Mercurial > repos > iuc > gatk4_mutect2
view test-data/Mutect2-out2.vcf @ 6:fb0bb7174530 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4 commit 301f94b20e29da22d5f4502c44344f4a0115930d
| author | iuc |
|---|---|
| date | Wed, 24 Aug 2022 17:59:05 +0000 |
| parents | 287c4af133e6 |
| children |
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##fileformat=VCFv4.2 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> ##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> ##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele"> ##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele"> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles"> ##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)"> ##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=Mutect2,CommandLine="Mutect2 --tumor-sample SRR8525881 --output output.vcf --input tumor.bam --reference reference.fa --QUIET true --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --allele-informative-reads-overlap-margin 2 --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-reads-per-alignment-start 50 --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 --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.7.0",Date="May 8, 2020 3:31:33 PM CEST"> ##INFO=<ID=AS_SB_TABLE,Number=1,Type=String,Description="Allele-specific forward/reverse read counts for strand bias tests. Includes the reference and alleles separated by |."> ##INFO=<ID=AS_UNIQ_ALT_READ_COUNT,Number=A,Type=Integer,Description="Number of reads with unique start and mate end positions for each alt at a variant site"> ##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> ##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype"> ##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants"> ##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality"> ##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length"> ##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality"> ##INFO=<ID=MPOS,Number=A,Type=Integer,Description="median distance from end of read"> ##INFO=<ID=NALOD,Number=A,Type=Float,Description="Negative log 10 odds of artifact in normal with same allele fraction as tumor"> ##INFO=<ID=NCount,Number=1,Type=Integer,Description="Count of N bases in the pileup"> ##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes"> ##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig."> ##INFO=<ID=PON,Number=0,Type=Flag,Description="site found in panel of normals"> ##INFO=<ID=POPAF,Number=A,Type=Float,Description="negative log 10 population allele frequencies of alt alleles"> ##INFO=<ID=ROQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to read orientation artifact"> ##INFO=<ID=RPA,Number=R,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)"> ##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)"> ##INFO=<ID=SEQQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not sequencing errors"> ##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat"> ##INFO=<ID=STRANDQ,Number=1,Type=Integer,Description="Phred-scaled quality of strand bias artifact"> ##INFO=<ID=STRQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles in STRs are not polymerase slippage errors"> ##INFO=<ID=TLOD,Number=A,Type=Float,Description="Log 10 likelihood ratio score of variant existing versus not existing"> ##MutectVersion=2.2 ##contig=<ID=K03455,length=9719> ##filtering_status=Warning: unfiltered Mutect 2 calls. Please run FilterMutectCalls to remove false positives. ##source=Mutect2 ##tumor_sample=SRR8525881 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881 K03455 4861 . A G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;MBQ=0,37;MFRL=0,400;MMQ=60,60;MPOS=10;POPAF=7.30;TLOD=3.88 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,1:0.667:1:0,1:0,0:0,0,1,0 K03455 4918 . G A . . AS_SB_TABLE=4,1|1,5;DP=11;ECNT=13;MBQ=35,32;MFRL=299,328;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=17.13 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:5,6:0.538:11:2,1:3,3:4,1,1,5 K03455 4923 . A G . . AS_SB_TABLE=0,0|6,6;DP=12;ECNT=13;MBQ=0,33;MFRL=0,301;MMQ=60,60;MPOS=10;POPAF=7.30;TLOD=53.71 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,12:0.929:12:0,4:0,6:0,0,6,6 K03455 4949 . G A . . AS_SB_TABLE=3,3|5,6;DP=17;ECNT=13;MBQ=38,37;MFRL=281,293;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=44.63 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:6,11:0.667:17:2,3:2,7:0|1:4949_G_A:4949:3,3,5,6 K03455 4952 . C T . . AS_SB_TABLE=3,3|5,6;DP=19;ECNT=13;MBQ=25,37;MFRL=281,293;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=44.61 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:6,11:0.667:17:2,3:2,8:0|1:4949_G_A:4949:3,3,5,6 K03455 4988 . T C . . AS_SB_TABLE=15,13|4,4;DP=36;ECNT=13;MBQ=34,35;MFRL=254,290;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=23.46 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:28,8:0.229:36:10,4:14,3:15,13,4,4 K03455 4991 . T C . . AS_SB_TABLE=16,15|3,2;DP=36;ECNT=13;MBQ=33,36;MFRL=264,238;MMQ=60,60;MPOS=17;POPAF=7.30;TLOD=12.68 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:31,5:0.171:36:13,2:17,2:16,15,3,2 K03455 4996 . AC GA . . AS_SB_TABLE=17,16|3,3;DP=40;ECNT=13;MBQ=34,26;MFRL=260,256;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=12.38 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:33,6:0.161:39:11,2:15,3:17,16,3,3 K03455 4997 . C T,A . . AS_SB_TABLE=6,5|4,3|10,10;DP=40;ECNT=13;MBQ=20,35,38;MFRL=278,158,261;MMQ=60,60,60;MPOS=14,31;POPAF=7.30,7.30;TLOD=21.98,46.07 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:11,7,20:0.187,0.536:38:6,2,7:3,4,13:6,5,14,13 K03455 5015 . A G . . AS_SB_TABLE=6,8|16,17;DP=49;ECNT=13;MBQ=27,37;MFRL=245,251;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=138.05 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:14,33:0.728:47:7,9:6,22:6,8,16,17 K03455 5018 . A G . . AS_SB_TABLE=18,23|4,4;DP=49;ECNT=13;MBQ=34,20;MFRL=260,194;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=21.59 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:41,8:0.173:49:13,2:22,5:18,23,4,4 K03455 5027 . G A . . AS_SB_TABLE=18,23|4,7;DP=52;ECNT=13;MBQ=37,20;MFRL=260,158;MMQ=60,60;MPOS=35;POPAF=7.30;TLOD=33.61 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:41,11:0.208:52:14,2:24,8:0|1:5027_G_A:5027:18,23,4,7 K03455 5036 . G A . . AS_SB_TABLE=18,22|4,7;DP=52;ECNT=13;MBQ=34,20;MFRL=259,158;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=33.71 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:40,11:0.212:51:13,2:26,8:0|1:5027_G_A:5027:18,22,4,7 K03455 5076 . A G . . AS_SB_TABLE=11,36|1,8;DP=56;ECNT=29;MBQ=37,20;MFRL=260,190;MMQ=60,60;MPOS=49;POPAF=7.30;TLOD=27.26 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:47,9:0.173:56:15,1:29,8:0|1:5076_A_G:5076:11,36,1,8 K03455 5098 . A G . . AS_SB_TABLE=1,11|10,40;DP=63;ECNT=29;MBQ=20,33;MFRL=198,269;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=196.26 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:12,50:0.785:62:0,11:10,27:1,11,10,40 K03455 5099 . C T . . AS_SB_TABLE=10,41|1,10;DP=63;ECNT=29;MBQ=34,20;MFRL=260,190;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=33.93 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:51,11:0.196:62:10,1:33,8:0|1:5076_A_G:5076:10,41,1,10 K03455 5121 . C T . . AS_SB_TABLE=7,39|4,13;DP=63;ECNT=29;MBQ=26,20;MFRL=246,260;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=57.26 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:46,17:0.250:63:8,6:34,9:7,39,4,13 K03455 5130 . TG CA . . AS_SB_TABLE=3,13|3,37;DP=56;ECNT=29;MBQ=27,37;MFRL=218,249;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=170.80 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:16,40:0.738:56:5,6:9,32:3,13,3,37 K03455 5131 . G A . . AS_SB_TABLE=0,1|3,13;DP=56;ECNT=29;MBQ=32,20;MFRL=206,216;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=56.78 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1,16:0.946:17:0,4:1,9:0,1,3,13 K03455 5133 . T C . . AS_SB_TABLE=5,34|0,13;DP=52;ECNT=29;MBQ=33,33;MFRL=278,222;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=42.34 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:39,13:0.280:52:7,1:26,11:0|1:5133_T_C:5133:5,34,0,13 K03455 5137 . GG AA,AG . . AS_SB_TABLE=3,13|1,21|0,13;DP=51;ECNT=29;MBQ=32,39,39;MFRL=218,320,222;MMQ=60,60,60;MPOS=34,39;POPAF=7.30,7.30;TLOD=86.50,42.93 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:16,22,13:0.452,0.274:51:5,4,1:9,17,10:3,13,1,34 K03455 5146 . AGG A . . AS_SB_TABLE=4,32|0,12;DP=48;ECNT=29;MBQ=37,37;MFRL=286,219;MMQ=60,60;MPOS=43;POPAF=7.30;RPA=4,2;RU=G;STR;TLOD=39.62 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:36,12:0.276:48:8,1:25,11:0|1:5133_T_C:5133:4,32,0,12 K03455 5147 . G A . . AS_SB_TABLE=3,12|1,20;DP=48;ECNT=29;MBQ=20,37;MFRL=229,331;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=83.42 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:15,21:0.640:36:5,3:9,14:0|1:5147_G_A:5147:3,12,1,20 K03455 5149 . G A . . AS_SB_TABLE=3,42|1,1;DP=47;ECNT=29;MBQ=36,18;MFRL=257,64;MMQ=60,60;MPOS=13;POPAF=7.30;TLOD=4.60 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:45,2:0.043:47:7,0:30,1:3,42,1,1 K03455 5153 . GGTTT G . . AS_SB_TABLE=3,28|0,12;DP=43;ECNT=29;MBQ=35,37;MFRL=278,219;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=40.38 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:31,12:0.309:43:7,1:22,11:0|1:5133_T_C:5133:3,28,0,12 K03455 5155 . T C . . AS_SB_TABLE=3,11|0,16;DP=42;ECNT=29;MBQ=27,38;MFRL=221,315;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=62.97 