankSum=-0.437 GT:AD:DP:GQ:PL:SB 0/1:38,38,0:76:99:1275,0,1248,1389,1365,2755:28,10,25,13 -20 10014991 . A . . END=10014991 GT:DP:GQ:MIN_DP:PL 0/0:88:0:88:0,0,402 -20 10014992 . T . . END=10015385 GT:DP:GQ:MIN_DP:PL 0/0:73:99:41:0,102,1530 +20 10014991 . A . . END=10015385 GT:DP:GQ:MIN_DP:PL 0/0:73:99:41:0,102,1530 20 10015386 . G . . END=10015388 GT:DP:GQ:MIN_DP:PL 0/0:39:90:39:0,90,1350 20 10015389 . A . . END=10015390 GT:DP:GQ:MIN_DP:PL 0/0:38:81:38:0,81,1215 20 10015391 . G . . END=10015392 GT:DP:GQ:MIN_DP:PL 0/0:37:78:36:0,78,1170 @@ -747,17 +633,11 @@ 20 10015662 . G . . END=10015675 GT:DP:GQ:MIN_DP:PL 0/0:13:33:11:0,33,418 20 10015676 . G . . END=10015678 GT:DP:GQ:MIN_DP:PL 0/0:11:27:11:0,27,405 20 10015679 . C T, 140.77 . BaseQRankSum=0.200;DP=10;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=36000.00;ReadPosRankSum=0.497 GT:AD:DP:GQ:PL:SB 0/1:5,5,0:10:99:169,0,166,184,181,365:5,0,5,0 -20 10015680 . G . . END=10015683 GT:DP:GQ:MIN_DP:PL 0/0:11:27:11:0,27,405 -20 10015684 . C . . END=10015687 GT:DP:GQ:MIN_DP:PL 0/0:12:30:11:0,30,450 -20 10015688 . C . . END=10015688 GT:DP:GQ:MIN_DP:PL 0/0:11:33:11:0,33,400 -20 10015689 . G . . END=10015689 GT:DP:GQ:MIN_DP:PL 0/0:10:30:10:0,30,292 -20 10015690 . G . . END=10015690 GT:DP:GQ:MIN_DP:PL 0/0:11:33:11:0,33,406 -20 10015691 . C . . END=10015693 GT:DP:GQ:MIN_DP:PL 0/0:11:30:11:0,30,450 -20 10015694 . C . . END=10015694 GT:DP:GQ:MIN_DP:PL 0/0:12:23:12:0,23,389 -20 10015695 . C . . END=10015697 GT:DP:GQ:MIN_DP:PL 0/0:12:27:12:0,27,405 -20 10015698 . C . . END=10015698 GT:DP:GQ:MIN_DP:PL 0/0:12:23:12:0,23,401 -20 10015699 . C . . END=10015701 GT:DP:GQ:MIN_DP:PL 0/0:12:27:11:0,27,405 -20 10015702 . C . . END=10015707 GT:DP:GQ:MIN_DP:PL 0/0:12:30:11:0,30,450 +20 10015680 . G . . END=10015683 GT:DP:GQ:MIN_DP:PL 0/0:10:24:10:0,24,360 +20 10015684 . C . . END=10015687 GT:DP:GQ:MIN_DP:PL 0/0:11:27:10:0,27,405 +20 10015688 . C . . END=10015690 GT:DP:GQ:MIN_DP:PL 0/0:10:30:10:0,30,292 +20 10015691 . C . . END=10015701 GT:DP:GQ:MIN_DP:PL 0/0:11:27:10:0,27,405 +20 10015702 . C . . END=10015707 GT:DP:GQ:MIN_DP:PL 0/0:11:30:11:0,30,450 20 10015708 . G . . END=10015708 GT:DP:GQ:MIN_DP:PL 0/0:12:33:12:0,33,495 20 10015709 . C . . END=10015714 GT:DP:GQ:MIN_DP:PL 0/0:13:36:13:0,36,540 20 10015715 . C . . END=10015716 GT:DP:GQ:MIN_DP:PL 0/0:13:33:13:0,33,495 @@ -810,9 +690,7 @@ 20 10020890 . A . . END=10020896 GT:DP:GQ:MIN_DP:PL 0/0:42:93:40:0,93,1395 20 10020897 . C . . END=10020918 GT:DP:GQ:MIN_DP:PL 0/0:41:99:37:0,102,1530 20 10020919 . T . . END=10020919 GT:DP:GQ:MIN_DP:PL 0/0:45:95:45:0,95,1765 -20 10020920 . T . . END=10021606 GT:DP:GQ:MIN_DP:PL 0/0:79:99:46:0,105,1721 -20 10021607 . C . . END=10021607 GT:DP:GQ:MIN_DP:PL 0/0:98:98:98:0,98,3341 -20 10021608 . T . . END=10023688 GT:DP:GQ:MIN_DP:PL 0/0:80:99:54:0,110,1800 +20 10020920 . T . . END=10023688 GT:DP:GQ:MIN_DP:PL 0/0:80:99:46:0,105,1721 20 10023689 . G A, 1852.77 . BaseQRankSum=2.144;DP=80;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.352;RAW_MQ=285769.00;ReadPosRankSum=1.162 GT:AD:DP:GQ:PL:SB 0/1:29,51,0:80:99:1881,0,946,1968,1099,3067:16,13,26,25 20 10023690 . G . . END=10024106 GT:DP:GQ:MIN_DP:PL 0/0:70:99:57:0,120,1800 20 10024107 . C T, 1694.77 . BaseQRankSum=5.770;DP=86;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.546;RAW_MQ=303563.00;ReadPosRankSum=0.148 GT:AD:DP:GQ:PL:SB 0/1:38,48,0:86:99:1723,0,1086,1837,1230,3068:21,17,28,20 @@ -822,20 +700,18 @@ 20 10024288 . C . . END=10024288 GT:DP:GQ:MIN_DP:PL 0/0:71:0:71:0,0,1411 20 10024289 . T . . END=10024293 GT:DP:GQ:MIN_DP:PL 0/0:72:99:70:0,120,1800 20 10024294 . C . . END=10024294 GT:DP:GQ:MIN_DP:PL 0/0:69:0:69:0,0,1358 -20 10024295 . T . . END=10024295 GT:DP:GQ:MIN_DP:PL 0/0:69:99:69:0,120,1800 -20 10024296 . T . . END=10024296 GT:DP:GQ:MIN_DP:PL 0/0:67:82:67:0,82,2254 +20 10024295 . T . . END=10024296 GT:DP:GQ:MIN_DP:PL 0/0:68:99:67:0,120,1800 20 10024297 . T . . END=10024297 GT:DP:GQ:MIN_DP:PL 0/0:68:65:68:0,65,2188 -20 10024298 . T . . END=10024298 GT:DP:GQ:MIN_DP:PL 0/0:66:37:66:0,37,2037 -20 10024299 . C . . END=10024299 GT:DP:GQ:MIN_DP:PL 0/0:62:0:62:0,0,1430 +20 10024298 . T . . END=10024298 GT:DP:GQ:MIN_DP:PL 0/0:66:59:66:0,59,2080 +20 10024299 . C . . END=10024299 GT:DP:GQ:MIN_DP:PL 0/0:62:0:62:0,0,1480 20 10024300 . CTT C,CT,CTTTT, 87.76 . BaseQRankSum=2.446;DP=50;ExcessHet=3.0103;MLEAC=1,0,1,0;MLEAF=0.500,0.00,0.500,0.00;MQRankSum=-0.600;RAW_MQ=134695.00;ReadPosRankSum=-1.073 GT:AD:DP:GQ:PL:SB 1/3:3,4,3,8,0:18:1:122,67,400,91,215,231,19,0,1,156,161,279,257,107,347:1,2,11,4 20 10024303 . T . . END=10024303 GT:DP:GQ:MIN_DP:PL 0/0:67:57:67:0,57,855 20 10024304 . T . . END=10024307 GT:DP:GQ:MIN_DP:PL 0/0:69:63:68:0,63,945 20 10024308 . T . . END=10024310 GT:DP:GQ:MIN_DP:PL 0/0:70:78:70:0,78,1170 -20 10024311 . T . . END=10024315 GT:DP:GQ:MIN_DP:PL 0/0:66:81:66:0,81,1215 -20 10024316 . T . . END=10024316 GT:DP:GQ:MIN_DP:PL 0/0:66:69:66:0,69,1035 -20 10024317 . T . . END=10024317 GT:DP:GQ:MIN_DP:PL 0/0:64:72:64:0,72,1080 -20 10024318 . T . . END=10024318 GT:DP:GQ:MIN_DP:PL 0/0:62:63:62:0,63,945 -20 10024319 . T . . END=10024320 GT:DP:GQ:MIN_DP:PL 0/0:63:75:62:0,75,1125 +20 10024311 . T . . END=10024314 GT:DP:GQ:MIN_DP:PL 0/0:66:81:66:0,81,1215 +20 10024315 . T . . END=10024315 GT:DP:GQ:MIN_DP:PL 0/0:66:72:66:0,72,1080 +20 10024316 . T . . END=10024318 GT:DP:GQ:MIN_DP:PL 0/0:64:60:62:0,60,900 +20 10024319 . T . . END=10024320 GT:DP:GQ:MIN_DP:PL 0/0:63:72:62:0,72,1080 20 10024321 . T . . END=10024321 GT:DP:GQ:MIN_DP:PL 0/0:62:90:62:0,90,1350 20 10024322 . T . . END=10024322 GT:DP:GQ:MIN_DP:PL 0/0:60:69:60:0,69,2100 20 10024323 . T . . END=10024323 GT:DP:GQ:MIN_DP:PL 0/0:56:27:56:0,27,1860 @@ -846,28 +722,21 @@ 20 10026357 . T C, 1166.77 . BaseQRankSum=-1.700;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.148;RAW_MQ=215117.00;ReadPosRankSum=-0.076 GT:AD:DP:GQ:PL:SB 0/1:28,35,0:63:99:1195,0,932,1279,1037,2316:10,18,20,15 20 10026358 . A . . END=10026793 GT:DP:GQ:MIN_DP:PL 0/0:72:99:41:0,102,1530 20 10026794 . C T, 1084.77 . BaseQRankSum=2.828;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.719;RAW_MQ=184441.00;ReadPosRankSum=-0.533 GT:AD:DP:GQ:PL:SB 0/1:19,33,0:52:99:1113,0,529,1170,627,1798:7,12,15,18 -20 10026795 . G . . END=10027227 GT:DP:GQ:MIN_DP:PL 0/0:71:99:52:0,105,1575 -20 10027228 . G . . END=10027228 GT:DP:GQ:MIN_DP:PL 0/0:66:96:66:0,96,1440 -20 10027229 . A . . END=10027229 GT:DP:GQ:MIN_DP:PL 0/0:67:99:67:0,99,1485 -20 10027230 . A . . END=10027230 GT:DP:GQ:MIN_DP:PL 0/0:66:96:66:0,96,1440 -20 10027231 . A . . END=10027233 GT:DP:GQ:MIN_DP:PL 0/0:70:99:68:0,102,1530 +20 10026795 . G . . END=10027233 GT:DP:GQ:MIN_DP:PL 0/0:70:99:52:0,115,1800 20 10027234 . A ATTAG, 1320.73 . BaseQRankSum=-0.406;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.845;RAW_MQ=236651.00;ReadPosRankSum=-0.979 GT:AD:DP:GQ:PL:SB 0/1:34,35,0:69:99:1358,0,1964,1461,2069,3531:18,16,15,20 -20 10027235 . T . . END=10027235 GT:DP:GQ:MIN_DP:PL 0/0:72:0:72:0,0,334 -20 10027236 . T . . END=10027867 GT:DP:GQ:MIN_DP:PL 0/0:78:99:56:0,120,1800 +20 10027235 . T . . END=10027867 GT:DP:GQ:MIN_DP:PL 0/0:78:99:56:0,120,1800 20 10027868 . A G, 1739.77 . BaseQRankSum=-5.793;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.032;RAW_MQ=314882.00;ReadPosRankSum=1.872 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:44,45,0:89:99:0|1:10027868_A_G:1768,0,3201,1901,3340,5240:19,25,26,19 20 10027869 . A . . END=10027871 GT:DP:GQ:MIN_DP:PL 0/0:86:99:85:0,120,1800 20 10027872 . A G, 1724.77 . BaseQRankSum=-5.491;DP=85;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.101;RAW_MQ=300482.00;ReadPosRankSum=1.053 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:40,45,0:85:99:0|1:10027868_A_G:1753,0,3136,1879,3272,5151:16,24,26,19 20 10027873 . G . . END=10028866 GT:DP:GQ:MIN_DP:PL 0/0:80:99:55:0,120,1800 20 10028867 . A ATG, 1106.73 . BaseQRankSum=-0.874;DP=92;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.711;RAW_MQ=338841.00;ReadPosRankSum=0.364 GT:AD:DP:GQ:PL:SB 0/1:32,39,0:71:99:1144,0,916,1242,1033,2275:11,21,18,21 -20 10028868 . T . . END=10028868 GT:DP:GQ:MIN_DP:PL 0/0:92:0:92:0,0,401 -20 10028869 . G . . END=10030187 GT:DP:GQ:MIN_DP:PL 0/0:80:99:60:0,120,1800 +20 10028868 . T . . END=10030187 GT:DP:GQ:MIN_DP:PL 0/0:80:99:60:0,120,1800 20 10030188 . T A, 1372.77 . BaseQRankSum=0.711;DP=81;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.013;RAW_MQ=288841.00;ReadPosRankSum=-0.553 GT:AD:DP:GQ:PL:SB 0/1:42,39,0:81:99:1401,0,1524,1527,1641,3168:24,18,15,24 20 10030189 . G . . END=10030566 GT:DP:GQ:MIN_DP:PL 0/0:71:99:41:0,103,1575 20 10030567 . G . . END=10030567 GT:DP:GQ:MIN_DP:PL 0/0:41:90:41:0,90,1511 -20 10030568 . C . . END=10031253 GT:DP:GQ:MIN_DP:PL 0/0:70:99:42:0,99,1485 +20 10030568 . C . . END=10031253 GT:DP:GQ:MIN_DP:PL 