Mercurial > repos > malex > bayesase
view test-data/update_genomes_test_data/W1118_snp_testGenes.vcf @ 0:e979cb57a5d5 draft default tip
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
| author | malex |
|---|---|
| date | Thu, 14 Jan 2021 21:51:36 +0000 |
| parents | |
| children |
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##fileformat=VCFv4.2 ##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location"> ##FILTER=<ID=Het,Description="isHet == 1"> ##FILTER=<ID=LowQual,Description="Low quality"> ##FILTER=<ID=PASS,Description="All filters passed"> ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> ##FORMAT=<ID=FT,Number=.,Type=String,Description="Genotype-level filter"> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block"> ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> ##GATKCommandLine=<ID=GenotypeGVCFs,Version=3.2-2-gec30cee,Date="Fri Aug 22 11:38:29 PDT 2014",Epoch=1408732709322,CommandLineOptions="analysis_type=GenotypeGVCFs input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/home/rcf-40/msalomon/cmb/CEGS_fly_sequencing/reference/dmel-all-chromosome-r5.41_edited_headers.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false variant=[(RodBindingCollection [(RodBinding name=variant source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/DGRP_48.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant2 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source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_68.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant227 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_69.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant228 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_70.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant229 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_74.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant230 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_76.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant231 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_79.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant232 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_80.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant233 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_82.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant234 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_84.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant235 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_86.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant236 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_87.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant237 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_114.raw.SNPs.and.indels.g.vcf)])] out=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub includeNonVariantSites=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 annotation=[InbreedingCoeff, FisherStrand, QualByDepth, ChromosomeCounts, GenotypeSummaries] dbsnp=(RodBinding name= source=UNBOUND) filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"> ##GATKCommandLine=<ID=SelectVariants,CommandLine="SelectVariants --output /ufrc/mcintyre/share/BASE_mclab/galaxy/vcf_by_genotype/W1118_snp.vcf --sample-name W1118 --exclude-non-variants true --variant /ufrc/mcintyre/share/mel_cegs_variant_info/vcf_files_v3/CEGS.237.lines.SNPs.filtered.set.1.recode.vcf --reference /ufrc/mcintyre/share/references/dmel_fb551/dmel-all-chromosome-r5.51.fasta --invertSelect false --exclude-filtered false --preserve-alleles false --remove-unused-alternates false --restrict-alleles-to ALL --keep-original-ac false --keep-original-dp false --mendelian-violation false --invert-mendelian-violation false --mendelian-violation-qual-threshold 0.0 --select-random-fraction 0.0 --remove-fraction-genotypes 0.0 --fully-decode false --max-indel-size 2147483647 --min-indel-size 0 --max-filtered-genotypes 2147483647 --min-filtered-genotypes 0 --max-fraction-filtered-genotypes 1.0 --min-fraction-filtered-genotypes 0.0 --max-nocall-number 2147483647 --max-nocall-fraction 1.0 --set-filtered-gt-to-nocall false --allow-nonoverlapping-command-line-samples false --suppress-reference-path false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version="4.1.4.0",Date="July 22, 2020 1:43:15 PM EDT"> ##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive) ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> ##INFO=<ID=CCC,Number=1,Type=Integer,Description="Number of called chromosomes"> ##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> ##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval"> ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> ##INFO=<ID=GQ_MEAN,Number=1,Type=Float,Description="Mean of all GQ values"> ##INFO=<ID=GQ_STDDEV,Number=1,Type=Float,Description="Standard deviation of all GQ values"> ##INFO=<ID=HWP,Number=1,Type=Float,Description="P value from test of Hardy Weinberg Equilibrium"> ##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes"> ##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"> ##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed"> ##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed"> ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> ##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads"> ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> ##INFO=<ID=NCC,Number=1,Type=Integer,Description="Number of no-called samples"> ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> ##SelectVariants="analysis_type=SelectVariants input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/Users/msalomon/Desktop/reference/dmel-all-chromosome-r5.41_edited_headers.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=8 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=CEGS.ALL.snp.and.indel.raw.HETS.marked.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] select_expressions=[] excludeNonVariants=true excludeFiltered=false restrictAllelesTo=ALL keepOriginalAC=false mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[SNP] keepIDs=null fullyDecode=false forceGenotypesDecode=false justRead=false maxIndelSize=2147483647 ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false" ##VariantFiltration="analysis_type=VariantFiltration input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/Users/msalomon/Desktop/reference/dmel-all-chromosome-r5.41_edited_headers.