diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/ReferenceConfidenceVariantContextMerger.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/ReferenceConfidenceVariantContextMerger.java index f57d50a7cad..344ec716f58 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/ReferenceConfidenceVariantContextMerger.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/ReferenceConfidenceVariantContextMerger.java @@ -439,7 +439,8 @@ protected static void removeStaleAttributesAfterMerge(final Map attributes.remove(GATKVCFConstants.MLE_ALLELE_COUNT_KEY); attributes.remove(GATKVCFConstants.MLE_ALLELE_FREQUENCY_KEY); attributes.remove(VCFConstants.END_KEY); - attributes.remove(GATKVCFConstants.EVENT_COUNT_IN_HAPLOTYPE_KEY); //median doesn't make sense here so drop it; used for ClusteredEventFilter, which doesn't apply to MT + attributes.remove(GATKVCFConstants.EVENT_COUNT_IN_HAPLOTYPE_KEY); + attributes.remove(GATKVCFConstants.EVENT_COUNT_IN_REGION_KEY); //median doesn't make sense here so drop it; used for ClusteredEventFilter, which doesn't apply to MT } /** diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2Engine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2Engine.java index 1d2096f3c2b..f2242947e37 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2Engine.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2Engine.java @@ -72,7 +72,7 @@ public final class Mutect2Engine implements AssemblyRegionEvaluator, AutoCloseable { private static final List STANDARD_MUTECT_INFO_FIELDS = Arrays.asList(GATKVCFConstants.NORMAL_LOG_10_ODDS_KEY, GATKVCFConstants.TUMOR_LOG_10_ODDS_KEY, GATKVCFConstants.NORMAL_ARTIFACT_LOG_10_ODDS_KEY, - GATKVCFConstants.EVENT_COUNT_IN_HAPLOTYPE_KEY, GATKVCFConstants.IN_PON_KEY, GATKVCFConstants.POPULATION_AF_KEY, + GATKVCFConstants.EVENT_COUNT_IN_REGION_KEY, GATKVCFConstants.EVENT_COUNT_IN_HAPLOTYPE_KEY, GATKVCFConstants.IN_PON_KEY, GATKVCFConstants.POPULATION_AF_KEY, GATKVCFConstants.GERMLINE_QUAL_KEY, GATKVCFConstants.CONTAMINATION_QUAL_KEY, GATKVCFConstants.SEQUENCING_QUAL_KEY, GATKVCFConstants.POLYMERASE_SLIPPAGE_QUAL_KEY, GATKVCFConstants.READ_ORIENTATION_QUAL_KEY, GATKVCFConstants.STRAND_QUAL_KEY, GATKVCFConstants.ORIGINAL_CONTIG_MISMATCH_KEY, GATKVCFConstants.N_COUNT_KEY, GATKVCFConstants.AS_UNIQUE_ALT_READ_SET_COUNT_KEY); diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/SomaticGenotypingEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/SomaticGenotypingEngine.java index e4504398998..5324df8f59a 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/SomaticGenotypingEngine.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/SomaticGenotypingEngine.java @@ -8,6 +8,7 @@ import htsjdk.variant.variantcontext.*; import htsjdk.variant.vcf.VCFConstants; import org.apache.commons.collections4.ListUtils; +import org.apache.commons.lang3.mutable.MutableInt; import org.apache.commons.math3.linear.Array2DRowRealMatrix; import org.apache.commons.math3.linear.DefaultRealMatrixChangingVisitor; import org.apache.commons.math3.linear.RealMatrix; @@ -113,12 +114,14 @@ public CalledHaplotypes callMutations( } final AlleleLikelihoods logFragmentLikelihoods = logReadLikelihoods.groupEvidence(MTAC.independentMates ? read -> read : GATKRead::getName, Fragment::createAndAvoidFailure); + final Set potentialSomaticEventsInRegion = new HashSet<>(); for( final int loc : eventStarts ) { final List eventsAtThisLoc = AssemblyBasedCallerUtils.getVariantsFromActiveHaplotypes(loc, haplotypes, false); - VariantContext mergedVC = AssemblyBasedCallerUtils.makeMergedVariantContext(eventsAtThisLoc); - if( mergedVC == null ) { + VariantContext merged = AssemblyBasedCallerUtils.makeMergedVariantContext(eventsAtThisLoc); + if( merged == null ) { continue; } + final VariantContext mergedVC = emitRefConf ? ReferenceConfidenceUtils.addNonRefSymbolicAllele(merged) : merged; // converting haplotype likelihoods to allele likelihoods final Map> alleleMapper = AssemblyBasedCallerUtils.createAlleleMapper(mergedVC, loc, haplotypes, true); @@ -127,7 +130,6 @@ public CalledHaplotypes callMutations( logLikelihoods.retainEvidence(variantCallingRelevantFragmentOverlap::overlaps); if (emitRefConf) { - mergedVC = ReferenceConfidenceUtils.addNonRefSymbolicAllele(mergedVC); logLikelihoods.addNonReferenceAllele(Allele.NON_REF_ALLELE); } final List> tumorMatrices = IntStream.range(0, logLikelihoods.numberOfSamples()) @@ -152,13 +154,21 @@ public CalledHaplotypes callMutations( .filter(allele -> forcedAlleles.contains(allele) || tumorLogOdds.getAlt(allele) > MTAC.getEmissionLogOdds()) .collect(Collectors.toList()); - final long somaticAltCount = tumorAltAlleles.stream() + final List allelesToGenotype = tumorAltAlleles.stream() .filter(allele -> forcedAlleles.contains(allele) || !hasNormal || MTAC.genotypeGermlineSites || normalLogOdds.getAlt(allele) > MathUtils.log10ToLog(MTAC.normalLog10Odds)) - .count(); + .toList(); + + // record somatic alleles for later use in the Event Count annotation + // note that in tumor-only calling it does not attempt to detect germline events + mergedVC.getAlternateAlleles().stream() + .filter(allele -> tumorLogOdds.getAlt(allele) > MTAC.getEmissionLogOdds()) + .filter(allele -> !hasNormal || normalLogOdds.getAlt(allele) > MathUtils.log10ToLog(MTAC.normalLog10Odds)) + .map(allele -> new Event(mergedVC.getContig(), mergedVC.getStart(), mergedVC.getReference(), allele)) + .forEach(potentialSomaticEventsInRegion::add); // if every alt allele is germline, skip this variant. However, if some alt alleles are germline and others // are not we emit them all so that the filtering engine can see them - if (somaticAltCount == 0) { + if (allelesToGenotype.isEmpty()) { continue; } @@ -222,8 +232,41 @@ public CalledHaplotypes callMutations( final List outputCalls = AssemblyBasedCallerUtils.phaseCalls(returnCalls, calledHaplotypes); final int eventCount = outputCalls.size(); + + // calculate the number of somatic events in the best haplotype of each called variant + final Map haplotypeSupportCounts = logReadLikelihoods.alleles().stream() + .collect(Collectors.toMap(hap -> hap, label -> new MutableInt(0))); + logReadLikelihoods.bestAllelesBreakingTies() + .forEach(bestHaplotype -> haplotypeSupportCounts.get(bestHaplotype.allele).increment()); + + final Map> haplotypesByEvent= new HashMap<>(); + for (final Haplotype haplotype : logReadLikelihoods.alleles()) { + for (final Event event : haplotype.getEventMap().getEvents()) { + haplotypesByEvent.computeIfAbsent(event, e -> new ArrayList<>()).add(haplotype); + } + } + final Map> eventCountAnnotations = new HashMap<>(); + for (final VariantContext outputCall : outputCalls) { + for (final Allele allele : outputCall.getAlternateAlleles()) { + // note: this creates the minimal representation behind the scenes + final Event event = new Event(outputCall.getContig(), outputCall.getStart(), outputCall.getReference(), allele); + // haplotypesByEvent contains every *assembled* event, including events injected into the original assembly, + // but there are some modes where we genotype events that were never in an assembly graph, in which case + // this annotation is irrelevant + if (haplotypesByEvent.containsKey(event)) { + final Haplotype bestHaplotype = haplotypesByEvent.get(event).stream() + .sorted(Comparator.comparingInt(h -> haplotypeSupportCounts.getOrDefault(h, new MutableInt(0)).intValue()).reversed()) + .findFirst().get(); + + eventCountAnnotations.computeIfAbsent(outputCall, vc -> new ArrayList<>()) + .add((int) bestHaplotype.getEventMap().getEvents().stream().filter(potentialSomaticEventsInRegion::contains).count()); + } + } + } final List outputCallsWithEventCountAnnotation = outputCalls.stream() - .map(vc -> new VariantContextBuilder(vc).attribute(GATKVCFConstants.EVENT_COUNT_IN_HAPLOTYPE_KEY, eventCount).make()) + .map(vc -> new VariantContextBuilder(vc) + .attribute(GATKVCFConstants.EVENT_COUNT_IN_HAPLOTYPE_KEY, eventCountAnnotations.get(vc)) + .attribute(GATKVCFConstants.EVENT_COUNT_IN_REGION_KEY, potentialSomaticEventsInRegion.size()).make()) .collect(Collectors.toList()); return new CalledHaplotypes(outputCallsWithEventCountAnnotation, calledHaplotypes); } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/ClusteredEventsFilter.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/ClusteredEventsFilter.java index b7212562bb2..88cb589ef29 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/ClusteredEventsFilter.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/ClusteredEventsFilter.java @@ -8,9 +8,11 @@ public class ClusteredEventsFilter extends HardFilter { private final int maxEventsInRegion; + private final int maxEventsInHaplotype; - public ClusteredEventsFilter(final int maxEventsInRegion) { + public ClusteredEventsFilter(final int maxEventsInRegion, final int maxEventsInHaplotype) { this.maxEventsInRegion = maxEventsInRegion; + this.maxEventsInHaplotype = maxEventsInHaplotype; } @Override @@ -18,8 +20,9 @@ public ClusteredEventsFilter(final int maxEventsInRegion) { @Override public boolean isArtifact(final VariantContext vc, final Mutect2FilteringEngine filteringEngine) { - final Integer eventCount = vc.getAttributeAsInt(GATKVCFConstants.EVENT_COUNT_IN_HAPLOTYPE_KEY, -1); - return eventCount > maxEventsInRegion; + final List haplotypeEventCounts = vc.getAttributeAsIntList(GATKVCFConstants.EVENT_COUNT_IN_HAPLOTYPE_KEY, 0); + final int regionEventCounts = vc.getAttributeAsInt(GATKVCFConstants.EVENT_COUNT_IN_REGION_KEY, 0); + return haplotypeEventCounts.stream().mapToInt(n -> n).max().getAsInt() > maxEventsInHaplotype || regionEventCounts > maxEventsInRegion; } @Override @@ -28,5 +31,5 @@ public String filterName() { } @Override - protected List requiredInfoAnnotations() { return Collections.singletonList(GATKVCFConstants.EVENT_COUNT_IN_HAPLOTYPE_KEY); } + protected List requiredInfoAnnotations() { return List.of(GATKVCFConstants.EVENT_COUNT_IN_REGION_KEY, GATKVCFConstants.EVENT_COUNT_IN_HAPLOTYPE_KEY); } } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/FilteredHaplotypeFilter.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/FilteredHaplotypeFilter.java index 9a6375931ae..b725ee2587e 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/FilteredHaplotypeFilter.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/FilteredHaplotypeFilter.java @@ -13,6 +13,7 @@ import java.util.*; public class FilteredHaplotypeFilter extends Mutect2VariantFilter { + private static final double GERMLINE_PROBABILITY_TO_IGNORE_NORMAL_ARTIFACT = 0.25; private final double maxIntraHaplotypeDistance; // for each pgt + pid phasing string, a list of loci-error probability pairs @@ -54,10 +55,21 @@ public double calculateErrorProbability(final VariantContext vc, final Mutect2Fi @Override protected void accumulateDataForLearning(final VariantContext vc, final ErrorProbabilities errorProbabilities, final Mutect2FilteringEngine filteringEngine) { - // we record the maximum non-sequencing artifact that is not this filter itself - final double artifactProbability = errorProbabilities.getProbabilitiesByFilter().entrySet().stream() - .filter(e -> e.getKey().errorType() != ErrorType.SEQUENCING) - .filter(e -> !e.getKey().filterName().equals(filterName())) + // we record the maximum non-sequencing, non-germline, artifact probability that is not from this filter itself + final Map> probabilitiesByFilter = errorProbabilities.getProbabilitiesByFilter(); + + final double germlineProbability = probabilitiesByFilter.entrySet().stream() + .filter(e -> e.getKey().filterName() == GATKVCFConstants.GERMLINE_RISK_FILTER_NAME) + .flatMap(e -> e.getValue().stream()) // the value is a list of double, we need the max of all the lists + .max(Double::compareTo).orElse(0.0); + + // the normal artifact filter often lights up when there's a non-artifactual germline event, which we don't want here + final boolean ignoreNormalArtifact = germlineProbability > GERMLINE_PROBABILITY_TO_IGNORE_NORMAL_ARTIFACT; + + final double artifactProbability = probabilitiesByFilter.entrySet().stream() + .filter(e -> e.getKey().errorType() != ErrorType.NON_SOMATIC) + .filter(e -> !(ignoreNormalArtifact && e.getKey().filterName() == GATKVCFConstants.ARTIFACT_IN_NORMAL_FILTER_NAME)) + .filter(e -> !e.getKey().filterName().equals(filterName())) // exclude the haplotype filter itself, which would be circular .flatMap(e -> e.getValue().stream()) // the value is a list of double, we need the max of all the lists .max(Double::compareTo).orElse(0.0); diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/M2FiltersArgumentCollection.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/M2FiltersArgumentCollection.java index cec046e4026..26218b5008d 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/M2FiltersArgumentCollection.