0/0:70:99:42:0,114,1710 20 10031254 . A AT, 1463.73 . BaseQRankSum=-0.091;DP=87;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.017;RAW_MQ=309510.00;ReadPosRankSum=0.495 GT:AD:DP:GQ:PL:SB 0/1:38,47,0:85:99:1501,0,1159,1616,1300,2916:27,11,25,22 -20 10031255 . T . . END=10031255 GT:DP:GQ:MIN_DP:PL 0/0:88:0:88:0,0,0 -20 10031256 . G . . END=10031341 GT:DP:GQ:MIN_DP:PL 0/0:96:99:87:0,120,1800 +20 10031255 . T . . END=10031341 GT:DP:GQ:MIN_DP:PL 0/0:95:99:86:0,120,1800 20 10031342 . G A, 1834.77 . BaseQRankSum=1.833;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.866;RAW_MQ=332041.00;ReadPosRankSum=-0.012 GT:AD:DP:GQ:PL:SB 0/1:41,52,0:93:99:1863,0,1375,1986,1531,3517:22,19,31,21 20 10031343 . A . . END=10031797 GT:DP:GQ:MIN_DP:PL 0/0:91:99:66:0,120,1800 20 10031798 . G A, 4296.77 . DP=104;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=369410.00 GT:AD:DP:GQ:PL:SB 1/1:0,104,0:104:99:4325,313,0,4325,313,4325:0,0,57,47 @@ -879,11 +748,9 @@ 20 10032413 . T G, 869.77 . BaseQRankSum=-6.142;DP=66;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.065;RAW_MQ=233138.00;ReadPosRankSum=-1.003 GT:AD:DP:GQ:PL:SB 0/1:35,31,0:66:99:898,0,1277,1003,1371,2374:15,20,20,11 20 10032414 . T . . END=10032881 GT:DP:GQ:MIN_DP:PL 0/0:70:99:55:0,120,1800 20 10032882 . A T, 1202.77 . BaseQRankSum=-3.697;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.014;RAW_MQ=267241.00;ReadPosRankSum=0.626 GT:AD:DP:GQ:PL:SB 0/1:39,36,0:75:99:1231,0,1406,1348,1514,2862:28,11,22,14 -20 10032883 . A . . END=10032966 GT:DP:GQ:MIN_DP:PL 0/0:67:99:61:0,99,1485 -20 10032967 . T . . END=10032971 GT:DP:GQ:MIN_DP:PL 0/0:68:90:67:0,90,1350 +20 10032883 . A . . END=10032971 GT:DP:GQ:MIN_DP:PL 0/0:67:99:61:0,120,1800 20 10032972 . C CAT, 1122.73 . BaseQRankSum=-0.354;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.017;RAW_MQ=231241.00;ReadPosRankSum=-1.232 GT:AD:DP:GQ:PL:SB 0/1:33,30,0:63:99:1160,0,1477,1260,1568,2827:17,16,11,19 -20 10032973 . T . . END=10032973 GT:DP:GQ:MIN_DP:PL 0/0:65:0:65:0,0,104 -20 10032974 . G . . END=10033636 GT:DP:GQ:MIN_DP:PL 0/0:78:99:50:0,120,1800 +20 10032973 . T . . END=10033636 GT:DP:GQ:MIN_DP:PL 0/0:78:99:50:0,120,1800 20 10033637 . C . . END=10033637 GT:DP:GQ:MIN_DP:PL 0/0:58:97:58:0,97,2210 20 10033638 . C . . END=10034305 GT:DP:GQ:MIN_DP:PL 0/0:85:99:53:0,120,1800 20 10034306 . T C, 782.77 . BaseQRankSum=-3.661;DP=76;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.150;RAW_MQ=268610.00;ReadPosRankSum=0.539 GT:AD:DP:GQ:PL:SB 0/1:46,29,0:75:99:811,0,1593,950,1680,2630:24,22,14,15 @@ -901,8 +768,7 @@ 20 10036161 . T . . END=10036161 GT:DP:GQ:MIN_DP:PL 0/0:42:82:42:0,82,1514 20 10036162 . G . . END=10036929 GT:DP:GQ:MIN_DP:PL 0/0:76:99:43:0,113,1513 20 10036930 . CGATAGCCCTAGCCCTAGATA C, 1036.73 . BaseQRankSum=0.200;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.048;RAW_MQ=274847.00;ReadPosRankSum=0.460 GT:AD:DP:GQ:PL:SB 0/1:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 -20 10036951 . G . . END=10036951 GT:DP:GQ:MIN_DP:PL 0/0:77:0:77:0,0,1197 -20 10036952 . A . . END=10036956 GT:DP:GQ:MIN_DP:PL 0/0:74:99:70:0,120,1800 +20 10036951 . G . . END=10036956 GT:DP:GQ:MIN_DP:PL 0/0:74:99:70:0,120,1800 20 10036957 . C . . END=10036957 GT:DP:GQ:MIN_DP:PL 0/0:70:37:70:0,37,2472 20 10036958 . C . . END=10036958 GT:DP:GQ:MIN_DP:PL 0/0:70:40:70:0,40,2490 20 10036959 . T . . END=10036959 GT:DP:GQ:MIN_DP:PL 0/0:70:99:70:0,120,1800 @@ -917,29 +783,11 @@ 20 10036968 . A . . END=10036968 GT:DP:GQ:MIN_DP:PL 0/0:74:64:74:0,64,2707 20 10036969 . T . . END=10037036 GT:DP:GQ:MIN_DP:PL 0/0:87:99:72:0,107,1800 20 10037037 . C T, 1436.77 . BaseQRankSum=3.504;DP=81;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.193;RAW_MQ=293262.00;ReadPosRankSum=-1.609 GT:AD:DP:GQ:PL:SB 0/1:39,42,0:81:99:1465,0,1124,1580,1251,2831:28,11,28,14 -20 10037038 . G . . END=10037097 GT:DP:GQ:MIN_DP:PL 0/0:92:99:80:0,111,1665 -20 10037098 . C . . END=10037098 GT:DP:GQ:MIN_DP:PL 0/0:86:9:86:0,9,2910 -20 10037099 . A . . END=10037100 GT:DP:GQ:MIN_DP:PL 0/0:89:90:88:0,90,1350 -20 10037101 . A . . END=10037101 GT:DP:GQ:MIN_DP:PL 0/0:87:81:87:0,81,1215 -20 10037102 . T . . END=10037102 GT:DP:GQ:MIN_DP:PL 0/0:90:72:90:0,72,1080 -20 10037103 . A . . END=10037103 GT:DP:GQ:MIN_DP:PL 0/0:90:66:90:0,66,990 -20 10037104 . T . . END=10037104 GT:DP:GQ:MIN_DP:PL 0/0:89:0:89:0,0,2830 -20 10037105 . A . . END=10037107 GT:DP:GQ:MIN_DP:PL 0/0:89:54:88:0,54,810 -20 10037108 . G . . END=10037108 GT:DP:GQ:MIN_DP:PL 0/0:85:21:85:0,21,315 -20 10037109 . A . . END=10037109 GT:DP:GQ:MIN_DP:PL 0/0:84:18:84:0,18,270 +20 10037038 . G . . END=10037109 GT:DP:GQ:MIN_DP:PL 0/0:88:99:75:0,120,1800 20 10037110 . T TGATA, 2780.73 . DP=74;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=240219.00 GT:AD:DP:GQ:PL:SB 1/1:0,61,0:61:99:2818,189,0,2819,190,2820:0,0,35,26 -20 10037111 . G . . END=10037111 GT:DP:GQ:MIN_DP:PL 0/0:84:0:84:0,0,0 -20 10037112 . A . . END=10037121 GT:DP:GQ:MIN_DP:PL 0/0:83:99:81:0,120,1800 -20 10037122 . A . . END=10037126 GT:DP:GQ:MIN_DP:PL 0/0:80:0:79:0,0,1989 -20 10037127 . A . . END=10037127 GT:DP:GQ:MIN_DP:PL 0/0:79:85:79:0,85,2945 -20 10037128 . T . . END=10037131 GT:DP:GQ:MIN_DP:PL 0/0:77:99:74:0,114,1710 -20 10037132 . T . . END=10037134 GT:DP:GQ:MIN_DP:PL 0/0:73:0:72:0,0,1990 -20 10037135 . A . . END=10037137 GT:DP:GQ:MIN_DP:PL 0/0:70:99:70:0,111,1665 -20 10037138 . G . . END=10037140 GT:DP:GQ:MIN_DP:PL 0/0:70:93:68:0,93,1395 -20 10037141 . A . . END=10037143 GT:DP:GQ:MIN_DP:PL 0/0:70:0:68:0,0,1786 +20 10037111 . G . . END=10037143 GT:DP:GQ:MIN_DP:PL 0/0:77:99:68:0,120,1800 20 10037144 . T TGATAGATA, 1823.73 . DP=70;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=187352.00 GT:AD:DP:GQ:PL:SB 1/1:0,36,0:36:99:1861,127,0,1864,129,1866:0,0,15,21 -20 10037145 . G . . END=10037145 GT:DP:GQ:MIN_DP:PL 0/0:75:0:75:0,0,8 -20 10037146 . A . . END=10037186 GT:DP:GQ:MIN_DP:PL 0/0:70:99:65:0,117,1755 +20 10037145 . G . . END=10037186 GT:DP:GQ:MIN_DP:PL 0/0:70:99:65:0,111,1665 20 10037187 . G . . END=10037187 GT:DP:GQ:MIN_DP:PL 0/0:68:0:68:0,0,2259 20 10037188 . A . . END=10037188 GT:DP:GQ:MIN_DP:PL 0/0:66:99:66:0,120,1800 20 10037189 . T . . END=10037189 GT:DP:GQ:MIN_DP:PL 0/0:67:50:67:0,50,2476 @@ -954,57 +802,24 @@ 20 10038583 . C . . END=10038583 GT:DP:GQ:MIN_DP:PL 0/0:55:91:55:0,91,1806 20 10038584 . A . . END=10039370 GT:DP:GQ:MIN_DP:PL 0/0:76:99:54:0,120,1800 20 10039371 . T G, 1324.77 . BaseQRankSum=-3.260;DP=74;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=266400.00;ReadPosRankSum=0.391 GT:AD:DP:GQ:PL:SB 0/1:34,40,0:74:99:1353,0,1194,1455,1315,2770:15,19,24,16 -20 10039372 . T . . END=10040748 GT:DP:GQ:MIN_DP:PL 0/0:76:99:56:0,105,1575 -20 10040749 . T . . END=10040752 GT:DP:GQ:MIN_DP:PL 0/0:87:87:84:0,87,1305 -20 10040753 . C . . END=10040753 GT:DP:GQ:MIN_DP:PL 0/0:88:90:88:0,90,1350 -20 10040754 . T . . END=10040754 GT:DP:GQ:MIN_DP:PL 0/0:91:81:91:0,81,1215 -20 10040755 . G . . END=10040755 GT:DP:GQ:MIN_DP:PL 0/0:89:69:89:0,69,1035 -20 10040756 . T . . END=10040758 GT:DP:GQ:MIN_DP:PL 0/0:89:45:89:0,45,675 -20 10040759 . T . . END=10040759 GT:DP:GQ:MIN_DP:PL 0/0:89:48:89:0,48,720 -20 10040760 . T . . END=10040760 GT:DP:GQ:MIN_DP:PL 0/0:89:51:89:0,51,765 -20 10040761 . C . . END=10040761 GT:DP:GQ:MIN_DP:PL 0/0:88:48:88:0,48,720 -20 10040762 . T . . END=10040762 GT:DP:GQ:MIN_DP:PL 0/0:87:42:87:0,42,630 -20 10040763 . T . . END=10040763 GT:DP:GQ:MIN_DP:PL 0/0:87:30:87:0,30,450 -20 10040764 . T . . END=10040766 GT:DP:GQ:MIN_DP:PL 0/0:85:39:84:0,39,585 -20 10040767 . C . . END=10040767 GT:DP:GQ:MIN_DP:PL 0/0:83:36:83:0,36,540 -20 10040768 . T . . END=10040771 GT:DP:GQ:MIN_DP:PL 0/0:83:15:81:0,15,225 +20 10039372 . T . . END=10040770 GT:DP:GQ:MIN_DP:PL 0/0:76:99:56:0,120,1800 +20 10040771 . T . . END=10040771 GT:DP:GQ:MIN_DP:PL 0/0:81:60:81:0,60,2763 20 10040772 . C CT, 1995.73 . DP=79;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=211048.00 GT:AD:DP:GQ:PL:SB 1/1:0,70,0:70:99:2033,210,0,2034,210,2034:0,0,37,33 -20 10040773 . T . . END=10040773 GT:DP:GQ:MIN_DP:PL 0/0:81:0:81:0,0,0 -20 10040774 . T . . END=10040795 GT:DP:GQ:MIN_DP:PL 0/0:80:99:77:0,99,1485 -20 10040796 . T . . END=10040797 GT:DP:GQ:MIN_DP:PL 0/0:78:93:77:0,93,1395 -20 10040798 . C . . END=10040798 GT:DP:GQ:MIN_DP:PL 0/0:78:84:78:0,84,1260 -20 10040799 . T . . END=10040801 GT:DP:GQ:MIN_DP:PL 0/0:79:72:78:0,72,1080 -20 10040802 . G . . END=10040803 GT:DP:GQ:MIN_DP:PL 0/0:79:63:78:0,63,945 -20 10040804 . A . . END=10040805 GT:DP:GQ:MIN_DP:PL 0/0:78:57:77:0,57,855 -20 10040806 . T . . END=10040807 GT:DP:GQ:MIN_DP:PL 0/0:79:48:78:0,48,720 -20 10040808 . A . . END=10040809 GT:DP:GQ:MIN_DP:PL 0/0:80:42:79:0,42,630 -20 10040810 . C . . END=10040810 GT:DP:GQ:MIN_DP:PL 0/0:81:15:81:0,15,225 -20 10040811 . A . . END=10040811 GT:DP:GQ:MIN_DP:PL 0/0:80:3:80:0,3,45 +20 10040773 . T . . END=10040811 GT:DP:GQ:MIN_DP:PL 0/0:77:99:75:0,120,1800 20 10040812 . AT A, 2607.73 . DP=79;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=203299.00 GT:AD:DP:GQ:PL:SB 1/1:0,71,0:71:99:2645,214,0,2645,214,2645:0,0,36,35 -20 10040814 . T . . END=10040814 GT:DP:GQ:MIN_DP:PL 0/0:82:0:82:0,0,0 -20 10040815 . T . . END=10040819 GT:DP:GQ:MIN_DP:PL 0/0:79:99:78:0,109,1800 -20 10040820 . T . . END=10040820 GT:DP:GQ:MIN_DP:PL 0/0:77:75:77:0,75,2723 +20 10040814 . T . . END=10040820 GT:DP:GQ:MIN_DP:PL 0/0:78:99:77:0,120,1800 20 10040821 . T A, 1171.77 . BaseQRankSum=-0.021;DP=78;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.097;RAW_MQ=199699.00;ReadPosRankSum=-1.385 GT:AD:DP:GQ:PL:SB 0/1:38,40,0:78:99:1200,0,1099,1314,1219,2533:20,18,21,19 20 10040822 . A . . END=10041303 GT:DP:GQ:MIN_DP:PL 0/0:71:99:54:0,119,1800 20 10041304 . C T, 2765.77 . DP=68;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=239810.00 GT:AD:DP:GQ:PL:SB 1/1:0,68,0:68:99:2794,204,0,2794,204,2794:0,0,34,34 -20 10041305 . G . . END=10041688 GT:DP:GQ:MIN_DP:PL 0/0:61:99:48:0,105,1575 -20 10041689 . T . . END=10041689 GT:DP:GQ:MIN_DP:PL 0/0:72:93:72:0,93,1395 -20 10041690 . C . . END=10041690 GT:DP:GQ:MIN_DP:PL 0/0:72:87:72:0,87,1305 -20 10041691 . A . . END=10041692 GT:DP:GQ:MIN_DP:PL 0/0:73:69:73:0,69,1035 -20 10041693 . T . . END=10041694 GT:DP:GQ:MIN_DP:PL 0/0:76:51:75:0,51,765 -20 10041695 . A . . END=10041695 GT:DP:GQ:MIN_DP:PL 0/0:75:48:75:0,48,720 -20 10041696 . A . . END=10041696 GT:DP:GQ:MIN_DP:PL 0/0:75:45:75:0,45,675 -20 10041697 . A . . END=10041697 GT:DP:GQ:MIN_DP:PL 0/0:75:12:75:0,12,180 +20 10041305 . G . . END=10041697 GT:DP:GQ:MIN_DP:PL 0/0:62:99:48:0,120,1800 20 10041698 . C CAT, 0.04 . BaseQRankSum=1.887;DP=74;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.844;RAW_MQ=265497.00;ReadPosRankSum=0.579 GT:AD:DP:GQ:PL:SB 0/1:48,6,0:54:17:17,0,1425,166,1446,1612:21,27,2,4 -20 10041699 . A . . END=10041699 GT:DP:GQ:MIN_DP:PL 0/0:77:5:77:0,5,2671 -20 10041700 . T . . END=10041700 GT:DP:GQ:MIN_DP:PL 0/0:77:27:77:0,27,405 +20 10041699 . A . . END=10041700 GT:DP:GQ:MIN_DP:PL 0/0:79:99:78:0,120,1800 20 10041701 . A ATG,ATATG, 1403.73 . BaseQRankSum=0.848;DP=78;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=0.340;RAW_MQ=270590.00;ReadPosRankSum=-0.223 GT:AD:DP:GQ:PL:SB 0/2:8,0,48,0:56:58:1441,1582,2726,0,261,58,1575,2317,264,2201:2,6,21,27 -20 10041702 . T . . END=10041702 GT:DP:GQ:MIN_DP:PL 0/0:75:0:75:0,0,0 -20 10041703 . G . . END=10042318 GT:DP:GQ:MIN_DP:PL 0/0:64:99:49:0,117,1800 +20 10041702 . T . . END=10042318 GT:DP:GQ:MIN_DP:PL 0/0:64:99:49:0,117,1800 20 10042319 . C T, 2658.77 . DP=66;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=229851.00 GT:AD:DP:GQ:PL:SB 1/1:0,66,0:66:99:2687,199,0,2687,199,2687:0,0,38,28 20 10042320 . C . . END=10042760 GT:DP:GQ:MIN_DP:PL 0/0:74:99:60:0,120,1800 20 10042761 . A G, 3553.77 . DP=91;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=327600.00 GT:AD:DP:GQ:PL:SB 1/1:0,91,0:91:99:3582,272,0,3582,272,3582:0,0,58,33 -20 10042762 . G . . END=10042828 GT:DP:GQ:MIN_DP:PL 0/0:91:99:79:0,120,1800 +20 10042762 . G . . END=10042828 GT:DP:GQ:MIN_DP:PL 0/0:90:99:78:0,120,1800 20 10042829 . A G, 3055.77 . DP=78;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=278569.00 GT:AD:DP:GQ:PL:SB 1/1:0,78,0:78:99:3084,235,0,3084,235,3084:0,0,42,36 20 10042830 . C . . END=10043001 GT:DP:GQ:MIN_DP:PL 0/0:65:99:56:0,120,1800 20 10043002 . A T, 1287.77 . BaseQRankSum=3.986;DP=86;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=309600.00;ReadPosRankSum=-0.035 GT:AD:DP:GQ:PL:SB 0/1:48,38,0:86:99:1316,0,1659,1460,1773,3233:19,29,18,20 @@ -1014,18 +829,9 @@ 20 10045078 . G T, 3271.77 . DP=81;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=279389.00 GT:AD:DP:GQ:PL:SB 1/1:0,81,0:81:99:3300,244,0,3300,244,3300:0,0,37,44 20 10045079 . C . . END=10045641 GT:DP:GQ:MIN_DP:PL 0/0:71:99:60:0,120,1800 20 10045642 . G C, 3107.77 . DP=81;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=286610.00 GT:AD:DP:GQ:PL:SB 1/1:0,81,0:81:99:3136,243,0,3136,243,3136:0,0,38,43 -20 10045643 . A . . END=10046154 GT:DP:GQ:MIN_DP:PL 0/0:80:99:64:0,108,1620 -20 10046155 . G . . END=10046155 GT:DP:GQ:MIN_DP:PL 0/0:69:93:69:0,93,1395 -20 10046156 . G . . END=10046156 GT:DP:GQ:MIN_DP:PL 0/0:66:81:66:0,81,1215 -20 10046157 . G . . END=10046163 GT:DP:GQ:MIN_DP:PL 0/0:65:72:64:0,72,1080 -20 10046164 . A . . END=10046167 GT:DP:GQ:MIN_DP:PL 0/0:60:54:58:0,54,810 -20 10046168 . A . . END=10046170 GT:DP:GQ:MIN_DP:PL 0/0:61:51:59:0,51,765 -20 10046171 . A . . END=10046172 GT:DP:GQ:MIN_DP:PL 0/0:64:39:63:0,39,585 -20 10046173 . A . . END=10046176 GT:DP:GQ:MIN_DP:PL 0/0:63:21:62:0,21,315 -20 10046177 . A . . END=10046177 GT:DP:GQ:MIN_DP:PL 0/0:60:15:60:0,15,225 +20 10045643 . A . . END=10046177 GT:DP:GQ:MIN_DP:PL 0/0:79:99:58:0,120,1800 20 10046178 . AAGAAAGAAAG A, 2159.73 . DP=61;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=140545.00 GT:AD:DP:GQ:PL:SB 1/1:0,50,0:50:99:2197,152,0,2197,152,2197:0,0,23,27 -20 10046189 . A . . END=10046189 GT:DP:GQ:MIN_DP:PL 0/0:55:0:55:0,0,0 -20 10046190 . G . . END=10046435 GT:DP:GQ:MIN_DP:PL 0/0:67:99:52:0,108,1620 +20 10046189 . A . . END=10046435 GT:DP:GQ:MIN_DP:PL 0/0:67:99:52:0,108,1620 20 10046436 . A . . END=10046438 GT:DP:GQ:MIN_DP:PL 0/0:68:96:65:0,96,1440 20 10046439 . G . . END=10046439 GT:DP:GQ:MIN_DP:PL 0/0:66:99:66:0,99,1485 20 10046440 . G . . END=10046440 GT:DP:GQ:MIN_DP:PL 0/0:66:93:66:0,93,1395 @@ -1061,39 +867,25 @@ 20 10052688 . C A, 1062.77 . BaseQRankSum=0.180;DP=77;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.870;RAW_MQ=274969.00;ReadPosRankSum=1.443 GT:AD:DP:GQ:PL:SB 0/1:45,32,0:77:99:1091,0,1645,1226,1741,2967:27,18,16,16 20 10052689 . A . . END=10058021 GT:DP:GQ:MIN_DP:PL 0/0:74:99:36:0,99,1485 20 10058022 . T C, 975.77 . BaseQRankSum=-2.346;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.466;RAW_MQ=237579.00;ReadPosRankSum=0.018 GT:AD:DP:GQ:PL:SB 0/1:36,32,0:68:99:1004,0,1261,1112,1357,2469:16,20,13,19 -20 10058023 . A . . END=10062927 GT:DP:GQ:MIN_DP:PL 0/0:76:99:47:0,99,1485 -20 10062928 . T . . END=10062929 GT:DP:GQ:MIN_DP:PL 0/0:47:90:46:0,90,1350 -20 10062930 . T . . END=10062930 GT:DP:GQ:MIN_DP:PL 0/0:48:81:48:0,81,1215 -20 10062931 . G . . END=10062931 GT:DP:GQ:MIN_DP:PL 0/0:47:78:47:0,78,1170 -20 10062932 . T . . END=10062934 GT:DP:GQ:MIN_DP:PL 0/0:48:81:47:0,81,1215 +20 10058023 . A . . END=10062934 GT:DP:GQ:MIN_DP:PL 0/0:76:99:46:0,105,1575 20 10062935 . CAAA C,CA,CAA,CAAAA, 92.84 . BaseQRankSum=1.336;DP=79;ExcessHet=3.0103;MLEAC=0,0,0,1,0;MLEAF=0.00,0.00,0.00,0.500,0.00;MQRankSum=-1.405;RAW_MQ=232368.00;ReadPosRankSum=-0.986 GT:AD:DP:GQ:PL:SB 0/4:5,2,2,4,10,0:23:16:130,219,1823,163,1171,1044,115,628,576,505,0,158,82,16,101,243,986,887,608,171,888:2,3,9,9 20 10062939 . A . . END=10062955 GT:DP:GQ:MIN_DP:PL 0/0:82:99:74:0,120,1800 20 10062956 . T . . END=10062956 GT:DP:GQ:MIN_DP:PL 0/0:69:80:69:0,80,2241 20 10062957 . C . . END=10065775 GT:DP:GQ:MIN_DP:PL 0/0:70:99:42:0,105,1575 20 10065776 . C . . END=10065776 GT:DP:GQ:MIN_DP:PL 0/0:49:76:49:0,76,1707 20 10065777 . A . . END=10065777 GT:DP:GQ:MIN_DP:PL 0/0:48:94:48:0,94,1738 -20 10065778 . T . . END=10065778 GT:DP:GQ:MIN_DP:PL 0/0:48:99:48:0,111,1665 -20 10065779 . G . . END=10065779 GT:DP:GQ:MIN_DP:PL 0/0:52:0:52:0,0,1215 +20 10065778 . T . . END=10065778 GT:DP:GQ:MIN_DP:PL 0/0:48:99:48:0,120,1800 +20 10065779 . G . . END=10065779 GT:DP:GQ:MIN_DP:PL 0/0:52:0:52:0,0,1441 20 10065780 . T . . END=10065780 GT:DP:GQ:MIN_DP:PL 0/0:61:38:61:0,38,2046 20 10065781 . T . . END=10065781 GT:DP:GQ:MIN_DP:PL 0/0:71:75:71:0,75,1125 20 10065782 . T . . END=10065802 GT:DP:GQ:MIN_DP:PL 0/0:82:99:65:0,108,1620 20 10065803 . G . . END=10065803 GT:DP:GQ:MIN_DP:PL 0/0:59:81:59:0,81,2051 -20 10065804 . C . . END=10067041 GT:DP:GQ:MIN_DP:PL 0/0:72:99:48:0,103,1665 -20 10067042 . A . . END=10067043 GT:DP:GQ:MIN_DP:PL 0/0:52:90:52:0,90,1350 -20 10067044 . T . . END=10067045 GT:DP:GQ:MIN_DP:PL 0/0:52:84:52:0,84,1260 -20 10067046 . T . . END=10067046 GT:DP:GQ:MIN_DP:PL 0/0:52:75:52:0,75,1125 -20 10067047 . A . . END=10067048 GT:DP:GQ:MIN_DP:PL 0/0:51:66:50:0,66,990 +20 10065804 . C . . END=10067046 GT:DP:GQ:MIN_DP:PL 0/0:72:99:48:0,102,1530 +20 10067047 . A . . END=10067048 GT:DP:GQ:MIN_DP:PL 0/0:51:96:50:0,96,1440 20 10067049 . TAAAAAAAAA T,TA,TAA, 613.73 . BaseQRankSum=0.177;DP=69;ExcessHet=3.0103;MLEAC=0,1,1,0;MLEAF=0.00,0.500,0.500,0.00;MQRankSum=-0.342;RAW_MQ=204256.00;ReadPosRankSum=-1.322 GT:AD:DP:GQ:PL:SB 2/3:2,4,7,9,0:22:99:651,365,925,164,381,340,135,101,0,106,443,591,394,170,627:1,1,12,8 -20 10067059 . A . . END=10067060 GT:DP:GQ:MIN_DP:PL 0/0:57:87:56:0,87,1305 -20 10067061 . A . . END=10067061 GT:DP:GQ:MIN_DP:PL 0/0:59:90:59:0,90,1350 -20 10067062 . A . . END=10067066 GT:DP:GQ:MIN_DP:PL 