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=CEGS.ALL.snp.and.indel.raw.vcf) mask=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub filterExpression=[] filterName=[] genotypeFilterExpression=[isHet == 1] genotypeFilterName=[Het] clusterSize=3 clusterWindowSize=0 maskExtension=0 maskName=Mask filterNotInMask=false missingValuesInExpressionsShouldEvaluateAsFailing=false invalidatePreviousFilters=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false" ##bcftools_viewCommand=view -O v -o /ufrc/mcintyre/share/mel_cegs_variant_info/vcf_files_v3/CEGS.237.lines.SNPs.filtered.set.1.recode.vcf /ufrc/mcintyre/share/mel_cegs_variant_info/vcf_files_v3/CEGS.237.lines.SNPs.filtered.set.1.recode.vcf.gz; Date=Wed Jul 22 13:40:32 2020 ##bcftools_viewVersion=1.10.2+htslib-1.10.2 ##contig=<ID=YHet,length=347038,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=dmel_mitochondrion_genome,length=19517,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=2L,length=23011544,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=X,length=22422827,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=3L,length=24543557,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=4,length=1351857,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=2R,length=21146708,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=3R,length=27905053,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=Uextra,length=29004656,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=2RHet,length=3288761,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=2LHet,length=368872,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=3LHet,length=2555491,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=3RHet,length=2517507,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=U,length=10049037,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=XHet,length=204112,assembly=dmel-all-chromosome-r5.51.fasta> ##reference=file:///ufrc/mcintyre/share/references/dmel_fb551/dmel-all-chromosome-r5.51.fasta ##source=SelectVariants #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT W1118 X 7781305 . G C 17318.70 PASS AC=2;AF=1.00;AN=2;DP=9 GT:AD:DP:GQ:PL 1/1:0,9:9:30:432,30,0 X 21889635 . C T 30606.60 PASS AC=2;AF=1.00;AN=2;DP=6 GT:AD:DP:GQ:PL 1/1:0,6:6:18:230,18,0 X 21889661 . G C 70712.10 PASS AC=2;AF=1.00;AN=2;DP=8 GT:AD:DP:GQ:PL 1/1:0,8:8:24:286,24,0 X 21889690 . A C 22562.60 PASS AC=2;AF=1.00;AN=2;DP=6 GT:AD:DP:GQ:PL 1/1:0,6:6:18:270,18,0 X 21889694 . G A 68972.30 PASS AC=2;AF=1.00;AN=2;DP=6 GT:AD:DP:GQ:PL 1/1:0,6:6:18:270,18,0 X 21890117 . A T 53529.60 PASS AC=2;AF=1.00;AN=2;DP=12 GT:AD:DP:GQ:PL 1/1:0,12:12:36:472,36,0 X 21893636 . C T 76735.40 PASS AC=2;AF=1.00;AN=2;DP=12 GT:AD:DP:GQ:PL 1/1:0,9:12:36:0,12,0 X 21893803 . C T 58173.10 PASS AC=2;AF=1.00;AN=2;DP=5 GT:AD:DP:GQ:PL 1/1:0,5:5:15:208,15,0 X 21894302 . T A 71351.10 PASS AC=2;AF=1.00;AN=2;DP=14 GT:AD:DP:GQ:PL 1/1:0,14:14:42:593,42,0 X 21895115 . T C 66417.80 PASS AC=2;AF=1.00;AN=2;DP=13 GT:AD:DP:GQ:PL 1/1:0,13:13:39:564,39,0 X 21895236 . T A 84196.40 PASS AC=2;AF=1.00;AN=2;DP=19 GT:AD:DP:GQ:PL 1/1:0,19:19:57:787,57,0 X 21895556 . A G 107863 PASS AC=2;AF=1.00;AN=2;DP=11 GT:AD:DP:GQ:PL 1/1:0,11:11:33:478,33,0 X 21895559 . G A 