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/M2FiltersArgumentCollection.java @@ -55,6 +55,7 @@ public class M2FiltersArgumentCollection { * Hard filter thresholds */ public static final String MAX_EVENTS_IN_REGION_LONG_NAME = "max-events-in-region"; + public static final String MAX_EVENTS_IN_HAPLOTYPE_LONG_NAME = "max-events-in-haplotype"; public static final String MAX_ALT_ALLELE_COUNT_LONG_NAME = "max-alt-allele-count"; public static final String UNIQUE_ALT_READ_COUNT_LONG_NAME = "unique-alt-read-count"; public static final String MIN_MEDIAN_MAPPING_QUALITY_LONG_NAME = "min-median-mapping-quality"; @@ -65,7 +66,8 @@ public class M2FiltersArgumentCollection { public static final String MIN_READS_ON_EACH_STRAND_LONG_NAME = "min-reads-per-strand"; public static final String MIN_AF_LONG_NAME = "min-allele-fraction"; - private static final int DEFAULT_MAX_EVENTS_IN_REGION = 2; + private static final int DEFAULT_MAX_EVENTS_IN_REGION = 3; + private static final int DEFAULT_MAX_EVENTS_IN_HAPLOTYPE = 2; private static final int DEFAULT_MAX_ALT_ALLELES = 1; private static final int DEFAULT_MIN_UNIQUE_ALT_READS = 0; private static final int DEFAULT_MIN_MEDIAN_MAPPING_QUALITY = 30; @@ -77,9 +79,12 @@ public class M2FiltersArgumentCollection { private static final int DEFAULT_MIN_READS_ON_EACH_STRAND = 0; private static final double DEFAULT_MIN_AF = 0; - @Argument(fullName = MAX_EVENTS_IN_REGION_LONG_NAME, optional = true, doc = "Maximum events in a single assembly region. Filter all variants if exceeded.") + @Argument(fullName = MAX_EVENTS_IN_REGION_LONG_NAME, optional = true, doc = "Maximum number of non-germline events in a single assembly region. Filter all variants if exceeded.") public int maxEventsInRegion = DEFAULT_MAX_EVENTS_IN_REGION; + @Argument(fullName = MAX_EVENTS_IN_HAPLOTYPE_LONG_NAME, optional = true, doc = "Maximum number of non-germline events in a variant allele's best haplotype.") + public int maxEventsInHaplotype = DEFAULT_MAX_EVENTS_IN_HAPLOTYPE; + @Argument(fullName = MAX_ALT_ALLELE_COUNT_LONG_NAME, optional = true, doc = "Maximum alt alleles per site.") public int numAltAllelesThreshold = DEFAULT_MAX_ALT_ALLELES; diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/Mutect2FilteringEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/Mutect2FilteringEngine.java index 159f67df68d..77d2055587c 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/Mutect2FilteringEngine.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/Mutect2FilteringEngine.java @@ -312,7 +312,7 @@ private void buildFiltersList(final M2FiltersArgumentCollection MTFAC) { } if (!MTFAC.mitochondria && !MTFAC.microbial) { - filters.add(new ClusteredEventsFilter(MTFAC.maxEventsInRegion)); + filters.add(new ClusteredEventsFilter(MTFAC.maxEventsInRegion, MTFAC.maxEventsInHaplotype)); filters.add(new MultiallelicFilter(MTFAC.numAltAllelesThreshold)); filters.add(new FragmentLengthFilter(MTFAC.maxMedianFragmentLengthDifference)); filters.add(new PolymeraseSlippageFilter(MTFAC.minSlippageLength, MTFAC.slippageRate)); diff --git a/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFConstants.java b/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFConstants.java index a81f3c853da..a63bd927865 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFConstants.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFConstants.java @@ -42,7 +42,8 @@ public final class GATKVCFConstants { public static final String CULPRIT_KEY = "culprit"; public static final String ORIGINAL_DP_KEY = "DP_Orig"; //SelectVariants public static final String DOWNSAMPLED_KEY = "DS"; - public static final String EVENT_COUNT_IN_HAPLOTYPE_KEY = "ECNT"; //M2 + public static final String EVENT_COUNT_IN_REGION_KEY = "ECNT"; //M2 + public static final String EVENT_COUNT_IN_HAPLOTYPE_KEY = "ECNTH"; //M2 public static final String FISHER_STRAND_KEY = "FS"; public static final String AS_FISHER_STRAND_KEY = "AS_FS"; public static final String AS_SB_TABLE_KEY = "AS_SB_TABLE"; diff --git a/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFHeaderLines.java b/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFHeaderLines.java index 0e00e84cc57..efdb4393361 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFHeaderLines.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFHeaderLines.java @@ -223,7 +223,8 @@ public static VCFFormatHeaderLine getEquivalentFormatHeaderLine(final String inf addInfoLine(new VCFInfoHeaderLine(TREE_SCORE, 1, VCFHeaderLineType.Float, "Score from single sample filtering with random forest model.")); // M2-related info lines - addInfoLine(new VCFInfoHeaderLine(EVENT_COUNT_IN_HAPLOTYPE_KEY, 1, VCFHeaderLineType.Integer, "Number of events in this haplotype")); + addInfoLine(new VCFInfoHeaderLine(EVENT_COUNT_IN_HAPLOTYPE_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Number of somatic events in best supporting haplotype for each alt allele")); + addInfoLine(new VCFInfoHeaderLine(EVENT_COUNT_IN_REGION_KEY, 1, VCFHeaderLineType.Integer, "Number of potential somatic events in the assembly region")); addInfoLine(new VCFInfoHeaderLine(NORMAL_LOG_10_ODDS_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Normal log 10 likelihood ratio of diploid het or hom alt genotypes")); addInfoLine(new VCFInfoHeaderLine(TUMOR_LOG_10_ODDS_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Log 10 likelihood ratio score of variant existing versus not existing")); addFormatLine(new VCFFormatHeaderLine(TUMOR_LOG_10_ODDS_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Log 10 likelihood ratio score of variant existing versus not existing")); diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2IntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2IntegrationTest.java index bce858e23e8..6066768fa69 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2IntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2IntegrationTest.java @@ -6,6 +6,7 @@ import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.vcf.VCFConstants; import htsjdk.variant.vcf.VCFHeader; +import htsjdk.variant.vcf.VCFUtils; import org.apache.commons.collections4.SetUtils; import org.apache.commons.lang3.tuple.Pair; import org.broadinstitute.hellbender.CommandLineProgramTest; @@ -102,14 +103,14 @@ public class Mutect2IntegrationTest extends CommandLineProgramTest { @DataProvider(name = "dreamSyntheticData") public Object[][] dreamSyntheticData() { return new Object[][]{ - {DREAM_1_TUMOR, Optional.of(DREAM_1_NORMAL), DREAM_1_TRUTH, DREAM_1_MASK, 0.97, false}, - {DREAM_2_TUMOR, Optional.of(DREAM_2_NORMAL), DREAM_2_TRUTH, DREAM_2_MASK, 0.95, false}, - {DREAM_2_TUMOR, Optional.empty(), DREAM_2_TRUTH, DREAM_2_MASK, 0.95, false}, - {DREAM_2_TUMOR, Optional.empty(), DREAM_2_TRUTH, DREAM_2_MASK, 0.95, true}, - {DREAM_3_TUMOR, Optional.of(DREAM_3_NORMAL), DREAM_3_TRUTH, DREAM_3_MASK, 0.90, false}, - {DREAM_4_TUMOR, Optional.of(DREAM_4_NORMAL), DREAM_4_TRUTH, DREAM_4_MASK, 0.65, false}, - {DREAM_4_TUMOR, Optional.of(DREAM_4_NORMAL), DREAM_4_TRUTH, DREAM_4_MASK, 0.65, true}, - {DREAM_4_TUMOR, Optional.empty(), DREAM_4_TRUTH, DREAM_4_MASK, 0.65, false}, + {DREAM_1_TUMOR, Optional.of(DREAM_1_NORMAL), DREAM_1_TRUTH, DREAM_1_MASK, 0.98, false}, + {DREAM_2_TUMOR, Optional.of(DREAM_2_NORMAL), DREAM_2_TRUTH, DREAM_2_MASK, 0.98, false}, + {DREAM_2_TUMOR, Optional.empty(), DREAM_2_TRUTH, DREAM_2_MASK, 0.98, false}, + {DREAM_2_TUMOR, Optional.empty(), DREAM_2_TRUTH, DREAM_2_MASK, 0.98, true}, + {DREAM_3_TUMOR, Optional.of(DREAM_3_NORMAL), DREAM_3_TRUTH, DREAM_3_MASK, 0.95, false}, + {DREAM_4_TUMOR, Optional.of(DREAM_4_NORMAL), DREAM_4_TRUTH, DREAM_4_MASK, 0.8, false}, + {DREAM_4_TUMOR, Optional.of(DREAM_4_NORMAL), DREAM_4_TRUTH, DREAM_4_MASK, 0.7, true}, + {DREAM_4_TUMOR, Optional.empty(), DREAM_4_TRUTH, DREAM_4_MASK, 0.7, false}, }; } @@ -203,7 +204,7 @@ public void testNA12878NormalNormalFiltering() { final long numPassVariants = VariantContextTestUtils.streamVcf(filteredVcf) .filter(vc -> vc.getFilters().isEmpty()).count(); - Assert.assertTrue(numPassVariants < 10); + Assert.assertTrue(numPassVariants < 13); } // tumorBams, normalBam, truthVcf, mask, requiredSensitivity @@ -417,6 +418,29 @@ public void testForceCalling() { } } + // regression test for PR: https://github.com/broadinstitute/gatk/pull/8717, which fixed an issue wherein germline events were + // incorrectly contributing to the bad haplotype and clustered events filters. In order to make the test more stringent we turn + // on the genotype-germline-sites flag + // The test is on two variants that caused particular trouble previously in the DREAM 2 sample + @Test + public void testFilteredHaplotypeAndClusteredEventsFilters() throws Exception { + Utils.resetRandomGenerator(); + final File tumor = DREAM_2_TUMOR; + final File normal = DREAM_2_NORMAL; + final File unfilteredVcf = createTempFile("unfiltered", ".vcf"); + final File filteredVcf = createTempFile("filtered", ".vcf"); + + for (final int locus : List.of(4567628, 20870771)) { + final String interval = "20:" + (locus - 500) + "-" + (locus + 500); + runMutect2(List.of(tumor), List.of(normal), unfilteredVcf, interval, b37Reference, Optional.of(GNOMAD), + args -> args.addFlag(M2ArgumentCollection.GENOTYPE_GERMLINE_SITES_LONG_NAME)); + runFilterMutectCalls(unfilteredVcf, filteredVcf, b37Reference); + final Optional vcShouldPass = VariantContextTestUtils.streamVcf(filteredVcf).filter(vc -> vc.getStart() == locus).findFirst(); + Assert.assertTrue(vcShouldPass.isPresent()); + Assert.assertFalse(vcShouldPass.get().isFiltered()); + } + } + // test that the dont-use-soft-clips option actually does something @Test public void testDontUseSoftClips() { @@ -528,7 +552,7 @@ public void testContaminationFilter() { filteredVariants.get(10).stream().filter(vc -> vc.getFilters().contains(GATKVCFConstants.CONTAMINATION_FILTER_NAME)).count()); final List missedObviousVariantsAtTenPercent = filteredVariants.get(10).stream() - .filter(vc -> !vc.getFilters().contains(GATKVCFConstants.CONTAMINATION_FILTER_NAME)) + .filter(vc -> !vc.isFiltered()) .filter(VariantContext::isBiallelic) .filter(vc -> { final int[] AD = vc.getGenotype(0).getAD(); @@ -1088,7 +1112,18 @@ public void testExposureOfSmithWatermanParametersIsConsistentWithPastResults(fin }; runCommandLine(args); - IntegrationTestSpec.assertEqualTextFiles(output, expected); + + // This used to be an exact text match, which cause hours of aggravation when the test passed locally and + // failed on the cloud. + final double[] outputTlods = VariantContextTestUtils.streamVcf(output) + .flatMap(vc -> vc.getAttributeAsDoubleList(GATKVCFConstants.TUMOR_LOG_10_ODDS_KEY, 0).stream()) + .mapToDouble(x -> x).toArray(); + + final double[] expectedTlods = VariantContextTestUtils.streamVcf(expected) + .flatMap(vc -> vc.getAttributeAsDoubleList(GATKVCFConstants.TUMOR_LOG_10_ODDS_KEY, 0).stream()) + .mapToDouble(x -> x).toArray(); + + Assert.assertEquals(outputTlods, expectedTlods); } @SafeVarargs diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/mutect/expected.testExposureOfSmithWatermanParameters.M2.gatk4.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/mutect/expected.testExposureOfSmithWatermanParameters.M2.gatk4.vcf index 5499d6371af..d4015319b6c 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/mutect/expected.testExposureOfSmithWatermanParameters.M2.gatk4.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/mutect/expected.testExposureOfSmithWatermanParameters.M2.gatk4.vcf @@ -16,7 +16,7 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= ##INFO= @@ -57,11 +57,11 @@ 20 10001628 . G A . . AS_SB_TABLE=0,0|55,40;DP=98;ECNT=4;MBQ=0,38;MFRL=0,400;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=390.73 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,95:0.990:95:0,48:0,46:0,95:0,0,55,40 20 10001661 . T C . . AS_SB_TABLE=0,0|49,34;DP=85;ECNT=4;MBQ=0,36;MFRL=0,398;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=361.55 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,83:0.988:83:0,44:0,36:0,83:0|1:10001661_T_C:10001661:0,0,49,34 20 10001670 . T G . . AS_SB_TABLE=0,0|46,38;DP=86;ECNT=4;MBQ=0,37;MFRL=0,398;MMQ=60,60;MPOS=20;POPAF=7.30;TLOD=368.22 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,84:0.988:84:0,48:0,33:0,84:0|1:10001661_T_C:10001661:0,0,46,38 -20 10002058 . T G . . AS_SB_TABLE=1,0|51,23;DP=79;ECNT=4;MBQ=12,38;MFRL=351,405;MMQ=29,60;MPOS=32;POPAF=7.30;TLOD=297.32 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:1,74:0.986:75:0,45:0,28:1,74:1,0,51,23 -20 10002099 . C T . . AS_SB_TABLE=19,8|23,15;DP=69;ECNT=4;MBQ=37,36;MFRL=407,406;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=121.87 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:27,38:0.581:65:11,19:16,18:27,38:19,8,23,15 -20 10002138 . C G . . AS_SB_TABLE=0,0|27,29;DP=57;ECNT=4;MBQ=0,37;MFRL=0,408;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=245.42 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,56:0.983:56:0,23:0,29:0,56:0|1:10002138_C_G:10002138:0,0,27,29 -20 10002142 . G C . . AS_SB_TABLE=0,0|26,29;DP=56;ECNT=4;MBQ=0,37;MFRL=0,408;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=241.85 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,55:0.983:55:0,23:0,28:0,55:0|1:10002138_C_G:10002138:0,0,26,29 -20 10002458 . G GT,GTTT,GTTTTT . . AS_SB_TABLE=0,0|3,3|5,1|4,2;DP=65;ECNT=2;MBQ=0,27,38,37;MFRL=0,398,363,419;MMQ=60,60,60,29;MPOS=35,39,13;POPAF=7.30,7.30,7.30;RPA=11,12,14,16;RU=T;STR;TLOD=11.36,12.81,8.50 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2/3:0,6,6,6:0.208,0.397,0.379:18:0,3,4,2:0,2,2,2:0,6,6,6:0,0,12,6 +20 10002058 . T G . . AS_SB_TABLE=1,0|51,23;DP=79;ECNT=1;MBQ=12,38;MFRL=351,405;MMQ=29,60;MPOS=32;POPAF=7.30;TLOD=297.32 