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:14,16:0.601:30:5,2:8,13:0|1:5147_G_A:5147:3,11,0,16 K03455 5156 . T A . . AS_SB_TABLE=1,17|2,10;DP=42;ECNT=29;MBQ=37,35;MFRL=296,269;MMQ=60,60;MPOS=15;POPAF=7.30;TLOD=43.10 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:18,12:0.365:30:2,5:16,7:0|1:5156_T_A:5156:1,17,2,10 K03455 5157 . T G,C . . AS_SB_TABLE=2,10|0,16|1,1;DP=42;ECNT=29;MBQ=28,37,20;MFRL=269,315,64;MMQ=60,60,60;MPOS=56,5;POPAF=7.30,7.30;TLOD=63.04,5.63 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:12,16,2:0.584,0.061:30:5,2,0:7,14,2:2,10,1,17 K03455 5169 . C T . . AS_SB_TABLE=1,19|1,10;DP=31;ECNT=29;MBQ=38,32;MFRL=275,190;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=37.40 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:20,11:0.355:31:2,4:17,7:1,19,1,10 K03455 5175 . A T . . AS_SB_TABLE=0,15|1,12;DP=28;ECNT=29;MBQ=28,38;MFRL=222,293;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=52.25 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:15,13:0.448:28:3,2:10,11:0|1:5147_G_A:5147:0,15,1,12 K03455 5177 . G C . . AS_SB_TABLE=1,16|0,10;DP=27;ECNT=29;MBQ=37,35;MFRL=293,219;MMQ=60,60;MPOS=52;POPAF=7.30;TLOD=36.84 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:17,10:0.393:27:4,1:12,9:0|1:5133_T_C:5133:1,16,0,10 K03455 5179 . CC AA,AC . . AS_SB_TABLE=0,4|1,11|0,10;DP=26;ECNT=29;MBQ=38,38,34;MFRL=339,296,219;MMQ=60,60,60;MPOS=51,61;POPAF=7.30,7.30;TLOD=48.82,37.25 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:4,12,10:0.429,0.393:26:2,2,1:2,10,7:0,4,1,21 K03455 5189 . G A . . AS_SB_TABLE=1,12|1,11;DP=25;ECNT=29;MBQ=39,39;MFRL=222,296;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=48.64 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:13,12:0.462:25:4,2:9,10:1,12,1,11 K03455 5190 . A G . . AS_SB_TABLE=1,19|1,4;DP=25;ECNT=29;MBQ=39,20;MFRL=252,278;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=15.35 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:20,5:0.231:25:3,2:17,2:0|1:5156_T_A:5156:1,19,1,4 K03455 5196 . T C . . AS_SB_TABLE=1,20|1,3;DP=25;ECNT=29;MBQ=38,20;MFRL=246,339;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=6.08 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:21,4:0.191:25:3,3:18,1:1,20,1,3 K03455 5220 . G A . . AS_SB_TABLE=2,14|0,7;DP=23;ECNT=29;MBQ=37,37;MFRL=286,222;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=24.08 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:16,7:0.344:23:5,1:11,6:0|1:5220_G_A:5220:2,14,0,7 K03455 5223 . T A . . AS_SB_TABLE=1,16|1,4;DP=22;ECNT=29;MBQ=37,37;MFRL=257,278;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=17.16 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:17,5:0.269:22:2,3:14,2:0|1:5223_T_A:5223:1,16,1,4 K03455 5226 . T C . . AS_SB_TABLE=1,15|1,5;DP=22;ECNT=29;MBQ=34,35;MFRL=268,253;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=12.23 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:16,6:0.231:22:4,1:12,5:1,15,1,5 K03455 5230 . T C . . AS_SB_TABLE=1,15|1,4;DP=21;ECNT=29;MBQ=33,38;MFRL=275,278;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=17.08 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:16,5:0.281:21:2,3:13,2:0|1:5223_T_A:5223:1,15,1,4 K03455 5233 . G A . . AS_SB_TABLE=2,9|0,5;DP=16;ECNT=29;MBQ=38,38;MFRL=293,216;MMQ=60,60;MPOS=17;POPAF=7.30;TLOD=17.95 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:11,5:0.369:16:3,0:7,5:0|1:5220_G_A:5220:2,9,0,5 K03455 5236 . A G . . AS_SB_TABLE=0,5|2,9;DP=16;ECNT=29;MBQ=37,38;MFRL=216,293;MMQ=60,60;MPOS=14;POPAF=7.30;TLOD=40.42 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:5,11:0.631:16:0,4:5,6:0,5,2,9 K03455 5240 . C T . . AS_SB_TABLE=2,10|0,3;DP=15;ECNT=29;MBQ=37,37;MFRL=250,162;MMQ=60,60;MPOS=5;POPAF=7.30;TLOD=9.14 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:12,3:0.250:15:3,0:8,3:2,10,0,3 K03455 6822 . GT AC . . AS_SB_TABLE=0,0|2,2;DP=4;ECNT=1;MBQ=0,38;MFRL=0,117;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=7.34 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,4:0.750:4:0,0:0,4:0,0,2,2 K03455 6902 . A C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=65;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 K03455 6905 . A G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 K03455 6911 . T C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 K03455 6917 . G A . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 K03455 6920 . G A . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=47;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 K03455 6923 . C T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=44;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 K03455 6931 . C A . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 K03455 6936 . C G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 K03455 7141 . GAATCC G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,0;MFRL=0,310;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,0:0|1:7141_GAATCC_G:7141:0,0,0,1 K03455 7149 . A G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,15;MFRL=0,310;MMQ=60,60;MPOS=7;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,0:0|1:7141_GAATCC_G:7141:0,0,0,1 K03455 7151 . C G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,38;MFRL=0,310;MMQ=60,60;MPOS=9;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,1:0,0:0|1:7141_GAATCC_G:7141:0,0,0,1 K03455 7154 . G T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,24;MFRL=0,310;MMQ=60,60;MPOS=12;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,1:0,0:0|1:7141_GAATCC_G:7141:0,0,0,1 K03455 7156 . G T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,25;MFRL=0,310;MMQ=60,60;MPOS=14;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,1:0,0:0|1:7141_GAATCC_G:7141:0,0,0,1 K03455 7163 . A C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,13;MFRL=0,310;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,1:0.667:1:0,0:0,0:0,0,0,1 K03455 7372 . T C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=2;MBQ=0,34;MFRL=0,451;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=3.58 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7372_T_C:7372:0,0,0,1 K03455 7392 . C T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=2;MBQ=0,32;MFRL=0,451;MMQ=60,60;MPOS=5;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7372_T_C:7372:0,0,0,1 K03455 7441 . A ACCT . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=77;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 K03455 7443 . A AGTG . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=82;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 K03455 7449 . G A . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=91;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 K03455 7452 . GGA G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=94;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 K03455 7455 . A ATG . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=95;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 K03455 7457 . TGA T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=99;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 K03455 7460 . CA C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,37;MFRL=0,486;MMQ=60,60;MPOS=100;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 K03455 7468 . CC TA . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=107;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,2 K03455 7478 . C T . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=117;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 K03455 7491 . A T . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=118;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 K03455 7494 . A G . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=115;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 K03455 7508 . GA AG . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=101;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 K03455 7541 . C CGA . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=68;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 K03455 7542 . AGT A . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=65;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 K03455 7548 . C A . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=61;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 K03455 7555 . GA AT . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=54;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 K03455 7560 . TC GT . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,38;MFRL=0,586;MMQ=60,50;MPOS=49;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 K03455 7568 . T C . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=41;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 K03455 7571 . T C . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=38;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 K03455 7581 . C A . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=28;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 K03455 7584 . T C . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=25;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 K03455 7603 . A AGGG . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,37;MFRL=0,586;MMQ=60,50;MPOS=6;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 K03455 7604 . T G . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,33;MFRL=0,586;MMQ=60,50;MPOS=2;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0|1:7541_C_CGA:7541:0,0,0,2