52330.70 PASS AC=2;AF=1.00;AN=2;DP=9 GT:AD:DP:GQ:PL 1/1:0,9:9:30:444,30,0 X 21895697 . T C 110094 PASS AC=2;AF=1.00;AN=2;DP=17 GT:AD:DP:GQ:PL 1/1:0,17:17:51:690,51,0 X 21896185 . C A 5071.21 PASS AC=2;AF=1.00;AN=2;DP=17 GT:AD:DP:GQ:PL 1/1:0,17:17:51:720,51,0 X 21897092 . G T 14573.70 PASS AC=2;AF=1.00;AN=2;DP=15 GT:AD:DP:GQ:PL 1/1:0,15:15:45:650,45,0 X 21898037 . T G 99430.60 PASS AC=2;AF=1.00;AN=2;DP=8 GT:AD:DP:GQ:PL 1/1:0,8:8:30:440,30,0 X 21898046 . T G 88654.70 PASS AC=2;AF=1.00;AN=2;DP=13 GT:AD:DP:GQ:PL 1/1:0,13:13:39:544,39,0 X 21898238 . C T 51144.70 PASS AC=2;AF=1.00;AN=2;DP=13 GT:AD:DP:GQ:PL 1/1:0,13:13:39:519,39,0 X 21898641 . T C 66103.40 PASS AC=2;AF=1.00;AN=2;DP=14 GT:AD:DP:GQ:PL 1/1:0,14:14:42:569,42,0 X 21899027 . T G 42283.40 PASS AC=2;AF=1.00;AN=2;DP=11 GT:AD:DP:GQ:PL 1/1:0,11:11:33:420,33,0 X 21899043 . T A 61169.20 PASS AC=2;AF=1.00;AN=2;DP=8 GT:AD:DP:GQ:PL 1/1:0,8:8:24:337,24,0 X 21899576 . C T 83305.10 PASS AC=2;AF=1.00;AN=2;DP=12 GT:AD:DP:GQ:PL 1/1:0,12:12:36:473,36,0 X 21899675 . T C 139002 PASS AC=2;AF=1.00;AN=2;DP=17 GT:AD:DP:GQ:PL 1/1:0,17:17:51:708,51,0 X 21899720 . C T 10772.70 PASS AC=2;AF=1.00;AN=2;DP=20 GT:AD:DP:GQ:PL 1/1:0,20:20:60:862,60,0 X 21899903 . T C 12674 PASS AC=2;AF=1.00;AN=2;DP=18 GT:AD:DP:GQ:PL 1/1:0,18:18:54:768,54,0 X 21900307 . A G 80133.80 PASS AC=2;AF=1.00;AN=2;DP=11 GT:AD:DP:GQ:PL 1/1:0,11:11:33:472,33,0 X 21900768 . G T 74693.30 PASS AC=2;AF=1.00;AN=2;DP=14 GT:AD:DP:GQ:PL 1/1:0,14:14:42:592,42,0 X 21900780 . A G 65714.90 PASS AC=2;AF=1.00;AN=2;DP=14 GT:AD:DP:GQ:PL 1/1:0,14:14:42:571,42,0 X 21901775 . T C 22131.50 PASS AC=2;AF=1.00;AN=2;DP=10 GT:AD:DP:GQ:PL 1/1:0,10:10:30:429,30,0 X 21902059 . C T 10715.30 PASS AC=2;AF=1.00;AN=2;DP=11 GT:AD:DP:GQ:PL 1/1:0,11:11:33:453,33,0 X 21902804 . C T 75910.80 PASS AC=2;AF=1.00;AN=2;DP=6 GT:AD:DP:GQ:PL 1/1:0,6:6:18:251,18,0 X 21902864 . G A 62085.10 PASS AC=2;AF=1.00;AN=2;DP=10 GT:AD:DP:GQ:PL 1/1:0,10:10:30:450,30,0 X 21902872 . T A 83073.30 PASS AC=2;AF=1.00;AN=2;DP=13 GT:AD:DP:GQ:PL 1/1:0,13:13:39:529,39,0 X 21903096 . G A 40162.90 PASS AC=2;AF=1.00;AN=2;DP=13 GT:AD:DP:GQ:PL 1/1:0,13:13:39:515,39,0 X 21903162 . T C 52615.90 PASS AC=2;AF=1.00;AN=2;DP=16 GT:AD:DP:GQ:PL 1/1:0,16:16:48:622,48,0 X 21903300 . A C 52197.30 PASS AC=2;AF=1.00;AN=2;DP=13 GT:AD:DP:GQ:PL 1/1:0,13:13:39:502,0,0 X 21903317 . C A 39534.20 PASS AC=2;AF=1.00;AN=2;DP=15 GT:AD:DP:GQ:PL 1/1:0,15:15:45:577,45,0 X 21903354 . T G 53570.10 PASS AC=2;AF=1.00;AN=2;DP=13 GT:AD:DP:GQ:PL 1/1:0,13:13:39:504,39,0 X 21903462 . G A 8890.18 PASS AC=2;AF=1.00;AN=2;DP=11 GT:AD:DP:GQ:PL 1/1:0,11:11:33:495,33,0 X 21903463 . T C 18923.90 PASS AC=2;AF=1.00;AN=2;DP=11 GT:AD:DP:GQ:PL 1/1:0,11:11:33:495,33,0 X 21903483 . C G 32472.90 PASS AC=2;AF=1.00;AN=2;DP=11 GT:AD:DP:GQ:PL 1/1:0,11:11:33:456,33,0 X 21903542 . G T 71035 PASS AC=2;AF=1.00;AN=2;DP=19 GT:AD:DP:GQ:PL 1/1:0,19:19:63:910,63,0 X 21903558 . C A 76925.70 PASS AC=2;AF=1.00;AN=2;DP=24 GT:AD:DP:GQ:PL 1/1:0,24:24:75:1090,75,0 X 21903657 . C T 38490.40 PASS AC=2;AF=1.00;AN=2;DP=16 GT:AD:DP:GQ:PL 1/1:0,16:16:48:665,48,0 X 21905635 . T A 35652 PASS AC=2;AF=1.00;AN=2;DP=16 GT:AD:DP:GQ:PL 1/1:0,16:16:48:585,48,0 X 21905664 . A C 34889.80 PASS AC=2;AF=1.00;AN=2;DP=18 GT:AD:DP:GQ:PL 