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:1,74:0.986:75:0,45:0,28:1,74:1,0,51,23 +20 10002099 . C T . . AS_SB_TABLE=19,8|23,15;DP=69;ECNT=2;MBQ=37,36;MFRL=407,406;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=121.87 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:27,38:0.581:65:11,19:16,18:27,38:19,8,23,15 +20 10002138 . C G . . AS_SB_TABLE=0,0|27,29;DP=57;ECNT=3;MBQ=0,37;MFRL=0,408;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=245.42 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,56:0.983:56:0,23:0,29:0,56:0|1:10002138_C_G:10002138:0,0,27,29 +20 10002142 . G C . . AS_SB_TABLE=0,0|26,29;DP=56;ECNT=3;MBQ=0,37;MFRL=0,408;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=241.85 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,55:0.983:55:0,23:0,28:0,55:0|1:10002138_C_G:10002138:0,0,26,29 +20 10002458 . G GT,GTTT,GTTTTT . . AS_SB_TABLE=0,0|3,3|5,1|4,2;DP=65;ECNT=2,2,2;MBQ=0,27,38,37;MFRL=0,398,363,419;MMQ=60,60,60,29;MPOS=35,39,13;POPAF=7.30,7.30,7.30;RPA=11,12,14,16;RU=T;STR;TLOD=11.36,12.81,8.50 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2/3:0,6,6,6:0.208,0.397,0.379:18:0,3,4,2:0,2,2,2:0,6,6,6:0,0,12,6 20 10002470 . C T . . AS_SB_TABLE=0,0|34,29;DP=68;ECNT=2;MBQ=0,35;MFRL=0,405;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=253.24 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,63:0.985:63:0,28:0,32:0,63:0,0,34,29 20 10002625 . G T . . AS_SB_TABLE=0,0|26,38;DP=66;ECNT=1;MBQ=0,38;MFRL=0,389;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=267.63 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,64:0.985:64:0,31:0,33:0,64:0,0,26,38 20 10003021 . C T . . AS_SB_TABLE=0,0|35,25;DP=63;ECNT=1;MBQ=0,38;MFRL=0,404;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=239.40 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,60:0.984:60:0,28:0,31:0,60:0,0,35,25 @@ -69,23 +69,23 @@ 20 10003651 . T C . . AS_SB_TABLE=0,0|32,61;DP=98;ECNT=2;MBQ=0,36;MFRL=0,399;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=362.87 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,93:0.990:93:0,39:0,53:0,93:0,0,32,61 20 10003692 . A G . . AS_SB_TABLE=0,0|25,43;DP=72;ECNT=2;MBQ=0,36;MFRL=0,400;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=261.96 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,68:0.986:68:0,31:0,36:0,68:0,0,25,43 20 10003832 . G A . . AS_SB_TABLE=0,0|23,43;DP=67;ECNT=1;MBQ=0,38;MFRL=0,398;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=271.62 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,66:0.985:66:0,28:0,38:0,66:0,0,23,43 -20 10004094 . A C . . AS_SB_TABLE=0,0|35,18;DP=55;ECNT=5;MBQ=0,34;MFRL=0,405;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=183.61 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,53:0.982:53:0,22:0,26:0,53:0,0,35,18 -20 10004147 . A G . . AS_SB_TABLE=0,0|21,31;DP=54;ECNT=5;MBQ=0,33;MFRL=0,399;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=184.86 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,52:0.983:52:0,26:0,24:0,52:0,0,21,31 -20 10004193 . G T . . AS_SB_TABLE=12,11|12,16;DP=54;ECNT=5;MBQ=37,37;MFRL=386,379;MMQ=57,60;MPOS=33;POPAF=7.30;TLOD=93.80 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:23,28:0.547:51:12,13:11,14:23,28:12,11,12,16 -20 10004222 . C CA . . AS_SB_TABLE=20,15|4,6;DP=69;ECNT=5;MBQ=34,36;MFRL=398,391;MMQ=60,60;MPOS=32;POPAF=7.30;RPA=18,19;RU=A;STR;TLOD=7.79 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:35,10:0.215:45:12,3:16,3:35,10:20,15,4,6 -20 10004223 . A AG . . AS_SB_TABLE=18,20|4,6;DP=69;ECNT=5;MBQ=35,29;MFRL=400,383;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=9.07 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:38,10:0.204:48:19,4:16,5:38,10:18,20,4,6 +20 10004094 . A C . . AS_SB_TABLE=0,0|35,18;DP=55;ECNT=1;MBQ=0,34;MFRL=0,405;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=183.61 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,53:0.982:53:0,22:0,26:0,53:0,0,35,18 +20 10004147 . A G . . AS_SB_TABLE=0,0|21,31;DP=54;ECNT=2;MBQ=0,33;MFRL=0,399;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=184.86 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,52:0.983:52:0,26:0,24:0,52:0,0,21,31 +20 10004193 . G T . . AS_SB_TABLE=12,11|12,16;DP=54;ECNT=2;MBQ=37,37;MFRL=386,379;MMQ=57,60;MPOS=33;POPAF=7.30;TLOD=93.80 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:23,28:0.547:51:12,13:11,14:23,28:12,11,12,16 +20 10004222 . C CA . . AS_SB_TABLE=20,15|4,6;DP=69;ECNT=1;MBQ=34,36;MFRL=398,391;MMQ=60,60;MPOS=32;POPAF=7.30;RPA=18,19;RU=A;STR;TLOD=7.79 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:35,10:0.215:45:12,3:16,3:35,10:20,15,4,6 +20 10004223 . A AG . . AS_SB_TABLE=18,20|4,6;DP=69;ECNT=1;MBQ=35,29;MFRL=400,383;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=9.07 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:38,10:0.204:48:19,4:16,5:38,10:18,20,4,6 20 10004351 . C G . . AS_SB_TABLE=0,0|38,32;DP=71;ECNT=2;MBQ=0,37;MFRL=0,415;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=276.55 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,70:0.986:70:0,33:0,36:0,70:0,0,38,32 20 10004389 . T G . . AS_SB_TABLE=0,0|25,37;DP=67;ECNT=2;MBQ=0,37;MFRL=0,411;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=250.53 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,62:0.985:62:0,28:0,34:0,62:0,0,25,37 20 10004610 . A C . . AS_SB_TABLE=0,0|46,43;DP=93;ECNT=1;MBQ=0,37;MFRL=0,404;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=363.46 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,89:0.989:89:0,49:0,39:0,89:0,0,46,43 20 10004725 . A G . . AS_SB_TABLE=10,25|17,13;DP=67;ECNT=4;MBQ=37,36;MFRL=398,388;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=97.23 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:35,30:0.461:65:16,15:19,14:35,30:10,25,17,13 -20 10004766 . GACTAAA G . . AS_SB_TABLE=13,22|7,20;DP=78;ECNT=4;MBQ=37,37;MFRL=386,413;MMQ=60,29;MPOS=33;POPAF=7.30;TLOD=101.89 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:35,27:0.442:62:13,11:13,14:35,27:0|1:10004766_GACTAAA_G:10004766:13,22,7,20 -20 10004774 . CTA C . . AS_SB_TABLE=14,23|7,20;DP=77;ECNT=4;MBQ=37,38;MFRL=386,413;MMQ=60,29;MPOS=34;POPAF=7.30;TLOD=101.37 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:37,27:0.428:64:17,13:18,14:37,27:0|1:10004766_GACTAAA_G:10004766:14,23,7,20 -20 10004777 . TGC T . . AS_SB_TABLE=14,23|7,20;DP=77;ECNT=4;MBQ=37,38;MFRL=386,413;MMQ=60,29;MPOS=35;POPAF=7.30;TLOD=101.37 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:37,27:0.428:64:18,13:19,14:37,27:0|1:10004766_GACTAAA_G:10004766:14,23,7,20 -20 10004874 . A C . . AS_SB_TABLE=0,0|54,33;DP=90;ECNT=2;MBQ=0,36;MFRL=0,398;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=361.12 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,87:0.989:87:0,47:0,38:0,87:0|1:10004874_A_C:10004874:0,0,54,33 +20 10004766 . GACTAAA G . . AS_SB_TABLE=13,22|7,20;DP=78;ECNT=3;MBQ=37,37;MFRL=386,413;MMQ=60,29;MPOS=33;POPAF=7.30;TLOD=101.89 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:35,27:0.442:62:13,11:13,14:35,27:0|1:10004766_GACTAAA_G:10004766:13,22,7,20 +20 10004774 . CTA C . . AS_SB_TABLE=14,23|7,20;DP=77;ECNT=3;MBQ=37,38;MFRL=386,413;MMQ=60,29;MPOS=34;POPAF=7.30;TLOD=101.37 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:37,27:0.428:64:17,13:18,14:37,27:0|1:10004766_GACTAAA_G:10004766:14,23,7,20 +20 10004777 . TGC T . . AS_SB_TABLE=14,23|7,20;DP=77;ECNT=3;MBQ=37,38;MFRL=386,413;MMQ=60,29;MPOS=35;POPAF=7.30;TLOD=101.37 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:37,27:0.428:64:18,13:19,14:37,27:0|1:10004766_GACTAAA_G:10004766:14,23,7,20 +20 10004874 . A C . . AS_SB_TABLE=0,0|54,33;DP=90;ECNT=1;MBQ=0,36;MFRL=0,398;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=361.12 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,87:0.989:87:0,47:0,38:0,87:0|1:10004874_A_C:10004874:0,0,54,33 20 10004887 . A G . . AS_SB_TABLE=24,21|24,16;DP=90;ECNT=2;MBQ=36,37;MFRL=398,400;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=134.37 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:45,40:0.471:85:27,24:18,16:45,40:0|1:10004874_A_C:10004874:24,21,24,16 20 10005010 . C T . . AS_SB_TABLE=0,0|44,28;DP=73;ECNT=1;MBQ=0,38;MFRL=0,394;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=294.41 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,72:0.987:72:0,35:0,37:0,72:0,0,44,28 -20 10005427 . C T . . AS_SB_TABLE=0,0|27,28;DP=60;ECNT=2;MBQ=0,37;MFRL=0,385;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=222.54 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,55:0.983:55:0,29:0,25:0,55:0,0,27,28 -20 10005499 . A G . . AS_SB_TABLE=0,0|45,31;DP=78;ECNT=2;MBQ=0,36;MFRL=0,384;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=306.30 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,76:0.987:76:0,37:0,39:0,76:0,0,45,31 +20 10005427 . C T . . AS_SB_TABLE=0,0|27,28;DP=60;ECNT=1;MBQ=0,37;MFRL=0,385;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=222.54 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,55:0.983:55:0,29:0,25:0,55:0,0,27,28 +20 10005499 . A G . . AS_SB_TABLE=0,0|45,31;DP=78;ECNT=1;MBQ=0,36;MFRL=0,384;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=306.30 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,76:0.987:76:0,37:0,39:0,76:0,0,45,31 20 10005587 . A G . . AS_SB_TABLE=19,17|16,20;DP=76;ECNT=1;MBQ=38,37;MFRL=383,391;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=124.92 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:36,36:0.501:72:15,12:20,24:36,36:19,17,16,20 20 10005723 . A G . . AS_SB_TABLE=0,0|48,38;DP=88;ECNT=1;MBQ=0,30;MFRL=0,389;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=307.12 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,86:0.989:86:0,39:0,45:0,86:0,0,48,38 20 10006291 . G A . . AS_SB_TABLE=25,28|16,15;DP=85;ECNT=1;MBQ=37,37;MFRL=395,378;MMQ=60,60;MPOS=17;POPAF=7.30;TLOD=101.08 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:53,31:0.372:84:23,14:30,17:53,31:25,28,16,15 @@ -93,74 +93,74 @@ 20 10006682 . T A . . AS_SB_TABLE=0,0|44,29;DP=75;ECNT=1;MBQ=0,37;MFRL=0,408;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=288.39 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,73:0.987:73:0,38:0,34:0,73:0,0,44,29 20 10006816 . TAAA T . . AS_SB_TABLE=0,0|29,28;DP=80;ECNT=2;MBQ=0,36;MFRL=0,410;MMQ=60,60;MPOS=28;POPAF=7.30;RPA=6,3;RU=A;STR;TLOD=251.82 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,57:0.985:57:0,29:0,26:0,57:0|1:10006816_TAAA_T:10006816:0,0,29,28 20 10006822 . AC A . . AS_SB_TABLE=0,0|30,28;DP=77;ECNT=2;MBQ=0,36;MFRL=0,410;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=254.94 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,58:0.985:58:0,30:0,27:0,58:0|1:10006816_TAAA_T:10006816:0,0,30,28 -20 10007150 . G C . . AS_SB_TABLE=16,22|14,11;DP=64;ECNT=2;MBQ=37,30;MFRL=409,375;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=69.61 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:38,25:0.398:63:17,16:20,8:38,25:0|1:10007150_G_C:10007150:16,22,14,11 -20 10007175 . C T . . AS_SB_TABLE=9,14|18,20;DP=63;ECNT=2;MBQ=37,38;MFRL=386,407;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=137.92 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 1|0:23,38:0.619:61:15,21:8,17:23,38:1|0:10007150_G_C:10007150:9,14,18,20 +20 10007150 . G C . . AS_SB_TABLE=16,22|14,11;DP=64;ECNT=1;MBQ=37,30;MFRL=409,375;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=69.61 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:38,25:0.398:63:17,16:20,8:38,25:0|1:10007150_G_C:10007150:16,22,14,11 +20 10007175 . C T . . AS_SB_TABLE=9,14|18,20;DP=63;ECNT=1;MBQ=37,38;MFRL=386,407;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=137.92 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 1|0:23,38:0.619:61:15,21:8,17:23,38:1|0:10007150_G_C:10007150:9,14,18,20 20 10007352 . C T . . AS_SB_TABLE=0,0|29,40;DP=70;ECNT=1;MBQ=0,38;MFRL=0,403;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=277.49 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,69:0.986:69:0,37:0,32:0,69:0,0,29,40 20 10007531 . A G . . AS_SB_TABLE=0,0|48,24;DP=75;ECNT=1;MBQ=0,38;MFRL=0,396;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=293.08 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,72:0.987:72:0,41:0,31:0,72:0,0,48,24 -20 10007980 . A C . . AS_SB_TABLE=0,0|39,51;DP=92;ECNT=2;MBQ=0,37;MFRL=0,393;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=353.30 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,90:0.989:90:0,44:0,45:0,90:0,0,39,51 -20 10008029 . T TA . . AS_SB_TABLE=1,2|28,46;DP=97;ECNT=2;MBQ=33,35;MFRL=399,391;MMQ=60,60;MPOS=20;POPAF=7.30;RPA=9,10;RU=A;STR;TLOD=203.30 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:3,74:0.951:77:2,34:1,34:3,74:1,2,28,46 +20 10007980 . A C . . AS_SB_TABLE=0,0|39,51;DP=92;ECNT=1;MBQ=0,37;MFRL=0,393;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=353.30 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,90:0.989:90:0,44:0,45:0,90:0,0,39,51 +20 10008029 . T TA . . AS_SB_TABLE=1,2|28,46;DP=97;ECNT=1;MBQ=33,35;MFRL=399,391;MMQ=60,60;MPOS=20;POPAF=7.30;RPA=9,10;RU=A;STR;TLOD=203.30 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:3,74:0.951:77:2,34:1,34:3,74:1,2,28,46 20 