0/0:61:99:56:0,99,1485 -20 10067067 . A . . END=10067067 GT:DP:GQ:MIN_DP:PL 0/0:52:19:52:0,19,1692 -20 10067068 . A . . END=10067068 GT:DP:GQ:MIN_DP:PL 0/0:47:0:47:0,0,1430 -20 10067069 . A . . END=10067069 GT:DP:GQ:MIN_DP:PL 0/0:42:26:42:0,26,1402 -20 10067070 . A . . END=10067070 GT:DP:GQ:MIN_DP:PL 0/0:40:84:40:0,84,1498 -20 10067071 . A . . END=10067075 GT:DP:GQ:MIN_DP:PL 0/0:41:99:39:0,105,1471 -20 10067076 . A . . END=10067076 GT:DP:GQ:MIN_DP:PL 0/0:44:97:44:0,97,1535 -20 10067077 . G . . END=10067089 GT:DP:GQ:MIN_DP:PL 0/0:48:99:45:0,110,1645 +20 10067059 . A . . END=10067067 GT:DP:GQ:MIN_DP:PL 0/0:57:99:50:0,99,1485 +20 10067068 . A . . END=10067070 GT:DP:GQ:MIN_DP:PL 0/0:44:96:44:0,96,1440 +20 10067071 . A . . END=10067089 GT:DP:GQ:MIN_DP:PL 0/0:48:99:46:0,102,1530 20 10067090 . C A, 2004.77 . DP=55;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=165948.00 GT:AD:DP:GQ:PL:SB 1/1:0,55,0:55:99:2033,164,0,2033,164,2033:0,0,27,28 20 10067091 . T . . END=10067263 GT:DP:GQ:MIN_DP:PL 0/0:76:99:50:0,120,1800 20 10067264 . G A, 2922.77 . DP=73;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=257282.00 GT:AD:DP:GQ:PL:SB 1/1:0,73,0:73:99:2951,219,0,2951,219,2951:0,0,38,35 @@ -1110,16 +902,15 @@ 20 10068034 . G . . END=10068040 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 20 10068041 . T . . END=10068043 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,1350 20 10068044 . T . . END=10068135 GT:DP:GQ:MIN_DP:PL 0/0:43:99:34:0,99,1485 -20 10068136 . A . . END=10068140 GT:DP:GQ:MIN_DP:PL 0/0:40:84:39:0,84,1260 -20 10068141 . T . . END=10068141 GT:DP:GQ:MIN_DP:PL 0/0:39:90:39:0,90,1350 -20 10068142 . C . . END=10068142 GT:DP:GQ:MIN_DP:PL 0/0:38:84:38:0,84,1260 -20 10068143 . T . . END=10068148 GT:DP:GQ:MIN_DP:PL 0/0:35:75:31:0,75,1125 -20 10068149 . T . . END=10068151 GT:DP:GQ:MIN_DP:PL 0/0:31:63:31:0,63,945 -20 10068152 . A . . END=10068155 GT:DP:GQ:MIN_DP:PL 0/0:29:57:28:0,57,855 -20 10068156 . A . . END=10068157 GT:DP:GQ:MIN_DP:PL 0/0:27:51:27:0,51,765 +20 10068136 . A . . END=10068138 GT:DP:GQ:MIN_DP:PL 0/0:40:87:40:0,87,1305 +20 10068139 . T . . END=10068141 GT:DP:GQ:MIN_DP:PL 0/0:39:90:39:0,90,1350 +20 10068142 . C . . END=10068148 GT:DP:GQ:MIN_DP:PL 0/0:35:81:31:0,81,1215 +20 10068149 . T . . END=10068150 GT:DP:GQ:MIN_DP:PL 0/0:31:75:31:0,75,1125 +20 10068151 . A . . END=10068155 GT:DP:GQ:MIN_DP:PL 0/0:29:63:28:0,63,945 +20 10068156 . A . . END=10068157 GT:DP:GQ:MIN_DP:PL 0/0:27:57:27:0,57,855 20 10068158 . GTGTATATATATA G, 66.73 . BaseQRankSum=-0.652;DP=29;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.328;RAW_MQ=93364.00;ReadPosRankSum=0.524 GT:AD:DP:GQ:PL:SB 0/1:3,4,0:7:57:104,0,57,114,69,183:0,3,2,2 20 10068160 . GTATATATATATGTA G,*, 697.73 . DP=28;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;RAW_MQ=87005.00 GT:AD:DP:GQ:PL:SB 1/2:0,2,4,0:6:53:735,162,131,102,0,53,507,174,108,472:0,0,2,4 -20 10068175 . T . . END=10068175 GT:DP:GQ:MIN_DP:PL 0/0:20:17:20:0,17,729 +20 10068175 . T . . END=10068175 GT:DP:GQ:MIN_DP:PL 0/0:20:18:20:0,18,270 20 10068176 . A . . END=10068180 GT:DP:GQ:MIN_DP:PL 0/0:19:24:17:0,24,360 20 10068181 . T . . END=10068185 GT:DP:GQ:MIN_DP:PL 0/0:16:27:16:0,27,405 20 10068186 . A . . END=10068186 GT:DP:GQ:MIN_DP:PL 0/0:16:9:16:0,9,570 @@ -1133,16 +924,14 @@ 20 10068200 . A . . END=10068200 GT:DP:GQ:MIN_DP:PL 0/0:16:45:16:0,45,675 20 10068201 . T . . END=10068201 GT:DP:GQ:MIN_DP:PL 0/0:18:51:18:0,51,765 20 10068202 . A . . END=10068203 GT:DP:GQ:MIN_DP:PL 0/0:19:54:19:0,54,810 -20 10068204 . A . . END=10068206 GT:DP:GQ:MIN_DP:PL 0/0:21:57:20:0,57,855 -20 10068207 . C . . END=10068209 GT:DP:GQ:MIN_DP:PL 0/0:22:60:21:0,60,900 -20 10068210 . T . . END=10068215 GT:DP:GQ:MIN_DP:PL 0/0:26:75:26:0,75,960 -20 10068216 . C . . END=10068216 GT:DP:GQ:MIN_DP:PL 0/0:27:81:27:0,81,1065 -20 10068217 . C . . END=10068217 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20 10068218 . A . . END=10068223 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,1215 -20 10068224 . G . . END=10068225 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,1350 -20 10068226 . T . . END=10068227 GT:DP:GQ:MIN_DP:PL 0/0:32:87:31:0,87,1305 -20 10068228 . C . . END=10068228 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20 10068229 . T . . END=10068237 GT:DP:GQ:MIN_DP:PL 0/0:32:87:30:0,87,1305 +20 10068204 . A . . END=10068205 GT:DP:GQ:MIN_DP:PL 0/0:21:57:20:0,57,855 +20 10068206 . C . . END=10068206 GT:DP:GQ:MIN_DP:PL 0/0:21:54:21:0,54,810 +20 10068207 . C . . END=10068208 GT:DP:GQ:MIN_DP:PL 0/0:22:57:21:0,57,855 +20 10068209 . C . . END=10068209 GT:DP:GQ:MIN_DP:PL 0/0:23:63:23:0,63,945 +20 10068210 . T . . END=10068219 GT:DP:GQ:MIN_DP:PL 0/0:27:72:26:0,72,1080 +20 10068220 . C . . END=10068224 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 +20 10068225 . G . . END=10068225 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 +20 10068226 . T . . END=10068237 GT:DP:GQ:MIN_DP:PL 0/0:32:84:30:0,84,1260 20 10068238 . T . . END=10068247 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,1168 20 10068248 . T . . END=10068290 GT:DP:GQ:MIN_DP:PL 0/0:38:99:34:0,102,1384 20 10068291 . C . . END=10068299 GT:DP:GQ:MIN_DP:PL 0/0:40:90:36:0,90,1350 @@ -1168,20 +957,13 @@ 20 10068981 . G A, 2503.77 . DP=61;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=219600.00 GT:AD:DP:GQ:PL:SB 1/1:0,61,0:61:99:2532,184,0,2532,184,2532:0,0,27,34 20 10068982 . A . . END=10070601 GT:DP:GQ:MIN_DP:PL 0/0:74:99:46:0,120,1800 20 10070602 . T C, 2691.77 . DP=72;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=248164.00 GT:AD:DP:GQ:PL:SB 1/1:0,72,0:72:99:2720,216,0,2720,216,2720:0,0,37,35 -20 10070603 . A . . END=10070920 GT:DP:GQ:MIN_DP:PL 0/0:90:99:66:0,99,1485 -20 10070921 . C . . END=10070921 GT:DP:GQ:MIN_DP:PL 0/0:91:90:91:0,90,1350 -20 10070922 . A . . END=10070923 GT:DP:GQ:MIN_DP:PL 0/0:92:57:91:0,57,855 -20 10070924 . T . . END=10070924 GT:DP:GQ:MIN_DP:PL 0/0:89:18:89:0,18,270 -20 10070925 . C . . END=10070926 GT:DP:GQ:MIN_DP:PL 0/0:87:12:86:0,12,180 -20 10070927 . C . . END=10070928 GT:DP:GQ:MIN_DP:PL 0/0:84:3:83:0,3,45 -20 10070929 . A . . END=10070935 GT:DP:GQ:MIN_DP:PL 0/0:85:0:85:0,0,0 +20 10070603 . A . . END=10070935 GT:DP:GQ:MIN_DP:PL 0/0:90:99:66:0,120,1800 20 10070936 . T A, 3631.77 . DP=81;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=279633.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,81,0:81:99:0|1:10070936_T_A:3660,247,0,3660,247,3660:0,0,44,37 -20 10070937 . A . . END=10070937 GT:DP:GQ:MIN_DP:PL 0/0:84:3:84:0,3,45 +20 10070937 . A . . END=10070937 GT:DP:GQ:MIN_DP:PL 0/0:80:99:80:0,120,1800 20 10070938 . G GA, 3656.73 . DP=79;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=275964.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,79,0:79:99:0|1:10070936_T_A:3694,250,0,3694,250,3694:0,0,43,36 -20 10070939 . A . . END=10070939 GT:DP:GQ:MIN_DP:PL 0/0:83:0:83:0,0,0 -20 10070940 . G . . END=10071134 GT:DP:GQ:MIN_DP:PL 0/0:77:99:67:0,120,1800 +20 10070939 . A . . END=10071134 GT:DP:GQ:MIN_DP:PL 0/0:77:99:67:0,120,1800 20 10071135 . C T, 3257.77 . DP=79;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=276123.00 GT:AD:DP:GQ:PL:SB 1/1:0,79,0:79:99:3286,238,0,3286,238,3286:0,0,34,45 -20 10071136 . T . . END=10071186 GT:DP:GQ:MIN_DP:PL 0/0:83:99:78:0,120,1800 +20 10071136 . T . . END=10071186 GT:DP:GQ:MIN_DP:PL 0/0:83:99:77:0,120,1800 20 10071187 . G A, 3410.77 . DP=82;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=292441.00 GT:AD:DP:GQ:PL:SB 1/1:0,82,0:82:99:3439,246,0,3439,246,3439:0,0,30,52 20 10071188 . G . . END=10071889 GT:DP:GQ:MIN_DP:PL 0/0:61:99:44:0,111,1710 20 10071890 . T C, 1974.77 . DP=57;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=202969.00 GT:AD:DP:GQ:PL:SB 1/1:0,57,0:57:99:2003,171,0,2003,171,2003:0,0,28,29 @@ -1205,30 +987,19 @@ 20 10075142 . G . . END=10075142 GT:DP:GQ:MIN_DP:PL 0/0:65:91:65:0,91,2199 20 10075143 . A . . END=10075167 GT:DP:GQ:MIN_DP:PL 0/0:81:99:68:0,120,1800 20 10075168 . C T, 3612.77 . DP=88;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=309981.00 GT:AD:DP:GQ:PL:SB 1/1:0,88,0:88:99:3641,264,0,3641,264,3641:0,0,38,50 -20 10075169 . G . . END=10075488 GT:DP:GQ:MIN_DP:PL 0/0:67:99:49:0,99,1485 -20 10075489 . C . . END=10075490 GT:DP:GQ:MIN_DP:PL 0/0:70:90:70:0,90,1350 -20 10075491 . G . . END=10075492 GT:DP:GQ:MIN_DP:PL 0/0:71:75:70:0,75,1125 -20 10075493 . G . . END=10075495 GT:DP:GQ:MIN_DP:PL 0/0:72:63:71:0,63,945 -20 10075496 . G . . END=10075497 GT:DP:GQ:MIN_DP:PL 0/0:73:54:73:0,54,810 -20 10075498 . T . . END=10075498 GT:DP:GQ:MIN_DP:PL 0/0:72:42:72:0,42,630 -20 10075499 . G . . END=10075499 GT:DP:GQ:MIN_DP:PL 0/0:73:33:73:0,33,495 -20 10075500 . A . . END=10075500 GT:DP:GQ:MIN_DP:PL 0/0:73:27:73:0,27,405 -20 10075501 . T . . END=10075502 GT:DP:GQ:MIN_DP:PL 0/0:72:21:71:0,21,315 -20 