1/1:0,18:18:57:852,57,0 X 21905680 . T G 65074.20 PASS AC=2;AF=1.00;AN=2;DP=17 GT:AD:DP:GQ:PL 1/1:0,17:17:51:763,51,0 X 21906974 . T A 28938.20 PASS AC=2;AF=1.00;AN=2;DP=2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 X 21908181 . C A 92090.50 PASS AC=2;AF=1.00;AN=2;DP=11 GT:AD:DP:GQ:PL 1/1:0,11:11:33:444,33,0 X 21908786 . C A 33209.20 PASS AC=2;AF=1.00;AN=2;DP=17 GT:AD:DP:GQ:PL 1/1:0,17:17:51:708,51,0 X 21909025 . A T 38860.10 PASS AC=2;AF=1.00;AN=2;DP=10 GT:AD:DP:GQ:PL 1/1:0,10:10:30:354,30,0 X 21909294 . A G 47187.30 PASS AC=2;AF=1.00;AN=2;DP=11 GT:AD:DP:GQ:PL 1/1:0,11:11:33:0,21,0 X 21909380 . G A 42365.60 PASS AC=2;AF=1.00;AN=2;DP=14 GT:AD:DP:GQ:PL 1/1:0,14:14:42:499,42,0 X 21909429 . A C 9195.76 PASS AC=2;AF=1.00;AN=2;DP=11 GT:AD:DP:GQ:PL 1/1:0,11:11:33:495,33,0 2R 13755015 . A G 130642 PASS AC=2;AF=1.00;AN=2;DP=17 GT:AD:DP:GQ:PL 1/1:0,17:17:51:32,0,0 2R 13755189 . G A 58304.80 PASS AC=2;AF=1.00;AN=2;DP=14 GT:AD:DP:GQ:PL 1/1:0,14:14:42:592,42,0 2R 13755213 . T A 22562 PASS AC=2;AF=1.00;AN=2;DP=16 GT:AD:DP:GQ:PL 1/1:0,16:16:48:703,48,0 2R 13755269 . T C 116759 PASS AC=2;AF=1.00;AN=2;DP=17 GT:AD:DP:GQ:PL 1/1:0,17:17:51:691,51,0 2R 13755404 . G C 152785 PASS AC=2;AF=1.00;AN=2;DP=9 GT:AD:DP:GQ:PL 1/1:0,9:9:30:446,30,0 2R 13755408 . A C 153507 PASS AC=2;AF=1.00;AN=2;DP=8 GT:AD:DP:GQ:PL 1/1:0,8:8:30:446,30,0 2R 13755520 . A T 127979 PASS AC=2;AF=1.00;AN=2;DP=11 GT:AD:DP:GQ:PL 1/1:0,11:11:33:2,0,0 2R 13755699 . T C 129629 PASS AC=2;AF=1.00;AN=2;DP=8 GT:AD:DP:GQ:PL 1/1:0,8:8:24:332,24,630 2R 13755788 . A C 119974 PASS AC=2;AF=1.00;AN=2;DP=7 GT:AD:DP:GQ:PL 1/1:0,7:7:21:315,21,0 2R 13757022 . A G 35892.70 PASS AC=2;AF=1.00;AN=2;DP=13 GT:AD:DP:GQ:PL 1/1:0,13:13:39:559,39,0 2R 13757200 . C G 30041.40 PASS AC=2;AF=1.00;AN=2;DP=18 GT:AD:DP:GQ:PL 1/1:0,18:18:54:749,54,0 2R 13757682 . C T 34666.10 PASS AC=2;AF=1.00;AN=2;DP=18 GT:AD:DP:GQ:PL 1/1:0,18:18:54:771,54,0 2R 13759568 . T A 47736.70 PASS AC=2;AF=1.00;AN=2;DP=12 GT:AD:DP:GQ:PL 1/1:0,12:12:36:528,36,0 2R 13759577 . A G 150046 PASS AC=2;AF=1.00;AN=2;DP=12 GT:AD:DP:GQ:PL 1/1:0,12:12:36:521,36,0 2R 16206689 . G A 117640 PASS AC=2;AF=1.00;AN=2;DP=16 GT:AD:DP:GQ:PL 1/1:0,16:16:48:686,48,0 2R 16207027 . 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A C 141265 PASS AC=2;AF=1.00;AN=2;DP=17 GT:AD:DP:GQ:PL 1/1:12,0:17:51:0,24,360 2R 16210895 . C T 102435 PASS AC=2;AF=1.00;AN=2;DP=10 GT:AD:DP:GQ:PL 1/1:0,10:10:30:450,30,0 2R 16210904 . C T 2532.47 PASS AC=2;AF=1.00;AN=2;DP=11 GT:AD:DP:GQ:PL 1/1:0,0:11:33:13,0,0 2R 16210940 . C G 97625.90 PASS AC=2;AF=1.00;AN=2;DP=15 GT:AD:DP:GQ:PL 1/1:0,60:15:45:595,45,0 2R 16211041 . C A 2579.85 PASS AC=2;AF=1.00;AN=2;DP=15 GT:AD:DP:GQ:PL 1/1:0,15:15:45:11,0,0 2R 16211042 . A G 95462 PASS AC=2;AF=1.00;AN=2;DP=15 GT:AD:DP:GQ:PL 1/1:0,5:15:45:675,0,0 2R 16211108 . G A 77101.80 PASS AC=2;AF=1.00;AN=2;DP=18 GT:AD:DP:GQ:PL 1/1:0,18:18:54:706,54,0 2R 16211202 . C T 129728 PASS AC=2;AF=1.00;AN=2;DP=13 GT:AD:DP:GQ:PL 1/1:0,13:13:39:561,39,0 2R 16211857 . T C 143370 PASS AC=2;AF=1.00;AN=2;DP=17 GT:AD:DP:GQ:PL 1/1:0,17:17:51:28,0,0 2R 16212083 . C G 148987 PASS AC=2;AF=1.00;AN=2;DP=9 GT:AD:DP:GQ:PL 1/1:0,21:9:27:8,0,0 2R 16212251 . 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