10008146 . TA T . . AS_SB_TABLE=0,0|38,32;DP=77;ECNT=2;MBQ=0,36;MFRL=0,404;MMQ=60,60;MPOS=28;POPAF=7.30;RPA=7,6;RU=A;STR;TLOD=216.06 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,70:0.987:70:0,29:0,39:0,70:0,0,38,32 20 10008221 . T C . . AS_SB_TABLE=0,0|43,37;DP=83;ECNT=2;MBQ=0,37;MFRL=0,398;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=323.40 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,80:0.988:80:0,38:0,41:0,80:0,0,43,37 20 10008458 . T G . . AS_SB_TABLE=0,0|30,39;DP=72;ECNT=1;MBQ=0,37;MFRL=0,392;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=266.45 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,69:0.986:69:0,36:0,32:0,69:0,0,30,39 20 10008742 . G T . . AS_SB_TABLE=10,13|11,15;DP=50;ECNT=2;MBQ=30,38;MFRL=405,392;MMQ=29,29;MPOS=20;POPAF=7.30;TLOD=73.72 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:23,26:0.534:49:8,14:12,12:23,26:10,13,11,15 -20 10008758 . C CA . . AS_SB_TABLE=3,1|16,18;DP=51;ECNT=2;MBQ=32,29;MFRL=376,384;MMQ=33,29;MPOS=29;POPAF=7.30;RPA=14,15;RU=A;STR;TLOD=75.97 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:4,34:0.879:38:1,10:2,14:4,34:3,1,16,18 -20 10008921 . C CA . . AS_SB_TABLE=10,8|8,9;DP=60;ECNT=9;MBQ=32,34;MFRL=402,414;MMQ=60,60;MPOS=22;POPAF=7.30;RPA=13,14;RU=A;STR;TLOD=28.32 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:18,17:0.478:35:8,6:9,9:18,17:10,8,8,9 -20 10008948 . TAAACACACACAC T,TAC,TACACACACAC,TAACACACACAC . . AS_SB_TABLE=2,0|2,1|8,6|4,1|7,0;DP=62;ECNT=9;MBQ=34,36,32,36,37;MFRL=213,382,414,398,406;MMQ=43,29,29,60,60;MPOS=19,32,7,15;POPAF=7.30,7.30,7.30,7.30;TLOD=5.49,39.14,9.35,15.11 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2/3/4:2,3,14,5,7:0.085,0.326,0.177,0.306:31:1,2,7,4,4:1,0,5,0,3:2,3,14,5,7:2,0,21,8 -20 10008951 . AC A . . AS_SB_TABLE=12,0|4,1;DP=53;ECNT=9;MBQ=36,35;MFRL=408,398;MMQ=60,60;MPOS=1;POPAF=7.30;TLOD=9.02 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:12,5:0.312:17:7,4:5,1:12,5:0|1:10008951_AC_A:10008951:12,0,4,1 -20 10008952 . CA C . . AS_SB_TABLE=2,0|11,1;DP=50;ECNT=9;MBQ=32,36;MFRL=213,402;MMQ=43,60;MPOS=11;POPAF=7.30;TLOD=12.52 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:2,12:0.825:14:1,4:1,3:2,12:2,0,11,1 -20 10008954 . CA C . . AS_SB_TABLE=12,0|4,1;DP=51;ECNT=9;MBQ=36,34;MFRL=408,398;MMQ=60,60;MPOS=3;POPAF=7.30;TLOD=8.68 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:12,5:0.312:17:7,4:5,1:12,5:0|1:10008951_AC_A:10008951:12,0,4,1 -20 10008959 . AC A . . AS_SB_TABLE=20,5|10,7;DP=52;ECNT=9;MBQ=38,30;MFRL=412,414;MMQ=60,29;MPOS=30;POPAF=7.30;TLOD=38.90 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:25,17:0.407:42:12,5:10,5:25,17:0|1:10008959_AC_A:10008959:20,5,10,7 -20 10008961 . AC A . . AS_SB_TABLE=28,12|2,1;DP=52;ECNT=9;MBQ=37,36;MFRL=414,382;MMQ=60,29;MPOS=20;POPAF=7.30;TLOD=3.77 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:40,3:0.087:43:22,3:16,0:40,3:0|1:10008961_AC_A:10008961:28,12,2,1 -20 10008962 . CA C . . AS_SB_TABLE=20,6|10,7;DP=53;ECNT=9;MBQ=36,29;MFRL=413,414;MMQ=60,29;MPOS=29;POPAF=7.30;TLOD=39.04 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:26,17:0.398:43:13,4:10,4:26,17:0|1:10008959_AC_A:10008959:20,6,10,7 -20 10008964 . CA C . . AS_SB_TABLE=29,12|2,1;DP=55;ECNT=9;MBQ=36,35;MFRL=413,382;MMQ=60,29;MPOS=22;POPAF=7.30;TLOD=3.72 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:41,3:0.085:44:24,2:15,0:41,3:0|1:10008961_AC_A:10008961:29,12,2,1 +20 10008758 . C CA . . AS_SB_TABLE=3,1|16,18;DP=51;ECNT=1;MBQ=32,29;MFRL=376,384;MMQ=33,29;MPOS=29;POPAF=7.30;RPA=14,15;RU=A;STR;TLOD=75.97 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:4,34:0.879:38:1,10:2,14:4,34:3,1,16,18 +20 10008921 . C CA . . AS_SB_TABLE=10,8|8,9;DP=60;ECNT=4;MBQ=32,34;MFRL=402,414;MMQ=60,60;MPOS=22;POPAF=7.30;RPA=13,14;RU=A;STR;TLOD=28.32 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:18,17:0.478:35:8,6:9,9:18,17:10,8,8,9 +20 10008948 . TAAACACACACAC T,TAC,TACACACACAC,TAACACACACAC . . AS_SB_TABLE=2,0|2,1|8,6|4,1|7,0;DP=62;ECNT=4,3,3,2;MBQ=34,36,32,36,37;MFRL=213,382,414,398,406;MMQ=43,29,29,60,60;MPOS=19,32,7,15;POPAF=7.30,7.30,7.30,7.30;TLOD=5.49,39.14,9.35,15.11 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2/3/4:2,3,14,5,7:0.085,0.326,0.177,0.306:31:1,2,7,4,4:1,0,5,0,3:2,3,14,5,7:2,0,21,8 +20 10008951 . AC A . . AS_SB_TABLE=12,0|4,1;DP=53;ECNT=3;MBQ=36,35;MFRL=408,398;MMQ=60,60;MPOS=1;POPAF=7.30;TLOD=9.02 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:12,5:0.312:17:7,4:5,1:12,5:0|1:10008951_AC_A:10008951:12,0,4,1 +20 10008952 . CA C . . AS_SB_TABLE=2,0|11,1;DP=50;ECNT=2;MBQ=32,36;MFRL=213,402;MMQ=43,60;MPOS=11;POPAF=7.30;TLOD=12.52 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:2,12:0.825:14:1,4:1,3:2,12:2,0,11,1 +20 10008954 . CA C . . AS_SB_TABLE=12,0|4,1;DP=51;ECNT=3;MBQ=36,34;MFRL=408,398;MMQ=60,60;MPOS=3;POPAF=7.30;TLOD=8.68 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:12,5:0.312:17:7,4:5,1:12,5:0|1:10008951_AC_A:10008951:12,0,4,1 +20 10008959 . AC A . . AS_SB_TABLE=20,5|10,7;DP=52;ECNT=3;MBQ=38,30;MFRL=412,414;MMQ=60,29;MPOS=30;POPAF=7.30;TLOD=38.90 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:25,17:0.407:42:12,5:10,5:25,17:0|1:10008959_AC_A:10008959:20,5,10,7 +20 10008961 . AC A . . AS_SB_TABLE=28,12|2,1;DP=52;ECNT=4;MBQ=37,36;MFRL=414,382;MMQ=60,29;MPOS=20;POPAF=7.30;TLOD=3.77 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:40,3:0.087:43:22,3:16,0:40,3:0|1:10008961_AC_A:10008961:28,12,2,1 +20 10008962 . CA C . . AS_SB_TABLE=20,6|10,7;DP=53;ECNT=3;MBQ=36,29;MFRL=413,414;MMQ=60,29;MPOS=29;POPAF=7.30;TLOD=39.04 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:26,17:0.398:43:13,4:10,4:26,17:0|1:10008959_AC_A:10008959:20,6,10,7 +20 10008964 . CA C . . AS_SB_TABLE=29,12|2,1;DP=55;ECNT=4;MBQ=36,35;MFRL=413,382;MMQ=60,29;MPOS=22;POPAF=7.30;TLOD=3.72 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:41,3:0.085:44:24,2:15,0:41,3:0|1:10008961_AC_A:10008961:29,12,2,1 20 10009227 . A G . . AS_SB_TABLE=16,7|19,20;DP=63;ECNT=2;MBQ=38,37;MFRL=378,396;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=139.93 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:23,39:0.625:62:16,21:7,18:23,39:16,7,19,20 -20 10009246 . A G . . AS_SB_TABLE=0,0|42,35;DP=81;ECNT=2;MBQ=0,37;MFRL=0,395;MMQ=60,60;MPOS=16;POPAF=7.30;TLOD=301.21 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,77:0.988:77:0,37:0,39:0,77:0,0,42,35 +20 10009246 . A G . . AS_SB_TABLE=0,0|42,35;DP=81;ECNT=1;MBQ=0,37;MFRL=0,395;MMQ=60,60;MPOS=16;POPAF=7.30;TLOD=301.21 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,77:0.988:77:0,37:0,39:0,77:0,0,42,35 20 10009400 . T A . . AS_SB_TABLE=0,0|39,35;DP=75;ECNT=1;MBQ=0,38;MFRL=0,382;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=300.85 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,74:0.987:74:0,36:0,37:0,74:0,0,39,35 20 10009512 . C G . . AS_SB_TABLE=0,0|30,47;DP=80;ECNT=1;MBQ=0,37;MFRL=0,387;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=304.88 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,77:0.988:77:0,35:0,41:0,77:0,0,30,47 -20 10009719 . A G . . AS_SB_TABLE=0,0|24,33;DP=65;ECNT=9;MBQ=0,30;MFRL=0,393;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=189.68 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,57:0.984:57:0,24:0,27:0,57:0,0,24,33 -20 10009795 . A G . . AS_SB_TABLE=0,0|16,31;DP=49;ECNT=9;MBQ=0,37;MFRL=0,392;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=189.10 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,47:0.982:47:0,22:0,25:0,47:0,0,16,31 -20 10009842 . G GAA . . AS_SB_TABLE=9,10|8,7;DP=52;ECNT=9;MBQ=34,35;MFRL=396,392;MMQ=60,60;MPOS=37;POPAF=7.30;RPA=1,3;RU=A;STR;TLOD=41.97 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:19,15:0.416:34:8,4:11,9:19,15:0|1:10009842_G_GAA:10009842:9,10,8,7 -20 10009844 . G A . . AS_SB_TABLE=8,8|9,10;DP=54;ECNT=9;MBQ=35,36;MFRL=390,396;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=68.30 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:16,19:0.545:35:4,7:10,11:16,19:0|1:10009844_G_A:10009844:8,8,9,10 -20 10009871 . A G . . AS_SB_TABLE=10,8|9,10;DP=62;ECNT=9;MBQ=36,37;MFRL=390,396;MMQ=45,60;MPOS=37;POPAF=7.30;TLOD=67.80 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:18,19:0.526:37:6,7:11,11:18,19:0|1:10009844_G_A:10009844:10,8,9,10 -20 10009875 . A G,AGG . . AS_SB_TABLE=2,0|6,9|7,7;DP=58;ECNT=9;MBQ=35,37,34;MFRL=391,397,386;MMQ=29,60,45;MPOS=35,23;POPAF=7.30,7.30;TLOD=56.83,52.54 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2:2,15,14:0.503,0.481:31:0,4,5:2,10,8:2,15,14:2,0,13,16 -20 10009877 . A AGG . . AS_SB_TABLE=8,9|6,6;DP=59;ECNT=9;MBQ=32,33;MFRL=397,376;MMQ=60,45;MPOS=21;POPAF=7.30;RPA=1,3;RU=G;STR;TLOD=32.39 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:17,12:0.400:29:4,4:10,4:17,12:0|1:10009842_G_GAA:10009842:8,9,6,6 -20 10009879 . A G,AGG . . AS_SB_TABLE=2,0|5,9|4,6;DP=55;ECNT=9;MBQ=26,35,32;MFRL=391,403,380;MMQ=29,60,29;MPOS=39,20;POPAF=7.30,7.30;TLOD=56.16,24.88 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2:2,14,10:0.612,0.372:26:0,2,3:1,9,4:2,14,10:2,0,9,15 -20 10009883 . A G . . AS_SB_TABLE=2,0|15,34;DP=52;ECNT=9;MBQ=26,36;MFRL=391,396;MMQ=29,60;MPOS=22;POPAF=7.30;TLOD=215.81 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:2,49:0.982:51:0,16:2,26:2,49:2,0,15,34 +20 10009719 . A G . . AS_SB_TABLE=0,0|24,33;DP=65;ECNT=6;MBQ=0,30;MFRL=0,393;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=189.68 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,57:0.984:57:0,24:0,27:0,57:0,0,24,33 +20 10009795 . A G . . AS_SB_TABLE=0,0|16,31;DP=49;ECNT=6;MBQ=0,37;MFRL=0,392;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=189.10 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,47:0.982:47:0,22:0,25:0,47:0,0,16,31 +20 10009842 . G GAA . . AS_SB_TABLE=9,10|8,7;DP=52;ECNT=5;MBQ=34,35;MFRL=396,392;MMQ=60,60;MPOS=37;POPAF=7.30;RPA=1,3;RU=A;STR;TLOD=41.97 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:19,15:0.416:34:8,4:11,9:19,15:0|1:10009842_G_GAA:10009842:9,10,8,7 +20 10009844 . G A . . AS_SB_TABLE=8,8|9,10;DP=54;ECNT=6;MBQ=35,36;MFRL=390,396;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=68.30 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:16,19:0.545:35:4,7:10,11:16,19:0|1:10009844_G_A:10009844:8,8,9,10 +20 10009871 . A G . . AS_SB_TABLE=10,8|9,10;DP=62;ECNT=6;MBQ=36,37;MFRL=390,396;MMQ=45,60;MPOS=37;POPAF=7.30;TLOD=67.80 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:18,19:0.526:37:6,7:11,11:18,19:0|1:10009844_G_A:10009844:10,8,9,10 +20 10009875 . A G,AGG . . AS_SB_TABLE=2,0|6,9|7,7;DP=58;ECNT=6,5;MBQ=35,37,34;MFRL=391,397,386;MMQ=29,60,45;MPOS=35,23;POPAF=7.30,7.30;TLOD=56.83,52.54 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2:2,15,14:0.503,0.481:31:0,4,5:2,10,8:2,15,14:2,0,13,16 +20 10009877 . A AGG . . AS_SB_TABLE=8,9|6,6;DP=59;ECNT=5;MBQ=32,33;MFRL=397,376;MMQ=60,45;MPOS=21;POPAF=7.30;RPA=1,3;RU=G;STR;TLOD=32.39 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:17,12:0.400:29:4,4:10,4:17,12:0|1:10009842_G_GAA:10009842:8,9,6,6 +20 10009879 . A G,AGG . . AS_SB_TABLE=2,0|5,9|4,6;DP=55;ECNT=6,5;MBQ=26,35,32;MFRL=391,403,380;MMQ=29,60,29;MPOS=39,20;POPAF=7.30,7.30;TLOD=56.16,24.88 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2:2,14,10:0.612,0.372:26:0,2,3:1,9,4:2,14,10:2,0,9,15 +20 10009883 . A G . . AS_SB_TABLE=2,0|15,34;DP=52;ECNT=6;MBQ=26,36;MFRL=391,396;MMQ=29,60;MPOS=22;POPAF=7.30;TLOD=215.81 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:2,49:0.982:51:0,16:2,26:2,49:2,0,15,34 20 10010393 . T G . . AS_SB_TABLE=24,12|19,24;DP=79;ECNT=1;MBQ=38,36;MFRL=387,388;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=148.61 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:36,43:0.545:79:19,12:16,30:36,43:24,12,19,24 20 10010536 . G GA . . AS_SB_TABLE=0,0|37,43;DP=92;ECNT=1;MBQ=0,35;MFRL=0,395;MMQ=60,60;MPOS=28;POPAF=7.30;RPA=6,7;RU=A;STR;TLOD=245.00 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,80:0.989:80:0,34:0,43:0,80:0,0,37,43 20 10010766 . T G . . AS_SB_TABLE=0,0|35,31;DP=70;ECNT=2;MBQ=0,30;MFRL=0,401;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=242.19 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,66:0.986:66:0,34:0,32:0,66:0,0,35,31 20 10010832 . T C . . AS_SB_TABLE=0,0|31,44;DP=76;ECNT=2;MBQ=0,36;MFRL=0,388;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=296.11 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,75:0.987:75:0,38:0,36:0,74:0,0,31,44 20 10011075 . C T . . AS_SB_TABLE=22,22|22,17;DP=86;ECNT=1;MBQ=30,38;MFRL=406,390;MMQ=60,60;MPOS=18;POPAF=7.30;TLOD=134.56 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:44,39:0.471:83:20,18:22,20:44,39:22,22,22,17 20 10011309 . T C . . AS_SB_TABLE=0,0|30,47;DP=80;ECNT=1;MBQ=0,30;MFRL=0,396;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=270.20 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,77:0.988:77:0,38:0,37:0,77:0,0,30,47 -20 10011517 . GA G,GAA . . AS_SB_TABLE=23,14|15,15|4,2;DP=99;ECNT=1;MBQ=35,35,38;MFRL=398,389,421;MMQ=60,60,60;MPOS=35,18;POPAF=7.30,7.30;RPA=14,13,15;RU=A;STR;TLOD=52.21,4.87 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2:37,30,6:0.390,0.085:73:14,16,3:23,14,2:37,30,6:23,14,19,17 +20 10011517 . GA G,GAA . . AS_SB_TABLE=23,14|15,15|4,2;DP=99;ECNT=1,1;MBQ=35,35,38;MFRL=398,389,421;MMQ=60,60,60;MPOS=35,18;POPAF=7.30,7.30;RPA=14,13,15;RU=A;STR;TLOD=52.21,4.87 