10075503 . A . . END=10075506 GT:DP:GQ:MIN_DP:PL 0/0:75:3:72:0,3,45 -20 10075507 . A . . END=10075507 GT:DP:GQ:MIN_DP:PL 0/0:80:6:80:0,6,90 +20 10075169 . G . . END=10075507 GT:DP:GQ:MIN_DP:PL 0/0:68:99:49:0,119,1800 20 10075508 . GA G, 1928.73 . DP=77;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=288121.00 GT:AD:DP:GQ:PL:SB 1/1:0,70,0:70:99:1966,210,0,1966,210,1966:0,0,29,41 -20 10075510 . A . . END=10075510 GT:DP:GQ:MIN_DP:PL 0/0:80:0:80:0,0,0 -20 10075511 . A . . END=10076249 GT:DP:GQ:MIN_DP:PL 0/0:76:99:55:0,120,1800 +20 10075510 . A . . END=10076249 GT:DP:GQ:MIN_DP:PL 0/0:76:99:55:0,120,1800 20 10076250 . A G, 1107.77 . BaseQRankSum=-3.386;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.423;RAW_MQ=278666.00;ReadPosRankSum=0.270 GT:AD:DP:GQ:PL:SB 0/1:40,39,0:79:99:1136,0,1339,1257,1456,2712:14,26,20,19 20 10076251 . A . . END=10076338 GT:DP:GQ:MIN_DP:PL 0/0:70:99:62:0,120,1800 20 10076339 . A G, 1309.77 . BaseQRankSum=-0.069;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.866;RAW_MQ=256441.00;ReadPosRankSum=1.015 GT:AD:DP:GQ:PL:SB 0/1:32,40,0:72:99:1338,0,1035,1435,1156,2590:12,20,18,22 -20 10076340 . A . . END=10076398 GT:DP:GQ:MIN_DP:PL 0/0:88:99:72:0,120,1800 +20 10076340 . A . . END=10076398 GT:DP:GQ:MIN_DP:PL 0/0:88:99:71:0,120,1800 20 10076399 . G A, 1807.77 . BaseQRankSum=4.154;DP=94;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=338400.00;ReadPosRankSum=-1.058 GT:AD:DP:GQ:PL:SB 0/1:44,50,0:94:99:1836,0,1544,1969,1694,3663:22,22,22,28 -20 10076400 . G . . END=10076988 GT:DP:GQ:MIN_DP:PL 0/0:73:99:51:0,102,1530 +20 10076400 . G . . END=10076988 GT:DP:GQ:MIN_DP:PL 0/0:73:99:51:0,120,1800 20 10076989 . CAA C,CA,CAAA, 214.73 . BaseQRankSum=-0.625;DP=75;ExcessHet=3.0103;MLEAC=0,1,1,0;MLEAF=0.00,0.500,0.500,0.00;MQRankSum=-0.473;RAW_MQ=253446.00;ReadPosRankSum=-0.918 GT:AD:DP:GQ:PL:SB 2/3:7,3,13,7,0:30:41:252,271,1146,41,448,376,147,276,0,361,322,712,423,318,705:4,3,12,11 -20 10076992 . A . . END=10077007 GT:DP:GQ:MIN_DP:PL 0/0:72:99:61:0,113,1800 +20 10076992 . A . . END=10077007 GT:DP:GQ:MIN_DP:PL 0/0:69:99:59:0,120,1800 20 10077008 . T A, 0 . BaseQRankSum=-1.806;DP=51;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.608;RAW_MQ=175323.00;ReadPosRankSum=0.805 GT:AD:DP:GQ:PGT:PID:PL:SB 0/0:46,4,0:50:42:0|1:10077008_T_A:0,42,2066,148,2078,2184:18,28,4,0 -20 10077009 . A . . END=10077009 GT:DP:GQ:MIN_DP:PL 0/0:54:99:54:0,120,1800 +20 10077009 . A . . END=10077009 GT:DP:GQ:MIN_DP:PL 0/0:52:99:52:0,120,1800 20 10077010 . G A, 0 . BaseQRankSum=-1.841;DP=53;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.658;RAW_MQ=182523.00;ReadPosRankSum=0.911 GT:AD:DP:GQ:PGT:PID:PL:SB 0/0:48,4,0:52:42:0|1:10077008_T_A:0,42,2066,148,2078,2184:18,30,4,0 20 10077011 . A . . END=10077751 GT:DP:GQ:MIN_DP:PL 0/0:69:99:44:0,102,1654 20 10077752 . T C, 1345.77 . BaseQRankSum=-6.503;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=284400.00;ReadPosRankSum=-0.352 GT:AD:DP:GQ:PL:SB 0/1:34,45,0:79:99:1374,0,1187,1477,1322,2799:16,18,16,29 @@ -1273,25 +1044,27 @@ 20 10087394 . T G, 1688.77 . BaseQRankSum=-2.340;DP=84;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.207;RAW_MQ=299641.00;ReadPosRankSum=0.885 GT:AD:DP:GQ:PL:SB 0/1:35,49,0:84:99:1717,0,1186,1823,1334,3156:21,14,24,25 20 10087395 . T . . END=10087753 GT:DP:GQ:MIN_DP:PL 0/0:83:99:61:0,120,1800 20 10087754 . T G, 1347.77 . BaseQRankSum=0.355;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.193;RAW_MQ=288141.00;ReadPosRankSum=-0.551 GT:AD:DP:GQ:PL:SB 0/1:37,41,0:78:99:1376,0,1239,1488,1362,2849:23,14,24,17 -20 10087755 . G . . END=10087803 GT:DP:GQ:MIN_DP:PL 0/0:102:99:83:0,120,1800 +20 10087755 . G . . END=10087803 GT:DP:GQ:MIN_DP:PL 0/0:100:99:81:0,120,1800 20 10087804 . C T, 1619.77 . BaseQRankSum=1.940;DP=100;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.618;RAW_MQ=369310.00;ReadPosRankSum=0.341 GT:AD:DP:GQ:PL:SB 0/1:50,50,0:100:99:1648,0,1511,1797,1661,3458:33,17,28,22 -20 10087805 . G . . END=10087819 GT:DP:GQ:MIN_DP:PL 0/0:101:99:97:0,120,1800 +20 10087805 . G . . END=10087819 GT:DP:GQ:MIN_DP:PL 0/0:101:99:96:0,120,1800 20 10087820 . CAG C,CAGAG, 428.73 . BaseQRankSum=-1.974;DP=99;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=0.422;RAW_MQ=362700.00;ReadPosRankSum=-0.357 GT:AD:DP:GQ:PL:SB 0/2:35,0,18,0:53:99:466,669,2577,0,1197,1168,661,2237,1238,2189:17,18,8,10 -20 10087823 . A . . END=10087841 GT:DP:GQ:MIN_DP:PL 0/0:87:99:83:0,120,1800 -20 10087842 . A . . END=10087842 GT:DP:GQ:MIN_DP:PL 0/0:82:64:82:0,64,2763 -20 10087843 . A . . END=10088062 GT:DP:GQ:MIN_DP:PL 0/0:95:99:71:0,120,1800 +20 10087823 . A . . END=10087841 GT:DP:GQ:MIN_DP:PL 0/0:86:99:83:0,120,1800 +20 10087842 . A . . END=10087842 GT:DP:GQ:MIN_DP:PL 0/0:82:0:82:0,0,2206 +20 10087843 . A . . END=10087843 GT:DP:GQ:MIN_DP:PL 0/0:82:73:82:0,73,2973 +20 10087844 . G . . END=10087844 GT:DP:GQ:MIN_DP:PL 0/0:80:0:80:0,0,2190 +20 10087845 . A . . END=10088062 GT:DP:GQ:MIN_DP:PL 0/0:95:99:71:0,120,1800 20 10088063 . C T, 1417.77 . BaseQRankSum=3.405;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.515;RAW_MQ=327579.00;ReadPosRankSum=0.285 GT:AD:DP:GQ:PL:SB 0/1:49,44,0:93:99:1446,0,1403,1592,1535,3128:24,25,18,26 20 10088064 . G . . END=10088698 GT:DP:GQ:MIN_DP:PL 0/0:87:99:60:0,120,1800 20 10088699 . C T, 776.77 . BaseQRankSum=3.803;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.140;RAW_MQ=199738.00;ReadPosRankSum=-1.456 GT:AD:DP:GQ:PL:SB 0/1:36,26,0:62:99:805,0,1088,913,1166,2079:15,21,19,7 -20 10088700 . G . . END=10088729 GT:DP:GQ:MIN_DP:PL 0/0:54:99:52:0,120,1800 +20 10088700 . G . . END=10088729 GT:DP:GQ:MIN_DP:PL 0/0:53:99:51:0,120,1800 20 10088730 . G A, 972.77 . BaseQRankSum=0.224;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.839;RAW_MQ=148358.00;ReadPosRankSum=0.581 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:29,23,0:52:99:0|1:10088730_G_A:1001,0,1152,1092,1231,2322:11,18,16,7 -20 10088731 . G . . END=10088735 GT:DP:GQ:MIN_DP:PL 0/0:56:99:56:0,120,1800 +20 10088731 . G . . END=10088735 GT:DP:GQ:MIN_DP:PL 0/0:55:99:55:0,120,1800 20 10088736 . A C, 1081.77 . BaseQRankSum=0.282;DP=55;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.169;RAW_MQ=149682.00;ReadPosRankSum=0.573 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:28,27,0:55:99:0|1:10088730_G_A:1110,0,1194,1203,1281,2484:10,18,16,11 -20 10088737 . C . . END=10088746 GT:DP:GQ:MIN_DP:PL 0/0:57:99:53:0,120,1800 +20 10088737 . C . . END=10088746 GT:DP:GQ:MIN_DP:PL 0/0:56:99:53:0,120,1800 20 10088747 . A G, 1111.77 . BaseQRankSum=-3.877;DP=55;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.907;RAW_MQ=146239.00;ReadPosRankSum=0.009 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:25,29,0:54:99:0|1:10088730_G_A:1140,0,995,1219,1085,2304:10,15,18,11 -20 10088748 . G . . END=10088798 GT:DP:GQ:MIN_DP:PL 0/0:50:99:46:0,109,1710 +20 10088748 . G . . END=10088798 GT:DP:GQ:MIN_DP:PL 0/0:49:99:46:0,114,1710 20 10088799 . G A, 1018.77 . BaseQRankSum=5.503;DP=53;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.498;RAW_MQ=150040.00;ReadPosRankSum=1.075 GT:AD:DP:GQ:PL:SB 0/1:22,31,0:53:99:1047,0,617,1114,711,1824:14,8,12,19 -20 10088800 . T . . END=10088831 GT:DP:GQ:MIN_DP:PL 0/0:54:99:50:0,108,1800 +20 10088800 . T . . END=10088831 GT:DP:GQ:MIN_DP:PL 0/0:54:99:50:0,113,1800 20 10088832 . G . . END=10088842 GT:DP:GQ:MIN_DP:PL 0/0:53:63:36:0,63,945 20 10088843 . C . . END=10088843 GT:DP:GQ:MIN_DP:PL 0/0:25:16:25:0,16,759 20 10088844 . A . . END=10088844 GT:DP:GQ:MIN_DP:PL 0/0:25:37:25:0,37,718 @@ -1310,17 +1083,11 @@ 20 10088867 . A . . END=10088870 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 20 10088871 . T . . END=10088894 GT:DP:GQ:MIN_DP:PL 0/0:39:99:33:0,99,1294 20 10088895 . C T, 532.77 . BaseQRankSum=2.462;DP=41;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.577;RAW_MQ=134450.00;ReadPosRankSum=1.301 GT:AD:DP:GQ:PL:SB 0/1:23,18,0:41:99:561,0,673,630,726,1356:10,13,8,10 -20 10088896 . G . . END=10088963 GT:DP:GQ:MIN_DP:PL 0/0:50:99:42:0,99,1485 -20 10088964 . G . . END=10088964 GT:DP:GQ:MIN_DP:PL 0/0:68:61:68:0,61,1979 -20 10088965 . T . . END=10088965 GT:DP:GQ:MIN_DP:PL 0/0:68:55:68:0,55,2178 -20 10088966 . C . . END=10088967 GT:DP:GQ:MIN_DP:PL 0/0:71:0:70:0,0,2081 +20 10088896 . G . . END=10088967 GT:DP:GQ:MIN_DP:PL 0/0:49:99:42:0,110,1709 20 10088968 . C CAAA, 1175.73 . BaseQRankSum=0.552;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.750;RAW_MQ=177808.00;ReadPosRankSum=2.416 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:30,23,0:53:99:0|1:10088968_C_CAAA:1213,0,1367,1310,1463,2773:16,14,14,9 -20 10088969 . A . . END=10088969 GT:DP:GQ:MIN_DP:PL 0/0:72:0:72:0,0,1374 -20 10088970 . A . . END=10088978 GT:DP:GQ:MIN_DP:PL 0/0:76:99:75:0,120,1800 -20 10088979 . A . . END=10088979 GT:DP:GQ:MIN_DP:PL 0/0:78:57:78:0,57,2694 +20 10088969 . A . . END=10088979 GT:DP:GQ:MIN_DP:PL 0/0:71:99:70:0,120,1800 20 10088980 . T C, 1247.77 . BaseQRankSum=-1.585;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.232;RAW_MQ=176353.00;ReadPosRankSum=1.288 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:37,31,0:68:99:0|1:10088968_C_CAAA:1276,0,1627,1394,1729,3123:19,18,15,16 -20 10088981 . A . . END=10088981 GT:DP:GQ:MIN_DP:PL 0/0:78:40:78:0,40,2558 -20 10088982 . A . . END=10088984 GT:DP:GQ:MIN_DP:PL 0/0:78:99:77:0,120,1800 +20 10088981 . A . . END=10088984 GT:DP:GQ:MIN_DP:PL 0/0:71:99:69:0,120,1800 20 10088985 . T C, 1178.77 . BaseQRankSum=-0.192;DP=74;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.248;RAW_MQ=191764.00;ReadPosRankSum=1.228 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:42,32,0:74:99:0|1:10088968_C_CAAA:1207,0,1729,1333,1826,3159:22,20,15,17 20 10088986 . A . . END=10088989 GT:DP:GQ:MIN_DP:PL 0/0:82:99:81:0,120,1800 20 10088990 . A . . END=10088990 GT:DP:GQ:MIN_DP:PL 0/0:84:7:84:0,7,2771 @@ -1336,15 +1103,11 @@ 20 10089043 . T . . END=10089043 GT:DP:GQ:MIN_DP:PL 0/0:76:79:76:0,79,2231 20 10089044 . G . . END=10089440 GT:DP:GQ:MIN_DP:PL 0/0:82:99:74:0,120,1800 20 10089441 . A G, 1179.77 . BaseQRankSum=-4.885;DP=76;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.948;RAW_MQ=270841.00;ReadPosRankSum=-0.156 GT:AD:DP:GQ:PL:SB 0/1:37,39,0:76:99:1208,0,1313,1319,1430,2749:19,18,14,25 -20 10089442 . G . . END=10089524 GT:DP:GQ:MIN_DP:PL 0/0:82:99:74:0,120,1800 +20 10089442 . G . . END=10089524 GT:DP:GQ:MIN_DP:PL 0/0:81:99:74:0,120,1800 20 10089525 . C T, 1548.77 . BaseQRankSum=5.859;DP=81;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.531;RAW_MQ=286610.00;ReadPosRankSum=0.862 GT:AD:DP:GQ:PL:SB 0/1:38,43,0:81:99:1577,0,1088,1691,1217,2908:22,16,20,23 -20 10089526 . G . . END=10090283 GT:DP:GQ:MIN_DP:PL 0/0:73:99:55:0,108,1620 -20 10090284 . A . . END=10090284 GT:DP:GQ:MIN_DP:PL 0/0:69:87:69:0,87,1305 -20 10090285 . A . . END=10090287 GT:DP:GQ:MIN_DP:PL 0/0:70:90:70:0,90,1350 -20 10090288 . C . . END=10090288 GT:DP:GQ:MIN_DP:PL 0/0:70:78:70:0,78,1170 +20 10089526 . G . . END=10090288 GT:DP:GQ:MIN_DP:PL 0/0:72:99:55:0,111,1800 20 10090289 . CAA C,CA, 384.73 . BaseQRankSum=0.441;DP=80;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=1.393;RAW_MQ=287682.00;ReadPosRankSum=0.048 GT:AD:DP:GQ:PL:SB 0/2:14,4,20,0:38:99:422,360,986,0,261,230,477,867,348,928:7,7,11,13 -20 10090292 . A . . END=10090292 GT:DP:GQ:MIN_DP:PL 0/0:79:38:79:0,38,2756 -20 10090293 . A . . END=10090763 GT:DP:GQ:MIN_DP:PL 0/0:75:99:61:0,120,1800 +20 10090292 . A . . END=10090763 GT:DP:GQ:MIN_DP:PL 0/0:75:99:61:0,120,1800 20 10090764 . A G, 840.77 . BaseQRankSum=-2.659;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=226800.00;ReadPosRankSum=1.207 GT:AD:DP:GQ:PL:SB 0/1:34,29,0:63:99:869,0,1207,972,1294,2265:12,22,14,15 20 10090765 . A . . END=10090969 GT:DP:GQ:MIN_DP:PL 0/0:75:99:65:0,120,1800 20 10090970 . T C, 1257.77 . BaseQRankSum=-0.484;DP=69;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.509;RAW_MQ=243938.00;ReadPosRankSum=-0.072 GT:AD:DP:GQ:PL:SB 0/1:33,36,0:69:99:1286,0,1092,1384,1201,2585:20,13,20,16 @@ -1354,13 +1117,9 @@ 20 10092415 . A G, 1635.77 . BaseQRankSum=-6.731;DP=101;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=363600.00;ReadPosRankSum=0.082 GT:AD:DP:GQ:PL:SB 0/1:52,49,0:101:99:1664,0,1902,1820,2049,3870:27,25,24,25 20 10092416 . G . . END=10092926 GT:DP:GQ:MIN_DP:PL 0/0:80:99:60:0,120,1800 20 10092927 . G T, 106.77 . BaseQRankSum=-2.507;DP=73;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.009;RAW_MQ=257282.00;ReadPosRankSum=-0.220 GT:AD:DP:GQ:PL:SB 0/1:59,13,0:72:99:135,0,1864,310,1901,2211:43,16,0,13 -20 10092928 . T . . END=10093558 GT:DP:GQ:MIN_DP:PL 0/0:79:99:57:0,111,1665 -20 10093559 . T . . END=10093562 GT:DP:GQ:MIN_DP:PL 0/0:62:90:60:0,90,1350 -20 10093563 . G . . END=10093566 GT:DP:GQ:MIN_DP:PL 0/0:61:84:60:0,84,1260 -20 10093567 . G . . END=10093567 GT:DP:GQ:MIN_DP:PL 0/0:59:75:59:0,75,1125 +20 10092928 . T . . END=10093567 GT:DP:GQ:MIN_DP:PL 0/0:79:99:57:0,120,1800 20 10093568 . GTT G,GT,GTTT, 326.73 . BaseQRankSum=0.426;DP=59;ExcessHet=3.0103;MLEAC=0,1,0,0;MLEAF=0.00,0.500,0.00,0.00;MQRankSum=0.410;RAW_MQ=203561.00;ReadPosRankSum=1.257 GT:AD:DP:GQ:PL:SB 0/2:17,4,17,4,0:42:99:364,329,1122,0,430,386,377,710,293,909,431,838,449,780,885:7,10,10,15 -20 10093571 . T . . END=10093571 GT:DP:GQ:MIN_DP:PL 0/0:57:59:57:0,59,2043 -20 10093572 . T . . END=10093922 GT:DP:GQ:MIN_DP:PL 0/0:62:99:51:0,99,1485 +20 10093571 . T . . END=10093922 GT:DP:GQ:MIN_DP:PL 0/0:62:99:51:0,99,1485 20 10093923 . T A, 1075.77 . BaseQRankSum=-0.667;DP=67;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.358;RAW_MQ=234704.00;ReadPosRankSum=-1.583 GT:AD:DP:GQ:PL:SB 0/1:35,32,0:67:99:1104,0,1257,1209,1353,2563:18,17,15,17 20 10093924 . G . . END=10094250 GT:DP:GQ:MIN_DP:PL 0/0:66:99:53:0,120,1800 20 10094251 . T A, 1270.77 . BaseQRankSum=0.251;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=223200.00;ReadPosRankSum=1.806 GT:AD:DP:GQ:PL:SB 0/1:26,36,0:62:99:1299,0,781,1376,889,2265:10,16,23,13 @@ -1370,8 +1129,7 @@ 20 10094774 . C T, 1036.77 . BaseQRankSum=-0.784;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.962;RAW_MQ=267241.00;ReadPosRankSum=0.197 GT:AD:DP:GQ:PL:SB 0/1:40,35,0:75:99:1065,0,1282,1185,1385,2570:24,16,21,14 20 10094775 . A . . END=10095431 GT:DP:GQ:MIN_DP:PL 0/0:77:99:63:0,120,1800 20 10095432 . GTGATGATGA G, 839.73 . BaseQRankSum=1.265;DP=77;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.431;RAW_MQ=227748.00;ReadPosRankSum=0.396 GT:AD:DP:GQ:PL:SB 0/1:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11 -20 10095442 . T . . END=10095442 GT:DP:GQ:MIN_DP:PL 0/0:71:0:71:0,0,1080 -20 10095443 . G . . END=10095740 GT:DP:GQ:MIN_DP:PL 0/0:81:99:64:0,120,1800 +20 10095442 . T . . END=10095740 GT:DP:GQ:MIN_DP:PL 0/0:80:99:64:0,120,1800 20 10095741 . A G, 1075.77 . BaseQRankSum=-0.534;DP=71;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.313;RAW_MQ=233528.00;ReadPosRankSum=-0.500 GT:AD:DP:GQ:PL:SB 0/1:36,34,0:70:99:1104,0,1233,1213,1335,2547:14,22,18,16 20 10095742 . G . . END=10096292 GT:DP:GQ:MIN_DP:PL 0/0:73:99:63:0,120,1800 20 10096293 . C T, 1355.77 . BaseQRankSum=4.664;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.397;RAW_MQ=257261.00;ReadPosRankSum=-1.135 GT:AD:DP:GQ:PL:SB 0/1:37,38,0:75:99:1384,0,1258,1495,1372,2867:21,16,21,17 @@ -1379,32 +1137,22 @@ 20 10096596 . C T, 1562.77 . BaseQRankSum=2.728;DP=87;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.612;RAW_MQ=300461.00;ReadPosRankSum=-0.170 GT:AD:DP:GQ:PL:SB 0/1:40,47,0:87:99:1591,0,1273,1711,1414,3125:19,21,23,24 20 10096597 . T . . END=10096767 GT:DP:GQ:MIN_DP:PL 0/0:90:99:75:0,120,1800 20 10096768 . A C, 1682.77 . BaseQRankSum=-2.764;DP=91;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.609;RAW_MQ=319323.00;ReadPosRankSum=0.613 GT:AD:DP:GQ:PL:SB 0/1:42,49,0:91:99:1711,0,1452,1838,1600,3437:25,17,24,25 -20 10096769 . A . . END=10096898 GT:DP:GQ:MIN_DP:PL 0/0:78:99:65:0,99,1485 +20 10096769 . A . . END=10096898 GT:DP:GQ:MIN_DP:PL 0/0:78:99:65:0,120,1800 20 10096899 . G T, 1614.77 . BaseQRankSum=2.755;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.387;RAW_MQ=279938.00;ReadPosRankSum=0.422 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:39,40,0:79:99:0|1:10096899_G_T:1643,0,1520,1764,1649,3413:19,20,12,28 -20 10096900 . G . . END=10096904 GT:DP:GQ:MIN_DP:PL 0/0:83:99:79:0,108,1620 +20 10096900 . G . . END=10096904 GT:DP:GQ:MIN_DP:PL 0/0:82:99:78:0,120,1800 20 10096905 . TA T, 1600.73 . BaseQRankSum=-0.755;DP=83;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.677;RAW_MQ=291579.00;ReadPosRankSum=0.461 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:40,43,0:83:99:0|1:10096899_G_T:1638,0,1623,1768,1752,3520:20,20,13,30 -20 10096907 . A . . END=10096907 GT:DP:GQ:MIN_DP:PL 0/0:83:0:83:0,0,0 -20 10096908 . T . . END=10096932 GT:DP:GQ:MIN_DP:PL 0/0:85:99:83:0,120,1800 +20 10096907 . A . . END=10096932 GT:DP:GQ:MIN_DP:PL 0/0:84:99:82:0,120,1800 20 10096933 . G C, 1511.77 . BaseQRankSum=-1.914;DP=85;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.802;RAW_MQ=298779.00;ReadPosRankSum=0.334 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:44,41,0:85:99:0|1:10096933_G_C:1540,0,1770,1684,1896,3580:28,16,13,28 -20 10096934 . T . . END=10096957 GT:DP:GQ:MIN_DP:PL 0/0:91:99:87:0,120,1800 +20 10096934 . T . . END=10096957 GT:DP:GQ:MIN_DP:PL 0/0:90:99:86:0,120,1800 20 10096958 . G A, 1766.77 . BaseQRankSum=2.839;DP=92;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.701;RAW_MQ=323979.00;ReadPosRankSum=-1.833 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:45,47,0:92:99:0|1:10096933_G_C:1795,0,1629,1929,1773,3702:27,18,16,31 20 10096959 . G . . END=10097074 GT:DP:GQ:MIN_DP:PL 