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2:37,30,6:0.390,0.085:73:14,16,3:23,14,2:37,30,6:23,14,19,17 20 10011666 . C T . . AS_SB_TABLE=0,0|43,30;DP=74;ECNT=1;MBQ=0,38;MFRL=0,389;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=297.10 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,73:0.987:73:0,36:0,37:0,73:0,0,43,30 20 10011939 . C T . . AS_SB_TABLE=0,0|23,39;DP=66;ECNT=2;MBQ=0,38;MFRL=0,402;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=252.36 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,62:0.985:62:0,31:0,31:0,62:0,0,23,39 -20 10012021 . CA C . . AS_SB_TABLE=0,0|26,40;DP=71;ECNT=2;MBQ=0,35;MFRL=0,398;MMQ=60,60;MPOS=31;POPAF=7.30;RPA=8,7;RU=A;STR;TLOD=199.53 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,66:0.986:66:0,38:0,27:0,66:0,0,26,40 +20 10012021 . CA C . . AS_SB_TABLE=0,0|26,40;DP=71;ECNT=1;MBQ=0,35;MFRL=0,398;MMQ=60,60;MPOS=31;POPAF=7.30;RPA=8,7;RU=A;STR;TLOD=199.53 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,66:0.986:66:0,38:0,27:0,66:0,0,26,40 20 10012362 . G T . . AS_SB_TABLE=0,0|2,21;DP=25;ECNT=3;MBQ=0,36;MFRL=0,402;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=85.36 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,23:0.961:23:0,10:0,12:0,23:0,0,2,21 20 10012384 . T C . . AS_SB_TABLE=0,10|2,6;DP=18;ECNT=3;MBQ=39,36;MFRL=424,397;MMQ=60,59;MPOS=33;POPAF=7.30;TLOD=25.29 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:10,8:0.450:18:1,6:9,2:10,8:0,10,2,6 20 10012387 . T C . . AS_SB_TABLE=0,0|2,15;DP=18;ECNT=3;MBQ=0,26;MFRL=0,402;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=54.91 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,17:0.948:17:0,4:0,7:0,17:0,0,2,15 -20 10012479 . A G . . AS_SB_TABLE=0,0|9,8;DP=18;ECNT=8;MBQ=0,29;MFRL=0,397;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=59.04 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,17:0.949:17:0,5:0,9:0,17:0|1:10012479_A_G:10012479:0,0,9,8 -20 10012498 . C G . . AS_SB_TABLE=0,0|3,7;DP=10;ECNT=8;MBQ=0,36;MFRL=0,403;MMQ=60,33;MPOS=26;POPAF=7.30;TLOD=44.86 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,10:0.925:10:0,6:0,4:0,11:0|1:10012479_A_G:10012479:0,0,3,7 -20 10012518 . T C . . AS_SB_TABLE=0,0|4,7;DP=12;ECNT=8;MBQ=0,32;MFRL=0,402;MMQ=60,29;MPOS=13;POPAF=7.30;TLOD=47.79 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,11:0.932:11:0,6:0,3:0,12:0|1:10012479_A_G:10012479:0,0,4,7 -20 10012521 . C T . . AS_SB_TABLE=4,4|2,2;DP=12;ECNT=8;MBQ=29,37;MFRL=404,387;MMQ=33,29;MPOS=28;POPAF=7.30;TLOD=9.77 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:8,4:0.356:12:4,3:3,1:8,4:4,4,2,2 -20 10012570 . G GCA . . AS_SB_TABLE=0,0|10,1;DP=11;ECNT=8;MBQ=0,37;MFRL=0,403;MMQ=60,29;MPOS=28;POPAF=7.30;TLOD=48.38 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,11:0.927:11:0,4:0,4:0,11:0|1:10012570_G_GCA:10012570:0,0,10,1 -20 10012572 . GT G . . AS_SB_TABLE=0,0|10,1;DP=12;ECNT=8;MBQ=0,35;MFRL=0,403;MMQ=60,29;MPOS=24;POPAF=7.30;TLOD=48.37 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,11:0.929:11:0,5:0,6:0,11:0|1:10012570_G_GCA:10012570:0,0,10,1 -20 10012631 . C CG . . AS_SB_TABLE=8,0|9,4;DP=21;ECNT=8;MBQ=33,33;MFRL=411,403;MMQ=60,37;MPOS=18;POPAF=7.30;RPA=1,2;RU=G;STR;TLOD=51.84 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:8,13:0.609:21:3,5:5,6:8,13:0|1:10012631_C_CG:10012631:8,0,9,4 -20 10012636 . G C . . AS_SB_TABLE=8,0|10,4;DP=22;ECNT=8;MBQ=25,36;MFRL=411,404;MMQ=60,44;MPOS=17;POPAF=7.30;TLOD=55.33 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:8,14:0.625:22:3,7:4,6:8,14:0|1:10012631_C_CG:10012631:8,0,10,4 +20 10012479 . A G . . AS_SB_TABLE=0,0|9,8;DP=18;ECNT=3;MBQ=0,29;MFRL=0,397;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=59.04 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,17:0.949:17:0,5:0,9:0,17:0|1:10012479_A_G:10012479:0,0,9,8 +20 10012498 . C G . . AS_SB_TABLE=0,0|3,7;DP=10;ECNT=3;MBQ=0,36;MFRL=0,403;MMQ=60,33;MPOS=26;POPAF=7.30;TLOD=44.86 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,10:0.925:10:0,6:0,4:0,11:0|1:10012479_A_G:10012479:0,0,3,7 +20 10012518 . T C . . AS_SB_TABLE=0,0|4,7;DP=12;ECNT=3;MBQ=0,32;MFRL=0,402;MMQ=60,29;MPOS=13;POPAF=7.30;TLOD=47.79 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,11:0.932:11:0,6:0,3:0,12:0|1:10012479_A_G:10012479:0,0,4,7 +20 10012521 . C T . . AS_SB_TABLE=4,4|2,2;DP=12;ECNT=6;MBQ=29,37;MFRL=404,387;MMQ=33,29;MPOS=28;POPAF=7.30;TLOD=9.77 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:8,4:0.356:12:4,3:3,1:8,4:4,4,2,2 +20 10012570 . G GCA . . AS_SB_TABLE=0,0|10,1;DP=11;ECNT=2;MBQ=0,37;MFRL=0,403;MMQ=60,29;MPOS=28;POPAF=7.30;TLOD=48.38 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,11:0.927:11:0,4:0,4:0,11:0|1:10012570_G_GCA:10012570:0,0,10,1 +20 10012572 . GT G . . AS_SB_TABLE=0,0|10,1;DP=12;ECNT=2;MBQ=0,35;MFRL=0,403;MMQ=60,29;MPOS=24;POPAF=7.30;TLOD=48.37 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,11:0.929:11:0,5:0,6:0,11:0|1:10012570_G_GCA:10012570:0,0,10,1 +20 10012631 . C CG . . AS_SB_TABLE=8,0|9,4;DP=21;ECNT=2;MBQ=33,33;MFRL=411,403;MMQ=60,37;MPOS=18;POPAF=7.30;RPA=1,2;RU=G;STR;TLOD=51.84 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:8,13:0.609:21:3,5:5,6:8,13:0|1:10012631_C_CG:10012631:8,0,9,4 +20 10012636 . G C . . AS_SB_TABLE=8,0|10,4;DP=22;ECNT=2;MBQ=25,36;MFRL=411,404;MMQ=60,44;MPOS=17;POPAF=7.30;TLOD=55.33 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:8,14:0.625:22:3,7:4,6:8,14:0|1:10012631_C_CG:10012631:8,0,10,4 20 10012714 . G C . . AS_SB_TABLE=0,0|29,6;DP=36;ECNT=2;MBQ=0,36;MFRL=0,401;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=131.36 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,35:0.973:35:0,17:0,18:0,35:0,0,29,6 20 10012751 . T C . . AS_SB_TABLE=0,0|17,13;DP=31;ECNT=2;MBQ=0,31;MFRL=0,394;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=95.12 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,30:0.969:30:0,15:0,12:0,30:0,0,17,13 20 10013119 . C T . . AS_SB_TABLE=19,10|17,13;DP=61;ECNT=1;MBQ=37,37;MFRL=387,409;MMQ=57,50;MPOS=22;POPAF=7.30;TLOD=103.18 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:29,30:0.508:59:13,22:16,8:29,30:19,10,17,13 20 10013574 . G A . . AS_SB_TABLE=15,23|7,24;DP=73;ECNT=1;MBQ=36,38;MFRL=404,397;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=107.23 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:38,31:0.451:69:19,12:19,19:38,31:15,23,7,24 20 10014990 . C CAT . . AS_SB_TABLE=28,10|26,13;DP=89;ECNT=1;MBQ=37,37;MFRL=399,386;MMQ=60,60;MPOS=27;POPAF=7.30;RPA=5,6;RU=AT;STR;TLOD=126.64 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:38,39:0.506:77:23,17:14,21:38,39:28,10,26,13 20 10015679 . C T . . AS_SB_TABLE=5,0|5,0;DP=10;ECNT=2;MBQ=37,35;MFRL=397,380;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=16.44 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:5,5:0.500:10:2,4:3,1:5,5:5,0,5,0 -20 10015761 . T C . . AS_SB_TABLE=9,0|12,1;DP=23;ECNT=2;MBQ=37,32;MFRL=397,387;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=36.84 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:9,13:0.580:22:3,6:6,5:9,13:9,0,12,1 +20 10015761 . T C . . AS_SB_TABLE=9,0|12,1;DP=23;ECNT=1;MBQ=37,32;MFRL=397,387;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=36.84 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:9,13:0.580:22:3,6:6,5:9,13:9,0,12,1 20 10018158 . G C . . AS_SB_TABLE=18,22|20,28;DP=94;ECNT=1;MBQ=30,38;MFRL=402,399;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=166.02 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:40,48:0.545:88:13,26:25,21:40,48:18,22,20,28 20 10018555 . G A . . AS_SB_TABLE=20,15|21,24;DP=84;ECNT=1;MBQ=37,37;MFRL=392,395;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=159.00 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:35,45:0.561:80:11,22:24,23:35,45:20,15,21,24 20 10019093 . A G . . AS_SB_TABLE=15,18|19,17;DP=73;ECNT=1;MBQ=37,37;MFRL=401,405;MMQ=60,60;MPOS=20;POPAF=7.30;TLOD=126.46 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:33,36:0.523:69:14,24:18,12:33,36:15,18,19,17 20 10020229 . G A . . AS_SB_TABLE=22,16|24,20;DP=84;ECNT=1;MBQ=30,38;MFRL=404,392;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=155.97 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:38,44:0.536:82:18,22:20,22:38,44:22,16,24,20 20 10023689 . G A . . AS_SB_TABLE=16,13|26,25;DP=82;ECNT=1;MBQ=37,38;MFRL=399,401;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=188.55 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:29,51:0.634:80:14,22:15,29:29,51:16,13,26,25 20 10024107 . C T . . AS_SB_TABLE=21,17|28,20;DP=89;ECNT=1;MBQ=31,38;MFRL=398,400;MMQ=60,60;MPOS=20;POPAF=7.30;TLOD=172.09 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:38,48:0.565:86:14,29:22,19:37,48:21,17,28,20 -20 10024300 . CTT C,CTTTT . . AS_SB_TABLE=2,1|3,1|6,2;DP=53;ECNT=1;MBQ=33,37,37;MFRL=379,422,400;MMQ=60,29,60;MPOS=24,35;POPAF=7.30,7.30;RPA=23,21,25;RU=T;STR;TLOD=5.13,12.50 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2:3,4,8:0.227,0.527:15:2,3,2:0,1,5:3,4,8:2,1,9,3 +20 10024300 . CTT C,CTTTT . . AS_SB_TABLE=2,1|3,1|6,2;DP=53;ECNT=1,1;MBQ=33,37,37;MFRL=379,422,400;MMQ=60,29,60;MPOS=24,35;POPAF=7.30,7.30;RPA=23,21,25;RU=T;STR;TLOD=5.13,12.50 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2:3,4,8:0.227,0.527:15:2,3,2:0,1,5:3,4,8:2,1,9,3 20 10026357 . T C . . AS_SB_TABLE=10,18|20,15;DP=63;ECNT=1;MBQ=38,37;MFRL=391,399;MMQ=60,60;MPOS=17;POPAF=7.30;TLOD=118.85 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:28,35:0.554:63:15,14:13,21:28,35:10,18,20,15 20 10026794 . C T . . AS_SB_TABLE=7,12|15,18;DP=56;ECNT=1;MBQ=30,37;MFRL=403,397;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=111.32 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:19,33:0.628:52:9,15:10,16:19,33:7,12,15,18 20 10027228 . G GA . . AS_SB_TABLE=16,15|15,17;DP=72;ECNT=4;MBQ=37,37;MFRL=396,389;MMQ=60,60;MPOS=28;POPAF=7.30;RPA=4,5;RU=A;STR;TLOD=123.29 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:31,32:0.507:63:16,14:14,16:31,32:0|1:10027228_G_GA:10027228:16,15,15,17 @@ -173,7 +173,7 @@ 20 10030188 . T A . . AS_SB_TABLE=24,18|15,24;DP=82;ECNT=1;MBQ=39,39;MFRL=386,393;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=139.23 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:42,39:0.482:81:16,14:26,25:42,39:24,18,15,24 20 10031254 . A AT . . AS_SB_TABLE=27,11|25,22;DP=90;ECNT=1;MBQ=38,38;MFRL=396,405;MMQ=60,60;MPOS=32;POPAF=7.30;RPA=1,2;RU=T;STR;TLOD=149.40 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:38,47:0.552:85:19,22:17,24:38,47:27,11,25,22 20 10031342 . G A . . AS_SB_TABLE=22,19|31,21;DP=93;ECNT=1;MBQ=37,38;MFRL=403,399;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=185.69 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:41,52:0.558:93:22,28:18,24:41,52:22,19,31,21 -20 10031798 . G A . . AS_SB_TABLE=0,0|57,47;DP=107;ECNT=2;MBQ=0,38;MFRL=0,382;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=430.45 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,104:0.991:104:0,62:0,42:0,104:0,0,57,47 +20 10031798 . G A . . AS_SB_TABLE=0,0|57,47;DP=107;ECNT=1;MBQ=0,38;MFRL=0,382;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=430.45 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,104:0.991:104:0,62:0,42:0,104:0,0,57,47 20 10031827 . C T . . AS_SB_TABLE=32,20|29,27;DP=115;ECNT=2;MBQ=37,38;MFRL=380,392;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=202.36 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:52,56:0.518:108:29,29:23,27:52,56:32,20,29,27 20 10032094 . G A . . AS_SB_TABLE=14,33|16,20;DP=86;ECNT=1;MBQ=36,38;MFRL=380,376;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=124.34 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:47,36:0.436:83:25,23:21,13:47,36:14,33,16,20 20 10032413 . T G . . AS_SB_TABLE=15,20|20,11;DP=66;ECNT=1;MBQ=39,30;MFRL=400,384;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=89.01 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:35,31:0.470:66:22,14:13,17:35,31:15,20,20,11 @@ -188,16 +188,16 @@ 20 10036934 . AGCCC A . . AS_SB_TABLE=9,24|15,14;DP=86;ECNT=6;MBQ=39,38;MFRL=396,410;MMQ=60,39;MPOS=27;POPAF=7.30;TLOD=108.30 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:33,29:0.481:62:12,10:14,17:33,29:0|1:10036925_TAG_T:10036925:9,24,15,14 20 10036939 . TAGCC T . . AS_SB_TABLE=9,24|15,14;DP=80;ECNT=6;MBQ=38,38;MFRL=396,410;MMQ=60,39;MPOS=28;POPAF=7.30;TLOD=108.16 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:33,29:0.478:62:14,9:18,17:33,29:0|1:10036925_TAG_T:10036925:9,24,15,14 20 10036944 . CTAGATA C . . AS_SB_TABLE=11,28|15,14;DP=87;ECNT=6;MBQ=38,34;MFRL=396,410;MMQ=60,39;MPOS=29;POPAF=7.30;TLOD=106.58 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:39,29:0.437:68:14,10:18,17:39,29:0|1:10036925_TAG_T:10036925:11,28,15,14 -20 10037037 . C T . . AS_SB_TABLE=28,11|28,14;DP=88;ECNT=10;MBQ=36,38;MFRL=406,407;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=145.62 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:39,42:0.523:81:15,18:20,24:39,42:28,11,28,14 -20 10037106 . T TAG . . AS_SB_TABLE=0,0|35,27;DP=83;ECNT=10;MBQ=0,38;MFRL=0,394;MMQ=60,60;MPOS=33;POPAF=7.30;RPA=1,2;RU=AG;STR;TLOD=275.85 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,62:0.986:62:0,32:0,25:0,62:0|1:10037106_T_TAG:10037106:0,0,35,27 -20 10037107 . A AT . . AS_SB_TABLE=0,0|35,27;DP=82;ECNT=10;MBQ=0,38;MFRL=0,394;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=275.86 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,62:0.986:62:0,36:0,24:0,62:0|1:10037106_T_TAG:10037106:0,0,35,27 -20 10037110 . T TA . . AS_SB_TABLE=0,0|35,28;DP=84;ECNT=10;MBQ=0,38;MFRL=0,394;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=279.85 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,63:0.986:63:0,37:0,26:0,63:0|1:10037106_T_TAG:10037106:0,0,35,28 -20 10037121 . T TAG . . AS_SB_TABLE=0,0|11,15;DP=85;ECNT=10;MBQ=0,37;MFRL=0,402;MMQ=60,29;MPOS=12;POPAF=7.30;RPA=1,2;RU=AG;STR;TLOD=116.38 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,26:0.973:26:0,14:0,9:0,27:0|1:10037121_T_TAG:10037121:0,0,11,15 -20 10037122 . A AT . . AS_SB_TABLE=0,0|11,15;DP=84;ECNT=10;MBQ=0,38;MFRL=0,402;MMQ=60,29;MPOS=14;POPAF=7.30;TLOD=116.40 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,26:0.973:26:0,15:0,9:0,27:0|1:10037121_T_TAG:10037121:0,0,11,15 -20 10037125 . T TA . . AS_SB_TABLE=0,0|11,16;DP=83;ECNT=10;MBQ=0,37;MFRL=0,401;MMQ=60,29;MPOS=17;POPAF=7.30;TLOD=120.93 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,27:0.974:27:0,16:0,10:0,28:0|1:10037121_T_TAG:10037121:0,0,11,16 -20 10037136 . T TAG . . AS_SB_TABLE=0,0|15,21;DP=81;ECNT=10;MBQ=0,38;MFRL=0,397;MMQ=60,29;MPOS=28;POPAF=7.30;RPA=1,2;RU=AG;STR;TLOD=161.56 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,36:0.980:36:0,18:0,14:0,37:0|1:10037121_T_TAG:10037121:0,0,15,21 -20 10037137 . A AT . . AS_SB_TABLE=0,0|15,22;DP=79;ECNT=10;MBQ=0,38;MFRL=0,397;MMQ=60,29;MPOS=30;POPAF=7.30;TLOD=165.42 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,37:0.980:37:0,21:0,15:0,38:0|1:10037121_T_TAG:10037121:0,0,15,22 -20 10037144 . T TA . . AS_SB_TABLE=0,0|17,26;DP=81;ECNT=10;MBQ=0,38;MFRL=0,397;MMQ=60,29;MPOS=36;POPAF=7.30;TLOD=184.14 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,43:0.982:43:0,23:0,17:0,43:0|1:10037121_T_TAG:10037121:0,0,17,26 +20 10037037 . C T . . AS_SB_TABLE=28,11|28,14;DP=88;ECNT=1;MBQ=36,38;MFRL=406,407;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=145.62 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:39,42:0.523:81:15,18:20,24:39,42:28,11,28,14 +20 10037106 . T TAG . . AS_SB_TABLE=0,0|35,27;DP=83;ECNT=3;MBQ=0,38;MFRL=0,394;MMQ=60,60;MPOS=33;POPAF=7.30;RPA=1,2;RU=AG;STR;TLOD=275.85 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,62:0.986:62:0,32:0,25:0,62:0|1:10037106_T_TAG:10037106:0,0,35,27 +20 10037107 . A AT . . AS_SB_TABLE=0,0|35,27;DP=82;ECNT=3;MBQ=0,38;MFRL=0,394;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=275.86 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,62:0.986:62:0,36:0,24:0,62:0|1:10037106_T_TAG:10037106:0,0,35,27 +20 10037110 . T TA . . AS_SB_TABLE=0,0|35,28;DP=84;ECNT=3;MBQ=0,38;MFRL=0,394;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=279.85 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,63:0.986:63:0,37:0,26:0,63:0|1:10037106_T_TAG:10037106:0,0,35,28 +20 10037121 . T TAG . . AS_SB_TABLE=0,0|11,15;DP=85;ECNT=6;MBQ=0,37;MFRL=0,402;MMQ=60,29;MPOS=12;POPAF=7.30;RPA=1,2;RU=AG;STR;TLOD=116.38 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,26:0.973:26:0,14:0,9:0,27:0|1:10037121_T_TAG:10037121:0,0,11,15 +20 10037122 . A AT . . AS_SB_TABLE=0,0|11,15;DP=84;ECNT=6;MBQ=0,38;MFRL=0,402;MMQ=60,29;MPOS=14;POPAF=7.30;TLOD=116.40 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,26:0.973:26:0,15:0,9:0,27:0|1:10037121_T_TAG:10037121:0,0,11,15 +20 10037125 . T TA . . AS_SB_TABLE=0,0|11,16;DP=83;ECNT=6;MBQ=0,37;MFRL=0,401;MMQ=60,29;MPOS=17;POPAF=7.30;TLOD=120.93 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,27:0.974:27:0,16:0,10:0,28:0|1:10037121_T_TAG:10037121:0,0,11,16 +20 10037136 . T TAG . . AS_SB_TABLE=0,0|15,21;DP=81;ECNT=6;MBQ=0,38;MFRL=0,397;MMQ=60,29;MPOS=28;POPAF=7.30;RPA=1,2;RU=AG;STR;TLOD=161.56 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,36:0.980:36:0,18:0,14:0,37:0|1:10037121_T_TAG:10037121:0,0,15,21 +20 10037137 . A AT . . AS_SB_TABLE=0,0|15,22;DP=79;ECNT=6;MBQ=0,38;MFRL=0,397;MMQ=60,29;MPOS=30;POPAF=7.30;TLOD=165.42 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,37:0.980:37:0,21:0,15:0,38:0|1:10037121_T_TAG:10037121:0,0,15,22 +20 10037144 . T TA . . AS_SB_TABLE=0,0|17,26;DP=81;ECNT=6;MBQ=0,38;MFRL=0,397;MMQ=60,29;MPOS=36;POPAF=7.30;TLOD=184.14 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,43:0.982:43:0,23:0,17:0,43:0|1:10037121_T_TAG:10037121:0,0,17,26 20 10037709 . A T . . AS_SB_TABLE=24,15|19,13;DP=73;ECNT=1;MBQ=38,37;MFRL=401,401;MMQ=60,60;MPOS=20;POPAF=7.30;TLOD=102.53 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:39,32:0.450:71:23,15:16,16:39,32:24,15,19,13 20 10039371 . T G . . AS_SB_TABLE=15,19|24,16;DP=76;ECNT=1;MBQ=38,37;MFRL=380,385;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=134.76 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:34,40:0.533:74:14,28:20,11:34,39:15,19,24,16 20 10040772 . C CT . . AS_SB_TABLE=0,0|37,33;DP=85;ECNT=3;MBQ=0,34;MFRL=0,394;MMQ=60,60;MPOS=27;POPAF=7.30;RPA=8,9;RU=T;STR;TLOD=201.44 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,70:0.987:70:0,33:0,35:0,70:0,0,37,33 @@ -207,8 +207,8 @@ 20 10041698 . C CAT . . AS_SB_TABLE=0,1|30,42;DP=80;ECNT=2;MBQ=21,36;MFRL=392,391;MMQ=60,60;MPOS=27;POPAF=7.30;RPA=2,3;RU=AT;STR;TLOD=281.37 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:1,72:0.986:73:1,26:0,41:1,72:0,1,30,42 20 10041701 . A ATG . . AS_SB_TABLE=2,6|22,28;DP=80;ECNT=2;MBQ=38,38;MFRL=404,387;MMQ=60,60;MPOS=36;POPAF=7.30;RPA=13,14;RU=TG;STR;TLOD=150.93 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:8,50:0.859:58:4,18:3,31:8,50:2,6,22,28 20 10042319 . C T . . AS_SB_TABLE=0,0|38,28;DP=69;ECNT=1;MBQ=0,37;MFRL=0,407;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=266.88 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,66:0.986:66:0,30:0,35:0,66:0,0,38,28 -20 10042761 . A G . . AS_SB_TABLE=0,0|58,33;DP=94;ECNT=2;MBQ=0,37;MFRL=0,392;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=356.27 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,91:0.989:91:0,41:0,46:0,91:0,0,58,33 -20 10042829 . A G . . AS_SB_TABLE=0,0|42,36;DP=82;ECNT=2;MBQ=0,37;MFRL=0,391;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=306.47 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,78:0.988:78:0,35:0,42:0,78:0,0,42,36 +20 10042761 . A G . . AS_SB_TABLE=0,0|58,33;DP=94;ECNT=1;MBQ=0,37;MFRL=0,392;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=356.27 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,91:0.989:91:0,41:0,46:0,91:0,0,58,33 +20 10042829 . A G . . AS_SB_TABLE=0,0|42,36;DP=82;ECNT=1;MBQ=0,37;MFRL=0,391;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=306.47 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,78:0.988:78:0,35:0,42:0,78:0,0,42,36 20 10043002 . A T . . AS_SB_TABLE=19,29|18,20;DP=89;ECNT=1;MBQ=36,38;MFRL=399,385;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=130.93 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:48,38:0.443:86:30,20:18,18:48,38:19,29,18,20 20 10044849 . A G . . AS_SB_TABLE=0,0|22,37;DP=59;ECNT=1;MBQ=0,31;MFRL=0,393;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=210.23 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,59:0.984:59:0,32:0,25:0,59:0,0,22,37 20 10045078 . G T . . AS_SB_TABLE=0,0|37,44;DP=84;ECNT=1;MBQ=0,38;MFRL=0,399;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=328.07 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,81:0.988:81:0,38:0,43:0,81:0,0,37,44 @@ -223,8 +223,8 @@ 20 10051448 . T C . . AS_SB_TABLE=27,8|23,12;DP=71;ECNT=1;MBQ=37,37;MFRL=405,393;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=115.47 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:35,35:0.500:70:15,19:19,15:35,35:27,8,23,12 20 10052688 . C A . . AS_SB_TABLE=27,18|16,16;DP=83;ECNT=1;MBQ=37,37;MFRL=408,394;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=108.68 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:45,32:0.418:77:15,19:30,13:45,32:27,18,16,16 20 10058022 . T C . . AS_SB_TABLE=16,20|13,19;DP=72;ECNT=1;MBQ=37,35;MFRL=406,405;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=99.59 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:36,32:0.470:68:21,16:15,15:36,32:16,20,13,19 -20 10062935 . CA C,CAA . . AS_SB_TABLE=2,3|5,3|4,6;DP=89;ECNT=1;MBQ=28,35,35;MFRL=382,372,394;MMQ=60,60,60;MPOS=24,18;POPAF=7.30,7.30;RPA=20,19,21;RU=A;STR;TLOD=3.57,14.67 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2:5,8,10:0.198,0.517:23:1,3,1:2,4,3:5,8,10:2,3,9,9 -20 10067049 . TAAAAAAAAA T,TA,TAA . . AS_SB_TABLE=1,1|3,1|5,2|4,5;DP=73;ECNT=2;MBQ=36,32,37,29;MFRL=434,443,407,416;MMQ=45,45,29,29;MPOS=32,31,11;POPAF=7.30,7.30,7.30;RPA=25,16,17,18;RU=A;STR;TLOD=3.68,9.22,18.38 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2/3:2,4,7,9:0.095,0.238,0.541:22:0,1,5,5:1,2,1,2:2,4,7,9:1,1,12,8 +20 10062935 . CA C,CAA . . AS_SB_TABLE=2,3|5,3|4,6;DP=89;ECNT=1,1;MBQ=28,35,35;MFRL=382,372,394;MMQ=60,60,60;MPOS=24,18;POPAF=7.30,7.30;RPA=20,19,21;RU=A;STR;TLOD=3.57,14.67 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2:5,8,10:0.198,0.517:23:1,3,1:2,4,3:5,8,10:2,3,9,9 +20 10067049 . TAAAAAAAAA T,TA,TAA . . AS_SB_TABLE=1,1|3,1|5,2|4,5;DP=73;ECNT=2,2,2;MBQ=36,32,37,29;MFRL=434,443,407,416;MMQ=45,45,29,29;MPOS=32,31,11;POPAF=7.30,7.30,7.30;RPA=25,16,17,18;RU=A;STR;TLOD=3.68,9.22,18.38 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2/3:2,4,7,9:0.095,0.238,0.541:22:0,1,5,5:1,2,1,2:2,4,7,9:1,1,12,8 20 10067090 . C A . . AS_SB_TABLE=0,0|27,28;DP=56;ECNT=2;MBQ=0,37;MFRL=0,408;MMQ=60,60;MPOS=18;POPAF=7.30;TLOD=201.54 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,55:0.983:55:0,22:0,29:0,55:0,0,27,28 20 10067264 . G A . . AS_SB_TABLE=0,0|38,35;DP=73;ECNT=1;MBQ=0,37;MFRL=0,392;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=293.24 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,73:0.987:73:0,26:0,46:0,73:0,0,38,35 20 10067722 . A C . . AS_SB_TABLE=0,0|25,29;DP=59;ECNT=1;MBQ=0,37;MFRL=0,385;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=215.70 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,54:0.983:54:0,25:0,29:0,54:0,0,25,29 @@ -245,14 +245,14 @@ 20 10074806 . G A . . AS_SB_TABLE=0,0|33,38;DP=75;ECNT=1;MBQ=0,37;MFRL=0,402;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=282.69 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,71:0.987:71:0,34:0,36:0,71:0,0,33,38 20 10075043 . T C . . AS_SB_TABLE=0,0|36,25;DP=64;ECNT=1;MBQ=0,37;MFRL=0,402;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=241.55 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,61:0.984:61:0,24:0,37:0,61:0,0,36,25 20 10075142 . G A . . AS_SB_TABLE=36,25|0,4;DP=74;ECNT=2;MBQ=37,26;MFRL=402,388;MMQ=60,60;MPOS=20;POPAF=7.30;TLOD=3.01 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:61,4:0.064:65:16,2:41,1:61,4:36,25,0,4 -20 10075168 . C T . . AS_SB_TABLE=0,0|38,50;DP=91;ECNT=2;MBQ=0,38;MFRL=0,408;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=362.10 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,88:0.989:88:0,33:0,54:0,88:0,0,38,50 +20 10075168 . C T . . AS_SB_TABLE=0,0|38,50;DP=91;ECNT=1;MBQ=0,38;MFRL=0,408;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=362.10 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,88:0.989:88:0,33:0,54:0,88:0,0,38,50 20 10075508 . GA G . . AS_SB_TABLE=0,0|29,41;DP=81;ECNT=1;MBQ=0,34;MFRL=0,407;MMQ=60,60;MPOS=25;POPAF=7.30;RPA=11,10;RU=A;STR;TLOD=194.68 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,70:0.987:70:0,31:0,37:0,70:0,0,29,41 20 10076250 . A G . . AS_SB_TABLE=14,26|20,19;DP=82;ECNT=1;MBQ=37,30;MFRL=404,399;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=112.78 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:40,39:0.492:79:13,20:27,17:40,39:14,26,20,19 20 10076339 . A G . . AS_SB_TABLE=12,20|18,22;DP=76;ECNT=2;MBQ=35,35;MFRL=399,400;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=133.18 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:32,40:0.554:72:15,19:17,21:32,40:12,20,18,22 20 10076399 . G A . . AS_SB_TABLE=22,22|22,28;DP=95;ECNT=2;MBQ=38,38;MFRL=398,403;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=182.82 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:44,50:0.531:94:19,21:25,28:44,50:22,22,22,28 -20 10076989 . CA C . . AS_SB_TABLE=18,8|7,10;DP=82;ECNT=3;MBQ=37,34;MFRL=411,409;MMQ=60,60;MPOS=33;POPAF=7.30;RPA=18,17;RU=A;STR;TLOD=18.94 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:26,17:0.378:43:6,10:15,6:26,17:0|1:10076989_CA_C:10076989:18,8,7,10 -20 10077008 . T A . . AS_SB_TABLE=18,31|5,0;DP=68;ECNT=3;MBQ=35,15;MFRL=400,413;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=5.54 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 1|0:49,5:0.100:54:21,0:17,2:49,5:1|0:10076989_CA_C:10076989:18,31,5,0 -20 10077010 . G A . . AS_SB_TABLE=18,31|5,0;DP=58;ECNT=3;MBQ=37,15;MFRL=400,413;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=5.57 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 1|0:49,5:0.101:54:23,0:17,1:49,5:1|0:10076989_CA_C:10076989:18,31,5,0 +20 10076989 . CA C . . AS_SB_TABLE=18,8|7,10;DP=82;ECNT=1;MBQ=37,34;MFRL=411,409;MMQ=60,60;MPOS=33;POPAF=7.30;RPA=18,17;RU=A;STR;TLOD=18.94 