0/0:92:99:84:0,120,1800 20 10097075 . T G, 1445.77 . BaseQRankSum=-2.533;DP=92;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.389;RAW_MQ=315628.00;ReadPosRankSum=0.082 GT:AD:DP:GQ:PL:SB 0/1:44,48,0:92:99:1474,0,1482,1606,1626,3232:18,26,26,22 -20 10097076 . A . . END=10097100 GT:DP:GQ:MIN_DP:PL 0/0:92:99:79:0,99,1485 +20 10097076 . A . . END=10097100 GT:DP:GQ:MIN_DP:PL 0/0:91:99:77:0,120,1800 20 10097101 . C CTTT,CTTTT, 1091.73 . BaseQRankSum=-1.134;DP=76;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=-2.428;RAW_MQ=252294.00;ReadPosRankSum=2.086 GT:AD:DP:GQ:PL:SB 0/1:34,26,4,0:64:99:1129,0,1306,558,1324,2012,982,1430,2052,2377:22,12,15,15 -20 10097102 . T . . END=10097102 GT:DP:GQ:MIN_DP:PL 0/0:77:0:77:0,0,200 -20 10097103 . T . . END=10097435 GT:DP:GQ:MIN_DP:PL 0/0:70:99:60:0,99,1485 +20 10097102 . T . . END=10097435 GT:DP:GQ:MIN_DP:PL 0/0:70:99:60:0,120,1800 20 10097436 . CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT C, 1054.73 . BaseQRankSum=1.820;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-6.464;RAW_MQ=262143.00;ReadPosRankSum=-3.097 GT:AD:DP:GQ:PL:SB 0/1:57,32,0:89:99:1092,0,2241,1263,2338,3601:23,34,11,21 20 10097437 . TTTTC *,T, 2089.73 . DP=76;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;RAW_MQ=217330.00 GT:AD:DP:GQ:PL:SB 1/2:0,32,23,0:55:99:2127,940,1799,1195,0,1125,2201,1453,1262,2642:0,0,16,39 -20 10097442 . T . . END=10097442 GT:DP:GQ:MIN_DP:PL 0/0:63:0:63:0,0,698 -20 10097443 . T . . END=10097445 GT:DP:GQ:MIN_DP:PL 0/0:63:75:63:0,75,1125 -20 10097446 . T . . END=10097450 GT:DP:GQ:MIN_DP:PL 0/0:64:81:63:0,81,1215 -20 10097451 . T . . END=10097452 GT:DP:GQ:MIN_DP:PL 0/0:63:90:61:0,90,1350 -20 10097453 . C . . END=10097455 GT:DP:GQ:MIN_DP:PL 0/0:63:71:62:0,71,2168 -20 10097456 . T . . END=10097458 GT:DP:GQ:MIN_DP:PL 0/0:64:0:61:0,0,1556 -20 10097459 . T . . END=10097459 GT:DP:GQ:MIN_DP:PL 0/0:60:21:60:0,21,2116 -20 10097460 . T . . END=10097460 GT:DP:GQ:MIN_DP:PL 0/0:61:24:61:0,24,2071 -20 10097461 . C . . END=10097475 GT:DP:GQ:MIN_DP:PL 0/0:61:0:58:0,0,1102 +20 10097442 . T . . END=10097475 GT:DP:GQ:MIN_DP:PL 0/0:78:0:63:0,0,557 20 10097476 . T . . END=10097476 GT:DP:GQ:MIN_DP:PL 0/0:66:11:66:0,11,2255 20 10097477 . C . . END=10097625 GT:DP:GQ:MIN_DP:PL 0/0:69:99:45:0,109,1710 20 10097626 . C A, 626.77 . BaseQRankSum=1.085;DP=48;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.331;RAW_MQ=162820.00;ReadPosRankSum=1.015 GT:AD:DP:GQ:PL:SB 0/1:28,20,0:48:99:655,0,957,739,1017,1757:8,20,8,12 @@ -1457,34 +1205,24 @@ 20 10098149 . T . . END=10098150 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 20 10098151 . A . . END=10098160 GT:DP:GQ:MIN_DP:PL 0/0:33:83:31:0,83,1260 20 10098161 . A . . END=10098176 GT:DP:GQ:MIN_DP:PL 0/0:33:90:31:0,90,1350 -20 10098177 . C . . END=10098185 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,1215 -20 10098186 . A . . END=10098199 GT:DP:GQ:MIN_DP:PL 0/0:29:72:27:0,72,1080 -20 10098200 . C . . END=10098203 GT:DP:GQ:MIN_DP:PL 0/0:28:60:28:0,60,900 -20 10098204 . G . . END=10098204 GT:DP:GQ:MIN_DP:PL 0/0:28:48:28:0,48,720 -20 10098205 . T . . END=10098206 GT:DP:GQ:MIN_DP:PL 0/0:28:45:28:0,45,675 -20 10098207 . T . . END=10098208 GT:DP:GQ:MIN_DP:PL 0/0:28:42:27:0,42,630 -20 10098209 . T . . END=10098214 GT:DP:GQ:MIN_DP:PL 0/0:24:36:24:0,36,540 -20 10098215 . T . . END=10098216 GT:DP:GQ:MIN_DP:PL 0/0:22:33:21:0,33,495 -20 10098217 . T . . END=10098217 GT:DP:GQ:MIN_DP:PL 0/0:21:27:21:0,27,405 -20 10098218 . G . . END=10098218 GT:DP:GQ:MIN_DP:PL 0/0:21:22:21:0,22,768 +20 10098177 . C . . END=10098197 GT:DP:GQ:MIN_DP:PL 0/0:30:81:27:0,81,1116 +20 10098198 . A . . END=10098203 GT:DP:GQ:MIN_DP:PL 0/0:28:72:27:0,72,1080 +20 10098204 . G . . END=10098216 GT:DP:GQ:MIN_DP:PL 0/0:24:60:21:0,60,900 +20 10098217 . T . . END=10098218 GT:DP:GQ:MIN_DP:PL 0/0:21:54:21:0,54,810 20 10098219 . TATATATA T, 295.73 . BaseQRankSum=3.147;DP=21;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.205;RAW_MQ=65705.00;ReadPosRankSum=0.427 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:12,9,0:21:99:0|1:10098219_TATATATA_T:333,0,461,369,488,858:0,12,0,9 -20 10098227 . T . . END=10098227 GT:DP:GQ:MIN_DP:PL 0/0:18:0:18:0,0,86 -20 10098228 . T . . END=10098228 GT:DP:GQ:MIN_DP:PL 0/0:18:14:18:0,14,662 -20 10098229 . A . . END=10098229 GT:DP:GQ:MIN_DP:PL 0/0:18:21:18:0,21,315 -20 10098230 . T . . END=10098230 GT:DP:GQ:MIN_DP:PL 0/0:18:16:18:0,16,657 -20 10098231 . A . . END=10098231 GT:DP:GQ:MIN_DP:PL 0/0:18:19:18:0,19,656 -20 10098232 . T . . END=10098232 GT:DP:GQ:MIN_DP:PL 0/0:17:11:17:0,11,615 -20 10098233 . A . . END=10098236 GT:DP:GQ:MIN_DP:PL 0/0:15:21:12:0,21,315 +20 10098227 . T . . END=10098228 GT:DP:GQ:MIN_DP:PL 0/0:18:30:18:0,30,450 +20 10098229 . A . . END=10098236 GT:DP:GQ:MIN_DP:PL 0/0:17:21:13:0,21,315 20 10098237 . A T, 244.77 . BaseQRankSum=0.006;DP=13;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.742;RAW_MQ=37064.00;ReadPosRankSum=0.277 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:6,7,0:13:99:0|1:10098219_TATATATA_T:273,0,273,294,294,588:0,6,0,7 -20 10098238 . A . . END=10098244 GT:DP:GQ:MIN_DP:PL 0/0:10:21:8:0,21,315 -20 10098245 . T . . END=10098248 GT:DP:GQ:MIN_DP:PL 0/0:9:24:9:0,24,360 -20 10098249 . A . . END=10098255 GT:DP:GQ:MIN_DP:PL 0/0:8:18:8:0,18,270 +20 10098238 . A . . END=10098244 GT:DP:GQ:MIN_DP:PL 0/0:10:21:9:0,21,315 +20 10098245 . T . . END=10098248 GT:DP:GQ:MIN_DP:PL 0/0:10:24:10:0,24,360 +20 10098249 . A . . END=10098250 GT:DP:GQ:MIN_DP:PL 0/0:10:18:9:0,18,270 +20 10098251 . A . . END=10098255 GT:DP:GQ:MIN_DP:PL 0/0:8:15:8:0,15,225 20 10098256 . T . . END=10098264 GT:DP:GQ:MIN_DP:PL 0/0:8:9:6:0,9,135 20 10098265 . T C, 133.77 . BaseQRankSum=1.834;DP=6;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.834;RAW_MQ=10564.00;ReadPosRankSum=0.000 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:2,4,0:6:59:0|1:10098219_TATATATA_T:162,0,59,168,71,239:0,2,0,4 -20 10098266 . A . . END=10098276 GT:DP:GQ:MIN_DP:PL 0/0:4:9:3:0,9,121 -20 10098277 . T . . END=10098279 GT:DP:GQ:MIN_DP:PL 0/0:3:6:3:0,6,90 -20 10098280 . A . . END=10098296 GT:DP:GQ:MIN_DP:PL 0/0:4:9:3:0,9,114 -20 10098297 . A . . END=10098307 GT:DP:GQ:MIN_DP:PL 0/0:3:6:2:0,6,86 +20 10098266 . A . . END=10098272 GT:DP:GQ:MIN_DP:PL 0/0:4:9:4:0,9,135 +20 10098273 . A . . END=10098279 GT:DP:GQ:MIN_DP:PL 0/0:3:6:3:0,6,90 +20 10098280 . A . . END=10098290 GT:DP:GQ:MIN_DP:PL 0/0:4:9:3:0,9,126 +20 10098291 . A . . END=10098307 GT:DP:GQ:MIN_DP:PL 0/0:3:6:2:0,6,86 20 10098308 . AAT A, 0 . DP=2;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;RAW_MQ=7200.00 GT:AD:DP:GQ:PL:SB 0/0:2,0,0:2:6:0,6,81,6,81,81:0,2,0,0 20 10098311 . A . . END=10098321 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,80 20 10098322 . A . . END=10098327 GT:DP:GQ:MIN_DP:PL 0/0:3:9:3:0,9,121 @@ -1492,9 +1230,8 @@ 20 10098330 . A . . END=10098343 GT:DP:GQ:MIN_DP:PL 0/0:4:9:4:0,9,135 20 10098344 . A . . END=10098344 GT:DP:GQ:MIN_DP:PL 0/0:4:0:4:0,0,1 20 10098345 . T . . END=10098350 GT:DP:GQ:MIN_DP:PL 0/0:3:9:3:0,9,125 -20 10098351 . T . . END=10098357 GT:DP:GQ:MIN_DP:PL 0/0:3:6:3:0,6,90 -20 10098358 . T . . END=10098359 GT:DP:GQ:MIN_DP:PL 0/0:3:3:3:0,3,45 -20 10098360 . A . . END=10098380 GT:DP:GQ:MIN_DP:PL 0/0:1:0:1:0,0,0 +20 10098351 . T . . END=10098360 GT:DP:GQ:MIN_DP:PL 0/0:3:3:3:0,3,45 +20 10098361 . T . . END=10098380 GT:DP:GQ:MIN_DP:PL 0/0:1:0:1:0,0,0 20 10098381 . T . . END=10098454 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,37 20 10098455 . A . . END=10098551 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0 20 10098552 . T . . END=10098637 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,40 @@ -1543,24 +1280,21 @@ 20 10098821 . T . . END=10098823 GT:DP:GQ:MIN_DP:PL 0/0:17:51:17:0,51,677 20 10098824 . A . . END=10098826 GT:DP:GQ:MIN_DP:PL 0/0:18:54:18:0,54,705 20 10098827 . T . . END=10098827 GT:DP:GQ:MIN_DP:PL 0/0:19:57:19:0,57,752 -20 10098828 . T . . END=10098857 GT:DP:GQ:MIN_DP:PL 0/0:25:60:20:0,60,799 -20 10098858 . G . . END=10098858 GT:DP:GQ:MIN_DP:PL 0/0:24:57:24:0,57,855 +20 10098828 . T . . END=10098835 GT:DP:GQ:MIN_DP:PL 0/0:21:60:20:0,60,799 +20 10098836 . G . . END=10098841 GT:DP:GQ:MIN_DP:PL 0/0:24:72:24:0,72,906 +20 10098842 . C . . END=10098842 GT:DP:GQ:MIN_DP:PL 0/0:24:69:24:0,69,1035 +20 10098843 . A . . END=10098858 GT:DP:GQ:MIN_DP:PL 0/0:26:72:24:0,72,990 20 10098859 . G . . END=10098859 GT:DP:GQ:MIN_DP:PL 0/0:24:29:24:0,29,851 -20 10098860 . T . . END=10098861 GT:DP:GQ:MIN_DP:PL 0/0:24:57:23:0,57,855 -20 10098862 . T . . END=10098862 GT:DP:GQ:MIN_DP:PL 0/0:25:60:25:0,60,900 -20 10098863 . G . . END=10098867 GT:DP:GQ:MIN_DP:PL 0/0:25:57:25:0,57,855 -20 10098868 . C . . END=10098868 GT:DP:GQ:MIN_DP:PL 0/0:25:54:25:0,54,810 -20 10098869 . G . . END=10098870 GT:DP:GQ:MIN_DP:PL 0/0:27:60:27:0,60,900 -20 10098871 . C . . END=10098873 GT:DP:GQ:MIN_DP:PL 0/0:29:57:28:0,57,855 -20 10098874 . A . . END=10098874 GT:DP:GQ:MIN_DP:PL 0/0:30:54:30:0,54,810 -20 10098875 . C . . END=10098876 GT:DP:GQ:MIN_DP:PL 0/0:30:48:30:0,48,720 -20 10098877 . G . . END=10098880 GT:DP:GQ:MIN_DP:PL 0/0:31:45:30:0,45,675 -20 10098881 . C . . END=10098881 GT:DP:GQ:MIN_DP:PL 0/0:31:48:31:0,48,720 -20 10098882 . C . . END=10098883 GT:DP:GQ:MIN_DP:PL 0/0:32:51:32:0,51,765 -20 10098884 . C . . END=10098884 GT:DP:GQ:MIN_DP:PL 0/0:32:48:32:0,48,720 +20 10098860 . T . . END=10098860 GT:DP:GQ:MIN_DP:PL 0/0:23:69:23:0,69,881 +20 10098861 . G . . END=10098868 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,960 +20 10098869 . G . . END=10098877 GT:DP:GQ:MIN_DP:PL 0/0:29:81:27:0,81,902 +20 10098878 . C . . END=10098878 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,1170 +20 10098879 . A . . END=10098881 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,1215 +20 10098882 . C . . END=10098882 GT:DP:GQ:MIN_DP:PL 0/0:32:60:32:0,60,1207 +20 10098883 . T . . END=10098883 GT:DP:GQ:MIN_DP:PL 0/0:32:56:32:0,56,1237 +20 10098884 . C . . END=10098884 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,1260 20 10098885 . C CA, 433.73 . BaseQRankSum=0.165;DP=31;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.449;RAW_MQ=77157.00;ReadPosRankSum=-1.073 GT:AD:DP:GQ:PL:SB 0/1:17,14,0:31:99:471,0,572,523,614,1137:16,1,13,1 -20 10098886 . C . . END=10098886 GT:DP:GQ:MIN_DP:PL 0/0:31:0:31:0,0,240 -20 10098887 . C . . END=10098890 GT:DP:GQ:MIN_DP:PL 0/0:31:84:29:0,84,1260 +20 10098886 . C . . END=10098890 GT:DP:GQ:MIN_DP:PL 0/0:31:84:29:0,84,1260 20 10098891 . C . . END=10098891 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 20 10098892 . G . . END=10098900 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 20 10098901 . T . . END=10098907 GT:DP:GQ:MIN_DP:PL 0/0:29:72:28:0,72,1080 @@ -1603,28 +1337,28 @@ 20 10099044 . A C, 334.77 . BaseQRankSum=-1.148;DP=24;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.418;RAW_MQ=59851.00;ReadPosRankSum=-2.207 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:15,9,0:24:99:0|1:10099029_T_C:363,0,768,420,798,1218:12,3,7,2 20 10099045 . C . . END=10099045 GT:DP:GQ:MIN_DP:PL 0/0:24:60:24:0,60,900 20 10099046 . T C, 304.77 . BaseQRankSum=-2.165;DP=24;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.418;RAW_MQ=59851.00;ReadPosRankSum=-2.297 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:15,9,0:24:99:0|1:10099029_T_C:333,0,603,378,630,1008:12,3,7,2 -20 10099047 . G . . END=10099054 GT:DP:GQ:MIN_DP:PL 0/0:26:63:25:0,63,945 +20 10099047 . G . . END=10099052 GT:DP:GQ:MIN_DP:PL 0/0:24:57:23:0,57,855 +20 10099053 . G . . END=10099054 GT:DP:GQ:MIN_DP:PL 0/0:23:54:23:0,54,810 20 10099055 . T C, 256.77 . BaseQRankSum=-1.554;DP=23;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.316;RAW_MQ=58555.00;ReadPosRankSum=-1.970 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:15,8,0:23:99:0|1:10099029_T_C:285,0,673,336,697,1033:11,4,6,2 -20 10099056 . T . . END=10099059 GT:DP:GQ:MIN_DP:PL 0/0:29:75:28:0,75,1125 -20 10099060 . A . . END=10099065 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1118 -20 10099066 . C . . END=10099068 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,1172 -20 10099069 . A . . END=10099069 GT:DP:GQ:MIN_DP:PL 0/0:32:82:32:0,82,1208 -20 10099070 . G . . END=10099078 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 +20 10099056 . T . . END=10099061 GT:DP:GQ:MIN_DP:PL 0/0:24:60:23:0,60,900 +20 10099062 . A . . END=10099067 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,921 +20 10099068 . G . . END=10099072 GT:DP:GQ:MIN_DP:PL 0/0:27:81:27:0,81,1042 +20 10099073 . T . . END=10099077 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 +20 10099078 . G . . END=10099078 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 20 10099079 . C T, 116.77 . BaseQRankSum=1.434;DP=29;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.821;RAW_MQ=78698.00;ReadPosRankSum=0.969 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:23,6,0:29:99:0|1:10099029_T_C:145,0,886,217,904,1120:11,12,4,2 -20 10099080 . G . . END=10099087 GT:DP:GQ:MIN_DP:PL 0/0:36:90:35:0,90,1350 -20 10099088 . C . . END=10099090 GT:DP:GQ:MIN_DP:PL 0/0:37:87:37:0,87,1305 -20 10099091 . C . . END=10099091 GT:DP:GQ:MIN_DP:PL 0/0:39:90:39:0,90,1350 -20 10099092 . A . . END=10099098 GT:DP:GQ:MIN_DP:PL 0/0:40:81:39:0,81,1215 -20 10099099 . C . . END=10099105 GT:DP:GQ:MIN_DP:PL 0/0:42:72:41:0,72,1080 -20 10099106 . T . . END=10099108 GT:DP:GQ:MIN_DP:PL 0/0:45:66:42:0,66,990 -20 10099109 . T . . END=10099110 GT:DP:GQ:MIN_DP:PL 0/0:48:72:47:0,72,1080 +20 10099080 . G . . END=10099089 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 +20 10099090 . A . . END=10099095 GT:DP:GQ:MIN_DP:PL 0/0:34:90:31:0,90,1350 +20 10099096 . A . . END=10099096 GT:DP:GQ:MIN_DP:PL 0/0:35:74:35:0,74,1310 +20 10099097 . G . . END=10099100 GT:DP:GQ:MIN_DP:PL 0/0:35:93:34:0,93,1395 +20 10099101 . G . . END=10099105 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1485 +20 10099106 . T . . END=10099106 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1440 +20 10099107 . T . . END=10099110 GT:DP:GQ:MIN_DP:PL 0/0:41:99:39:0,99,1485 20 10099111 . T TTTTGTTTG, 656.73 . BaseQRankSum=-1.207;DP=42;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.071;RAW_MQ=109737.00;ReadPosRankSum=-0.273 GT:AD:DP:GQ:PL:SB 0/1:22,13,0:35:99:694,0,802,763,859,1622:13,9,7,6 -20 10099112 . T . . END=10099112 GT:DP:GQ:MIN_DP:PL 0/0:55:0:55:0,0,194 -20 10099113 . T . . END=10099139 GT:DP:GQ:MIN_DP:PL 0/0:63:99:57:0,120,1800 +20 10099112 . T . . END=10099139 GT:DP:GQ:MIN_DP:PL 0/0:57:99:49:0,114,1710 20 10099140 . G T, 1005.77 . BaseQRankSum=-0.114;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.469;RAW_MQ=192512.00;ReadPosRankSum=0.338 GT:AD:DP:GQ:PL:SB 0/1:30,32,0:62:99:1034,0,931,1122,1028,2150:18,12,22,10 20 10099141 . G . . END=10099189 GT:DP:GQ:MIN_DP:PL 0/0:67:99:64:0,120,1800 20 10099190 . G T, 1034.77 . BaseQRankSum=-0.034;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.711;RAW_MQ=215351.00;ReadPosRankSum=-1.260 GT:AD:DP:GQ:PL:SB 0/1:33,32,0:65:99:1063,0,1154,1162,1251,2413:21,12,21,11 -20 10099191 . C . . END=10099219 GT:DP:GQ:MIN_DP:PL 0/0:59:99:46:0,111,1665 +20 10099191 . C . . END=10099219 GT:DP:GQ:MIN_DP:PL 0/0:58:99:46:0,111,1665 20 10099220 . A G, 577.77 . BaseQRankSum=-1.664;DP=45;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.596;RAW_MQ=149477.00;ReadPosRankSum=0.629 GT:AD:DP:GQ:PL:SB 0/1:25,20,0:45:99:606,0,873,681,933,1614:15,10,11,9 20 10099221 . T . . END=10099229 GT:DP:GQ:MIN_DP:PL 0/0:44:99:42:0,102,1530 20 10099230 . T . . END=10099233 GT:DP:GQ:MIN_DP:PL 0/0:41:90:41:0,90,1350 @@ -1643,6 +1377,6 @@ 20 10099565 . C T, 1346.77 . BaseQRankSum=4.595;DP=69;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.266;RAW_MQ=243410.00;ReadPosRankSum=1.225 GT:AD:DP:GQ:PL:SB 0/1:31,38,0:69:99:1375,0,994,1468,1108,2576:23,8,21,17 20 10099566 . T . . END=10099754 GT:DP:GQ:MIN_DP:PL 0/0:77:99:66:0,120,1800 20 10099755 . C T, 1098.77 . BaseQRankSum=1.550;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.022;RAW_MQ=229010.00;ReadPosRankSum=-0.230 GT:AD:DP:GQ:PL:SB 0/1:33,32,0:65:99:1127,0,1148,1226,1245,2470:20,13,17,15 -20 10099756 . C . . END=10099831 GT:DP:GQ:MIN_DP:PL 0/0:64:99:59:0,120,1800 +20 10099756 . C . . END=10099831 GT:DP:GQ:MIN_DP:PL 0/0:63:99:58:0,120,1800 20 10099832 . A G, 1073.77 . BaseQRankSum=-4.563;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.869;RAW_MQ=250276.00;ReadPosRankSum=-1.023 GT:AD:DP:GQ:PL:SB 0/1:39,33,0:72:99:1102,0,1430,1220,1530,2749:22,17,14,19 20 10099833 . T . . END=10100000 GT:DP:GQ:MIN_DP:PL 0/0:85:99:73:0,120,1800 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf.idx index d937d465157e6e636af9610eb90dc9b56d0315ab..8090317b0b7c265ce93853c03ed9f5d907eea674 100644 GIT binary patch literal 40765 zcmeIyy=xO;9Ki9Xl~#)gzC!EZBrdhNw>+0zJB1`|12)xqZM8*WO_Lg%Cbf5lP!!yq zy7+=h#YxbD)R)1@LBvr9M_rtBs?br;OMetm{15yFj_-3v?(WIMlaHUvoM}@^?TC(Y zrCRDY45Kl#WR&aG+0s&AG_)~yVZNrT4Nn)fHGj!zE;jYza;+E?Yt3?D!SIc+6of+) z>A{iuY$+F{>$RW~gr!jnqF?7zQt+Rqd+*$HLarWx}b%Zn!Cd3I8(*8PR;XHKNXa;bbe z8@(+aw@fRhUDwo!xc&Qq>Cy4LuPn#Wsx|LuhVOSO_3D699}l*Egi?tPrQY?(n6eJ7 z6<{B*57-C%4{!hnZ~zBz00(dY2XFufZ~zBz00(dY2XFufZ~zBz00(dY2XFufZ~zBz z00(dY2XFufZ~zBz00(dY2XFufZ~zBz00(dY2XFufZ~zBz00(dY2XFufZ~zBz00(dY z2XFufZ~zBz00(dY2XFufZ~zBz00(dY2XFufZ~zBz00(dY2XFufZ~zBz00(dY2XFuf zZ~zBz00(dY2XFufZ~zBz00(dY2XFufZ~zBz00(dY2XFufZ~zBz00(dY2XFufZ~zBz z00(dY2XFufZ~zBz00(dY2XFufZ~zDXcL$Cf76-ceq~C|7yU$4%=A;`pq_a1r&%Q|q z_O@*eR`yBH9+KYcmVWAy_8paW^h)m@m##a~*Pc`jNRuPdW24fwN$HPi>8^rwwen{_ zRONhs?ceq5a(%n2m*xC^D80HY-LoQnbW8f=wzT`9^v+}H^)+e7Q|a^z>4TTj^*7Q} YpQUfVNY8(jc5XEe@7iBCyQ7vA`3tKki`pcG`ZaQd0Oqr@ kmY!d49xoRF-vCYye!{L0P5|E14i9nA!7K2uKj?q;2azg)PXGV_