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:26,17:0.378:43:6,10:15,6:26,17:0|1:10076989_CA_C:10076989:18,8,7,10 +20 10077008 . T A . . AS_SB_TABLE=18,31|5,0;DP=68;ECNT=2;MBQ=35,15;MFRL=400,413;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=5.54 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 1|0:49,5:0.100:54:21,0:17,2:49,5:1|0:10076989_CA_C:10076989:18,31,5,0 +20 10077010 . G A . . AS_SB_TABLE=18,31|5,0;DP=58;ECNT=2;MBQ=37,15;MFRL=400,413;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=5.57 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 1|0:49,5:0.101:54:23,0:17,1:49,5:1|0:10076989_CA_C:10076989:18,31,5,0 20 10077752 . T C . . AS_SB_TABLE=16,18|16,29;DP=83;ECNT=1;MBQ=38,30;MFRL=395,404;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=136.90 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:34,45:0.568:79:13,15:21,30:34,45:16,18,16,29 20 10079476 . T G . . AS_SB_TABLE=6,27|11,0;DP=55;ECNT=1;MBQ=38,15;MFRL=391,402;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=6.14 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:33,11:0.215:44:16,2:14,0:33,11:6,27,11,0 20 10081750 . C A . . AS_SB_TABLE=23,21|19,20;DP=92;ECNT=2;MBQ=36,38;MFRL=405,395;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=137.38 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:44,39:0.472:83:20,20:23,19:44,39:23,21,19,20 @@ -266,29 +266,29 @@ 20 10086954 . G A . . AS_SB_TABLE=16,18|21,13;DP=70;ECNT=1;MBQ=33,37;MFRL=401,392;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=111.57 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:34,34:0.499:68:14,16:19,17:34,34:16,18,21,13 20 10087230 . A G . . AS_SB_TABLE=22,20|23,31;DP=101;ECNT=1;MBQ=37,37;MFRL=398,386;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=186.54 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:42,54:0.561:96:20,30:22,24:42,54:22,20,23,31 20 10087394 . T G . . AS_SB_TABLE=21,14|24,25;DP=85;ECNT=1;MBQ=38,36;MFRL=390,392;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=171.36 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:35,49:0.581:84:15,26:20,23:35,49:21,14,24,25 -20 10087754 . T G . . AS_SB_TABLE=23,14|25,17;DP=87;ECNT=3;MBQ=36,37;MFRL=393,390;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=140.30 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:37,42:0.530:79:17,20:19,20:37,42:23,14,25,17 -20 10087804 . C T . . AS_SB_TABLE=33,17|28,22;DP=104;ECNT=3;MBQ=34,36;MFRL=388,390;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=163.83 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:50,50:0.501:100:21,19:26,28:50,50:33,17,28,22 +20 10087754 . T G . . AS_SB_TABLE=23,14|25,17;DP=87;ECNT=5;MBQ=36,37;MFRL=393,390;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=140.30 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:37,42:0.530:79:17,20:19,20:37,42:23,14,25,17 +20 10087804 . C T . . AS_SB_TABLE=33,17|28,22;DP=104;ECNT=5;MBQ=34,36;MFRL=388,390;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=163.83 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:50,50:0.501:100:21,19:26,28:50,50:33,17,28,22 20 10087820 . C CAG . . AS_SB_TABLE=18,19|8,10;DP=103;ECNT=3;MBQ=36,34;MFRL=387,393;MMQ=60,60;MPOS=38;POPAF=7.30;RPA=10,11;RU=AG;STR;TLOD=47.80 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:37,18:0.331:55:14,6:22,10:37,18:18,19,8,10 20 10088063 . C T . . AS_SB_TABLE=24,25|18,26;DP=94;ECNT=1;MBQ=30,37;MFRL=387,390;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=143.78 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:49,44:0.477:93:21,25:24,18:49,44:24,25,18,26 20 10088699 . C T . . AS_SB_TABLE=15,21|19,7;DP=67;ECNT=5;MBQ=30,37;MFRL=396,389;MMQ=60,60;MPOS=17;POPAF=7.30;TLOD=80.03 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:36,26:0.422:62:23,9:13,17:36,26:15,21,19,7 -20 10088730 . G A . . AS_SB_TABLE=11,19|16,10;DP=57;ECNT=5;MBQ=37,36;MFRL=398,389;MMQ=60,29;MPOS=23;POPAF=7.30;TLOD=99.42 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:30,26:0.466:56:17,6:11,17:30,26:0|1:10088730_G_A:10088730:11,19,16,10 -20 10088736 . A C . . AS_SB_TABLE=12,19|17,12;DP=60;ECNT=5;MBQ=35,37;MFRL=398,375;MMQ=60,29;MPOS=22;POPAF=7.30;TLOD=110.21 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:31,29:0.484:60:13,8:12,18:31,29:0|1:10088730_G_A:10088730:12,19,17,12 -20 10088747 . A G . . AS_SB_TABLE=10,16|19,11;DP=56;ECNT=5;MBQ=38,29;MFRL=399,389;MMQ=60,29;MPOS=25;POPAF=7.30;TLOD=113.33 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:26,30:0.534:56:13,10:12,18:26,30:0|1:10088730_G_A:10088730:10,16,19,11 -20 10088799 . G A . . AS_SB_TABLE=14,8|12,19;DP=54;ECNT=5;MBQ=30,38;MFRL=384,376;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=104.29 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:22,31:0.582:53:8,15:14,16:22,31:14,8,12,19 -20 10088895 . C T . . AS_SB_TABLE=10,12|8,10;DP=43;ECNT=5;MBQ=29,37;MFRL=386,384;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=55.74 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:22,18:0.450:40:10,8:11,9:22,18:10,12,8,10 -20 10088968 . C CAAA . . AS_SB_TABLE=17,15|17,15;DP=77;ECNT=5;MBQ=35,35;MFRL=397,394;MMQ=60,29;MPOS=28;POPAF=7.30;RPA=11,14;RU=A;STR;TLOD=120.43 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:32,32:0.499:64:14,12:15,10:32,32:0|1:10088968_C_CAAA:10088968:17,15,17,15 -20 10088980 . T C . . AS_SB_TABLE=20,19|18,16;DP=74;ECNT=5;MBQ=33,31;MFRL=398,390;MMQ=60,29;MPOS=21;POPAF=7.30;TLOD=126.85 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:39,34:0.467:73:18,13:17,15:39,34:0|1:10088968_C_CAAA:10088968:20,19,18,16 -20 10088985 . T C . . AS_SB_TABLE=22,20|15,17;DP=77;ECNT=5;MBQ=35,34;MFRL=398,389;MMQ=60,29;MPOS=26;POPAF=7.30;TLOD=120.13 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:42,32:0.434:74:22,16:18,15:42,32:0|1:10088968_C_CAAA:10088968:22,20,15,17 -20 10089026 . G T . . AS_SB_TABLE=22,40|10,0;DP=78;ECNT=5;MBQ=35,12;MFRL=399,403;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=5.32 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:62,10:0.109:72:33,0:24,3:62,10:22,40,10,0 -20 10089441 . A G . . AS_SB_TABLE=19,18|14,25;DP=79;ECNT=2;MBQ=39,37;MFRL=394,395;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=119.93 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:37,39:0.513:76:16,18:20,19:37,39:19,18,14,25 -20 10089525 . C T . . AS_SB_TABLE=22,16|20,23;DP=83;ECNT=2;MBQ=31,38;MFRL=397,401;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=156.93 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:38,43:0.533:81:20,22:15,21:38,43:22,16,20,23 -20 10090289 . CAA C,CA . . AS_SB_TABLE=7,7|3,1|8,12;DP=88;ECNT=1;MBQ=31,33,34;MFRL=395,390,394;MMQ=60,60,60;MPOS=10,29;POPAF=7.30,7.30;RPA=16,14,15;RU=A;STR;TLOD=4.41,37.82 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2:14,4,20:0.096,0.530:38:7,2,9:4,2,10:14,4,20:7,7,11,13 +20 10088730 . G A . . AS_SB_TABLE=11,19|16,10;DP=57;ECNT=4;MBQ=37,36;MFRL=398,389;MMQ=60,29;MPOS=23;POPAF=7.30;TLOD=99.42 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:30,26:0.466:56:17,6:11,17:30,26:0|1:10088730_G_A:10088730:11,19,16,10 +20 10088736 . A C . . AS_SB_TABLE=12,19|17,12;DP=60;ECNT=4;MBQ=35,37;MFRL=398,375;MMQ=60,29;MPOS=22;POPAF=7.30;TLOD=110.21 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:31,29:0.484:60:13,8:12,18:31,29:0|1:10088730_G_A:10088730:12,19,17,12 +20 10088747 . A G . . AS_SB_TABLE=10,16|19,11;DP=56;ECNT=4;MBQ=38,29;MFRL=399,389;MMQ=60,29;MPOS=25;POPAF=7.30;TLOD=113.33 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:26,30:0.534:56:13,10:12,18:26,30:0|1:10088730_G_A:10088730:10,16,19,11 +20 10088799 . G A . . AS_SB_TABLE=14,8|12,19;DP=54;ECNT=4;MBQ=30,38;MFRL=384,376;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=104.29 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:22,31:0.582:53:8,15:14,16:22,31:14,8,12,19 +20 10088895 . C T . . AS_SB_TABLE=10,12|8,10;DP=43;ECNT=1;MBQ=29,37;MFRL=386,384;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=55.74 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:22,18:0.450:40:10,8:11,9:22,18:10,12,8,10 +20 10088968 . C CAAA . . AS_SB_TABLE=17,15|17,15;DP=77;ECNT=3;MBQ=35,35;MFRL=397,394;MMQ=60,29;MPOS=28;POPAF=7.30;RPA=11,14;RU=A;STR;TLOD=120.43 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:32,32:0.499:64:14,12:15,10:32,32:0|1:10088968_C_CAAA:10088968:17,15,17,15 +20 10088980 . T C . . AS_SB_TABLE=20,19|18,16;DP=74;ECNT=3;MBQ=33,31;MFRL=398,390;MMQ=60,29;MPOS=21;POPAF=7.30;TLOD=126.85 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:39,34:0.467:73:18,13:17,15:39,34:0|1:10088968_C_CAAA:10088968:20,19,18,16 +20 10088985 . T C . . AS_SB_TABLE=22,20|15,17;DP=77;ECNT=3;MBQ=35,34;MFRL=398,389;MMQ=60,29;MPOS=26;POPAF=7.30;TLOD=120.13 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:42,32:0.434:74:22,16:18,15:42,32:0|1:10088968_C_CAAA:10088968:22,20,15,17 +20 10089026 . G T . . AS_SB_TABLE=22,40|10,0;DP=78;ECNT=1;MBQ=35,12;MFRL=399,403;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=5.32 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:62,10:0.109:72:33,0:24,3:62,10:22,40,10,0 +20 10089441 . A G . . AS_SB_TABLE=19,18|14,25;DP=79;ECNT=1;MBQ=39,37;MFRL=394,395;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=119.93 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:37,39:0.513:76:16,18:20,19:37,39:19,18,14,25 +20 10089525 . C T . . AS_SB_TABLE=22,16|20,23;DP=83;ECNT=1;MBQ=31,38;MFRL=397,401;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=156.93 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:38,43:0.533:81:20,22:15,21:38,43:22,16,20,23 +20 10090289 . CAA C,CA . . AS_SB_TABLE=7,7|3,1|8,12;DP=88;ECNT=1,1;MBQ=31,33,34;MFRL=395,390,394;MMQ=60,60,60;MPOS=10,29;POPAF=7.30,7.30;RPA=16,14,15;RU=A;STR;TLOD=4.41,37.82 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2:14,4,20:0.096,0.530:38:7,2,9:4,2,10:14,4,20:7,7,11,13 20 10090764 . A G . . AS_SB_TABLE=12,22|14,15;DP=67;ECNT=1;MBQ=37,30;MFRL=411,396;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=86.20 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:34,29:0.460:63:19,14:15,13:34,29:12,22,14,15 20 10090970 . T C . . AS_SB_TABLE=20,13|20,16;DP=70;ECNT=1;MBQ=38,38;MFRL=391,399;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=127.76 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:33,36:0.524:69:12,15:19,21:33,36:20,13,20,16 20 10091214 . C T . . AS_SB_TABLE=11,22|13,24;DP=73;ECNT=1;MBQ=36,37;MFRL=390,401;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=126.98 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:33,37:0.528:70:12,19:21,18:33,37:11,22,13,24 20 10092415 . A G . . AS_SB_TABLE=27,25|24,25;DP=103;ECNT=1;MBQ=39,37;MFRL=406,403;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=165.53 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:52,49:0.486:101:30,24:21,25:52,49:27,25,24,25 20 10092927 . G T . . AS_SB_TABLE=43,16|0,13;DP=83;ECNT=1;MBQ=38,27;MFRL=397,392;MMQ=60,60;MPOS=18;POPAF=7.30;TLOD=19.65 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:59,13:0.176:72:26,7:24,2:59,13:43,16,0,13 -20 10093568 . GTT G,GT,GTTT . . AS_SB_TABLE=7,10|2,2|7,10|1,3;DP=62;ECNT=1;MBQ=33,19,34,32;MFRL=383,363,390,367;MMQ=60,60,60,60;MPOS=39,29,32;POPAF=7.30,7.30,7.30;RPA=13,11,12,14;RU=T;STR;TLOD=4.11,33.39,5.30 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2/3:17,4,17,4:0.087,0.397,0.109:42:8,1,6,3:8,0,11,1:17,4,17,4:7,10,10,15 +20 10093568 . GTT G,GT,GTTT . . AS_SB_TABLE=7,10|2,2|7,10|1,3;DP=62;ECNT=1,1,1;MBQ=33,19,34,32;MFRL=383,363,390,367;MMQ=60,60,60,60;MPOS=39,29,32;POPAF=7.30,7.30,7.30;RPA=13,11,12,14;RU=T;STR;TLOD=4.11,33.39,5.30 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2/3:17,4,17,4:0.087,0.397,0.109:42:8,1,6,3:8,0,11,1:17,4,17,4:7,10,10,15 20 10093923 . T A . . AS_SB_TABLE=18,17|15,17;DP=73;ECNT=1;MBQ=38,38;MFRL=386,396;MMQ=60,60;MPOS=20;POPAF=7.30;TLOD=109.60 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:35,32:0.478:67:17,8:18,23:35,32:18,17,15,17 20 10094251 . T A . . AS_SB_TABLE=10,16|23,13;DP=67;ECNT=1;MBQ=38,37;MFRL=404,408;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=129.52 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:26,36:0.585:62:13,16:10,20:26,36:10,16,23,13 20 10094582 . A G . . AS_SB_TABLE=20,19|16,14;DP=73;ECNT=1;MBQ=37,36;MFRL=399,380;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=94.65 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:39,30:0.436:69:19,13:19,16:39,30:20,19,16,14 @@ -306,34 +306,34 @@ 20 10096933 . G C . . AS_SB_TABLE=29,18|14,28;DP=89;ECNT=4;MBQ=36,35;MFRL=398,401;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=153.41 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:47,42:0.471:89:22,18:22,23:47,42:0|1:10096933_G_C:10096933:29,18,14,28 20 10096958 . G A . . AS_SB_TABLE=27,17|16,32;DP=93;ECNT=4;MBQ=37,38;MFRL=397,402;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=178.87 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:44,48:0.521:92:23,21:20,25:44,48:0|1:10096933_G_C:10096933:27,17,16,32 20 10097075 . T G . . AS_SB_TABLE=18,26|26,22;DP=96;ECNT=2;MBQ=36,35;MFRL=396,400;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=146.49 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:44,48:0.519:92:20,22:24,24:44,48:18,26,26,22 -20 10097101 . C CTTT,CTTTT . . AS_SB_TABLE=21,12|12,14|3,1;DP=81;ECNT=2;MBQ=35,34,31;MFRL=405,396,396;MMQ=60,60,34;MPOS=33,19;POPAF=7.30,7.30;RPA=10,13,14;RU=T;STR;TLOD=60.13,4.31 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2:33,26,4:0.435,0.078:63:15,11,2:17,12,2:33,26,4:21,12,15,15 -20 10097433 . ACTCTTTTCTTTCTTTCTTTCTTTCTTTCTTT A . . AS_SB_TABLE=22,33|10,20;DP=86;ECNT=5;MBQ=34,35;MFRL=401,410;MMQ=60,29;MPOS=20;POPAF=7.30;TLOD=104.12 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:55,30:0.357:85:22,13:18,15:55,30:0|1:10097433_ACTCTTTTCTTTCTTTCTTTCTTTCTTTCTTT_A:10097433:22,33,10,20 -20 10097436 . CTTT C . . AS_SB_TABLE=0,0|5,18;DP=74;ECNT=5;MBQ=0,35;MFRL=0,402;MMQ=60,60;MPOS=32;POPAF=7.30;RPA=4,1;RU=T;STR;TLOD=92.92 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 1|0:0,23:0.972:23:0,13:0,8:0,23:1|0:10097433_ACTCTTTTCTTTCTTTCTTTCTTTCTTTCTTT_A:10097433:0,0,5,18 -20 10097440 . TC T . . AS_SB_TABLE=0,0|5,18;DP=76;ECNT=5;MBQ=0,35;MFRL=0,402;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=93.17 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 1|0:0,23:0.972:23:0,12:0,9:0,23:1|0:10097433_ACTCTTTTCTTTCTTTCTTTCTTTCTTTCTTT_A:10097433:0,0,5,18 -20 10097465 . CTT C . . AS_SB_TABLE=18,27|11,21;DP=77;ECNT=5;MBQ=34,36;MFRL=402,410;MMQ=60,29;MPOS=22;POPAF=7.30;RPA=3,1;RU=T;STR;TLOD=112.36 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:45,32:0.418:77:23,14:20,16:45,32:0|1:10097433_ACTCTTTTCTTTCTTTCTTTCTTTCTTTCTTT_A:10097433:18,27,11,21 -20 10097469 . CTTT C . . AS_SB_TABLE=19,28|11,21;DP=80;ECNT=5;MBQ=34,37;MFRL=401,410;MMQ=60,29;MPOS=20;POPAF=7.30;TLOD=111.93 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:47,32:0.408:79:25,14:19,18:47,32:0|1:10097433_ACTCTTTTCTTTCTTTCTTTCTTTCTTTCTTT_A:10097433:19,28,11,21 +20 10097101 . C CTTT,CTTTT . . AS_SB_TABLE=21,12|12,14|3,1;DP=81;ECNT=2,2;MBQ=35,34,31;MFRL=405,396,396;MMQ=60,60,34;MPOS=33,19;POPAF=7.30,7.30;RPA=10,13,14;RU=T;STR;TLOD=60.13,4.31 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2:33,26,4:0.435,0.078:63:15,11,2:17,12,2:33,26,4:21,12,15,15 +20 10097433 . ACTCTTTTCTTTCTTTCTTTCTTTCTTTCTTT A . . AS_SB_TABLE=22,33|10,20;DP=86;ECNT=3;MBQ=34,35;MFRL=401,410;MMQ=60,29;MPOS=20;POPAF=7.30;TLOD=104.12 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:55,30:0.357:85:22,13:18,15:55,30:0|1:10097433_ACTCTTTTCTTTCTTTCTTTCTTTCTTTCTTT_A:10097433:22,33,10,20 +20 10097436 . CTTT C . . AS_SB_TABLE=0,0|5,18;DP=74;ECNT=2;MBQ=0,35;MFRL=0,402;MMQ=60,60;MPOS=32;POPAF=7.30;RPA=4,1;RU=T;STR;TLOD=92.92 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 1|0:0,23:0.972:23:0,13:0,8:0,23:1|0:10097433_ACTCTTTTCTTTCTTTCTTTCTTTCTTTCTTT_A:10097433:0,0,5,18 +20 10097440 . TC T . . AS_SB_TABLE=0,0|5,18;DP=76;ECNT=2;MBQ=0,35;MFRL=0,402;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=93.17 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 1|0:0,23:0.972:23:0,12:0,9:0,23:1|0:10097433_ACTCTTTTCTTTCTTTCTTTCTTTCTTTCTTT_A:10097433:0,0,5,18 +20 10097465 . CTT C . . AS_SB_TABLE=18,27|11,21;DP=77;ECNT=3;MBQ=34,36;MFRL=402,410;MMQ=60,29;MPOS=22;POPAF=7.30;RPA=3,1;RU=T;STR;TLOD=112.36 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:45,32:0.418:77:23,14:20,16:45,32:0|1:10097433_ACTCTTTTCTTTCTTTCTTTCTTTCTTTCTTT_A:10097433:18,27,11,21 +20 10097469 . CTTT C . . AS_SB_TABLE=19,28|11,21;DP=80;ECNT=3;MBQ=34,37;MFRL=401,410;MMQ=60,29;MPOS=20;POPAF=7.30;TLOD=111.93 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:47,32:0.408:79:25,14:19,18:47,32:0|1:10097433_ACTCTTTTCTTTCTTTCTTTCTTTCTTTCTTT_A:10097433:19,28,11,21 20 10097626 . C A . . AS_SB_TABLE=8,20|8,12;DP=54;ECNT=1;MBQ=37,38;MFRL=396,404;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=65.03 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:28,20:0.421:48:13,14:14,6:28,20:8,20,8,12 20 10097789 . T C . . AS_SB_TABLE=14,20|13,10;DP=60;ECNT=1;MBQ=37,36;MFRL=404,388;MMQ=60,60;MPOS=20;POPAF=7.30;TLOD=71.38 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:34,23:0.407:57:13,4:21,19:34,23:14,20,13,10 20 10097928 . G A . . AS_SB_TABLE=9,8|8,11;DP=37;ECNT=1;MBQ=37,36;MFRL=381,392;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=59.24 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:17,19:0.526:36:11,13:6,6:17,19:9,8,8,11 20 10098110 . G C . . AS_SB_TABLE=0,19|2,15;DP=36;ECNT=2;MBQ=36,37;MFRL=403,383;MMQ=60,60;MPOS=20;POPAF=7.30;TLOD=60.84 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:19,17:0.474:36:9,4:10,13:19,17:0|1:10098110_G_C:10098110:0,19,2,15 20 10098135 . C A . . AS_SB_TABLE=0,24|1,13;DP=38;ECNT=2;MBQ=38,36;MFRL=406,391;MMQ=60,60;MPOS=8;POPAF=7.30;TLOD=50.13 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:24,14:0.375:38:13,6:10,8:24,14:0|1:10098110_G_C:10098110:0,24,1,13 20 10098786 . C T . . AS_SB_TABLE=7,0|2,0;DP=9;ECNT=1;MBQ=31,34;MFRL=388,369;MMQ=60,29;MPOS=8;POPAF=7.30;TLOD=4.17 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:7,2:0.273:9:5,2:2,0:7,2:7,0,2,0 -20 10098885 . C CA . . AS_SB_TABLE=16,1|13,1;DP=33;ECNT=1;MBQ=37,37;MFRL=389,378;MMQ=60,29;MPOS=23;POPAF=7.30;TLOD=46.53 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:17,14:0.454:31:9,5:8,7:17,14:16,1,13,1 -20 10098945 . T C . . AS_SB_TABLE=8,1|13,0;DP=22;ECNT=11;MBQ=35,37;MFRL=374,375;MMQ=60,33;MPOS=25;POPAF=7.30;TLOD=43.16 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:9,13:0.590:22:5,7:3,6:9,13:8,1,13,0 -20 10098987 . C T . . AS_SB_TABLE=9,2|13,0;DP=25;ECNT=11;MBQ=35,37;MFRL=389,387;MMQ=60,36;MPOS=38;POPAF=7.30;TLOD=40.10 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:11,13:0.539:24:7,9:4,4:11,13:9,2,13,0 -20 10099029 . T C . . AS_SB_TABLE=14,5|9,1;DP=30;ECNT=11;MBQ=38,36;MFRL=377,361;MMQ=60,33;MPOS=11;POPAF=7.30;TLOD=35.13 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:19,10:0.296:29:10,7:8,3:25,10:0|1:10099029_T_C:10099029:14,5,9,1 -20 10099034 . C A . . AS_SB_TABLE=14,5|9,1;DP=29;ECNT=11;MBQ=33,38;MFRL=377,361;MMQ=60,33;MPOS=10;POPAF=7.30;TLOD=35.13 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:19,10:0.296:29:10,7:8,3:25,10:0|1:10099029_T_C:10099029:14,5,9,1 -20 10099044 . A C . . AS_SB_TABLE=14,5|8,2;DP=29;ECNT=11;MBQ=38,36;MFRL=377,392;MMQ=60,29;MPOS=15;POPAF=7.30;TLOD=39.11 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:19,10:0.315:29:9,6:3,3:25,11:0|1:10099029_T_C:10099029:14,5,8,2 -20 10099046 . T C . . AS_SB_TABLE=12,3|7,2;DP=24;ECNT=11;MBQ=38,37;MFRL=388,397;MMQ=60,29;MPOS=16;POPAF=7.30;TLOD=39.82 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:15,9:0.352:24:9,6:6,3:21,11:0|1:10099029_T_C:10099029:12,3,7,2 -20 10099055 . T C . . AS_SB_TABLE=12,5|6,2;DP=25;ECNT=11;MBQ=39,37;MFRL=388,398;MMQ=60,29;MPOS=14;POPAF=7.30;TLOD=35.45 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:17,8:0.313:25:10,6:4,2:23,10:0|1:10099029_T_C:10099029:12,5,6,2 -20 10099079 . C T . . AS_SB_TABLE=12,12|4,2;DP=30;ECNT=11;MBQ=29,37;MFRL=384,362;MMQ=60,29;MPOS=36;POPAF=7.30;TLOD=23.29 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:24,6:0.217:30:11,3:10,2:30,8:0|1:10099029_T_C:10099029:12,12,4,2 -20 10099130 . T TG . . AS_SB_TABLE=18,12|12,7;DP=59;ECNT=11;MBQ=35,35;MFRL=386,387;MMQ=60,39;MPOS=23;POPAF=7.30;TLOD=54.49 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:30,19:0.366:49:10,12:15,5:33,19:0|1:10099130_T_TG:10099130:18,12,12,7 -20 10099134 . G GT . . AS_SB_TABLE=17,12|12,7;DP=58;ECNT=11;MBQ=35,35;MFRL=383,387;MMQ=60,39;MPOS=28;POPAF=7.30;RPA=5,6;RU=T;STR;TLOD=54.90 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:29,19:0.380:48:11,12:15,6:31,19:0|1:10099130_T_TG:10099130:17,12,12,7 -20 10099140 . G GTTTTTT . . AS_SB_TABLE=19,13|21,10;DP=64;ECNT=11;MBQ=35,35;MFRL=383,389;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=62.18 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:32,31:0.481:63:12,17:17,10:34,31:0|1:10099130_T_TG:10099130:19,13,21,10 -20 10099190 . G T . . AS_SB_TABLE=21,12|21,11;DP=65;ECNT=3;MBQ=37,37;MFRL=383,396;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=105.46 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:33,32:0.492:65:18,19:15,12:33,32:21,12,21,11 +20 10098885 . C CA . . AS_SB_TABLE=16,1|13,1;DP=33;ECNT=2;MBQ=37,37;MFRL=389,378;MMQ=60,29;MPOS=23;POPAF=7.30;TLOD=46.53 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:17,14:0.454:31:9,5:8,7:17,14:16,1,13,1 +20 10098945 . T C . . AS_SB_TABLE=8,1|13,0;DP=22;ECNT=8;MBQ=35,37;MFRL=374,375;MMQ=60,33;MPOS=25;POPAF=7.30;TLOD=43.16 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:9,13:0.590:22:5,7:3,6:9,13:8,1,13,0 +20 10098987 . C T . . AS_SB_TABLE=9,2|13,0;DP=25;ECNT=8;MBQ=35,37;MFRL=389,387;MMQ=60,36;MPOS=38;POPAF=7.30;TLOD=40.10 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:11,13:0.539:24:7,9:4,4:11,13:9,2,13,0 +20 10099029 . T C . . AS_SB_TABLE=14,5|9,1;DP=30;ECNT=8;MBQ=38,36;MFRL=377,361;MMQ=60,33;MPOS=11;POPAF=7.30;TLOD=35.13 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:19,10:0.296:29:10,7:8,3:25,10:0|1:10099029_T_C:10099029:14,5,9,1 +20 10099034 . C A . . AS_SB_TABLE=14,5|9,1;DP=29;ECNT=8;MBQ=33,38;MFRL=377,361;MMQ=60,33;MPOS=10;POPAF=7.30;TLOD=35.13 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:19,10:0.296:29:10,7:8,3:25,10:0|1:10099029_T_C:10099029:14,5,9,1 +20 10099044 . A C . . AS_SB_TABLE=14,5|8,2;DP=29;ECNT=8;MBQ=38,36;MFRL=377,392;MMQ=60,29;MPOS=15;POPAF=7.30;TLOD=39.11 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:19,10:0.315:29:9,6:3,3:25,11:0|1:10099029_T_C:10099029:14,5,8,2 +20 10099046 . T C . . AS_SB_TABLE=12,3|7,2;DP=24;ECNT=8;MBQ=38,37;MFRL=388,397;MMQ=60,29;MPOS=16;POPAF=7.30;TLOD=39.82 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:15,9:0.352:24:9,6:6,3:21,11:0|1:10099029_T_C:10099029:12,3,7,2 +20 10099055 . T C . . AS_SB_TABLE=12,5|6,2;DP=25;ECNT=8;MBQ=39,37;MFRL=388,398;MMQ=60,29;MPOS=14;POPAF=7.30;TLOD=35.45 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:17,8:0.313:25:10,6:4,2:23,10:0|1:10099029_T_C:10099029:12,5,6,2 +20 10099079 . C T . . AS_SB_TABLE=12,12|4,2;DP=30;ECNT=8;MBQ=29,37;MFRL=384,362;MMQ=60,29;MPOS=36;POPAF=7.30;TLOD=23.29 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:24,6:0.217:30:11,3:10,2:30,8:0|1:10099029_T_C:10099029:12,12,4,2 +20 10099130 . T TG . . AS_SB_TABLE=18,12|12,7;DP=59;ECNT=5;MBQ=35,35;MFRL=386,387;MMQ=60,39;MPOS=23;POPAF=7.30;TLOD=54.49 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:30,19:0.366:49:10,12:15,5:33,19:0|1:10099130_T_TG:10099130:18,12,12,7 +20 10099134 . G GT . . AS_SB_TABLE=17,12|12,7;DP=58;ECNT=5;MBQ=35,35;MFRL=383,387;MMQ=60,39;MPOS=28;POPAF=7.30;RPA=5,6;RU=T;STR;TLOD=54.90 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:29,19:0.380:48:11,12:15,6:31,19:0|1:10099130_T_TG:10099130:17,12,12,7 +20 10099140 . G GTTTTTT . . AS_SB_TABLE=19,13|21,10;DP=64;ECNT=5;MBQ=35,35;MFRL=383,389;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=62.18 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:32,31:0.481:63:12,17:17,10:34,31:0|1:10099130_T_TG:10099130:19,13,21,10 +20 10099190 . G T . . AS_SB_TABLE=21,12|21,11;DP=65;ECNT=2;MBQ=37,37;MFRL=383,396;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=105.46 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:33,32:0.492:65:18,19:15,12:33,32:21,12,21,11 20 10099220 . A G . . AS_SB_TABLE=15,10|11,9;DP=47;ECNT=3;MBQ=37,36;MFRL=373,396;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=59.94 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:25,20:0.444:45:13,12:12,7:25,20:15,10,11,9 -20 10099250 . G A . . AS_SB_TABLE=12,4|11,10;DP=39;ECNT=3;MBQ=30,36;MFRL=381,390;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=72.27 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:16,21:0.568:37:6,9:9,12:16,21:12,4,11,10 +20 10099250 . G A . . AS_SB_TABLE=12,4|11,10;DP=39;ECNT=2;MBQ=30,36;MFRL=381,390;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=72.27 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:16,21:0.568:37:6,9:9,12:16,21:12,4,11,10 20 10099535 . G A . . AS_SB_TABLE=17,9|22,17;DP=68;ECNT=2;MBQ=29,38;MFRL=392,403;MMQ=60,60;MPOS=17;POPAF=7.30;TLOD=136.15 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:26,39:0.598:65:13,20:12,18:26,39:17,9,22,17 20 10099565 . C T . . AS_SB_TABLE=23,8|21,17;DP=70;ECNT=2;MBQ=36,38;MFRL=390,397;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=136.78 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:31,38:0.549:69:12,22:19,16:31,38:23,8,21,17 -20 10099755 . C T . . AS_SB_TABLE=20,13|17,15;DP=66;ECNT=2;MBQ=37,38;MFRL=386,395;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=111.85 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:33,32:0.493:65:16,16:17,16:33,32:20,13,17,15 -20 10099832 . A G . . AS_SB_TABLE=22,17|14,19;DP=75;ECNT=2;MBQ=39,36;MFRL=392,394;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=109.48 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:39,33:0.459:72:21,20:18,13:39,33:22,17,14,19 +20 10099755 . C T . . AS_SB_TABLE=20,13|17,15;DP=66;ECNT=1;MBQ=37,38;MFRL=386,395;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=111.85 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:33,32:0.493:65:16,16:17,16:33,32:20,13,17,15 +20 10099832 . A G . . AS_SB_TABLE=22,17|14,19;DP=75;ECNT=1;MBQ=39,36;MFRL=392,394;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=109.48 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:39,33:0.459:72:21,20:18,13:39,33:22,17,14,19