bio-vcf 0.0.2 → 0.0.3
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/Gemfile +1 -0
- data/Gemfile.lock +8 -0
- data/README.md +376 -11
- data/VERSION +1 -1
- data/bin/bio-vcf +172 -39
- data/bio-vcf.gemspec +18 -3
- data/features/cli.feature +32 -0
- data/features/multisample.feature +28 -10
- data/features/step_definitions/cli-feature.rb +12 -0
- data/features/step_definitions/multisample.rb +64 -18
- data/features/support/env.rb +5 -0
- data/lib/bio-vcf.rb +2 -0
- data/lib/bio-vcf/utils.rb +23 -0
- data/lib/bio-vcf/vcfgenotypefield.rb +73 -28
- data/lib/bio-vcf/vcfheader.rb +8 -0
- data/lib/bio-vcf/vcfline.rb +1 -0
- data/lib/bio-vcf/vcfrecord.rb +142 -14
- data/lib/bio-vcf/vcfsample.rb +88 -0
- data/test/data/input/dbsnp.vcf +200 -0
- data/test/data/input/multisample.vcf +2 -2
- data/test/data/regression/eval_r.info.dp.ref +150 -0
- data/test/data/regression/r.info.dp.ref +147 -0
- data/test/data/regression/rewrite.info.sample.ref +150 -0
- data/test/data/regression/s.dp.ref +145 -0
- data/test/data/regression/seval_s.dp.ref +36 -0
- data/test/data/regression/sfilter001.ref +145 -0
- data/test/performance/metrics.md +98 -0
- metadata +28 -2
@@ -0,0 +1,150 @@
|
|
1
|
+
##fileformat=VCFv4.1
|
2
|
+
##FILTER=<ID=LowQual,Description="Low quality">
|
3
|
+
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
|
4
|
+
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
|
5
|
+
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
|
6
|
+
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
|
7
|
+
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
|
8
|
+
##GATKCommandLine=<ID=UnifiedGenotyper,Version=2.8-1-g932cd3a,Date="Sat Jan 25 10:33:56 CET 2014",Epoch=1390642436187,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[/data_fedor12/BAM/sander/Liver_clones/BIOPSY17513D/mapping/BIOPSY17513D_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone3/mapping/clone3_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone4/mapping/clone4_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone10/mapping/clone10_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone33/mapping/subclone33_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone46/mapping/subclone46_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone105/mapping/subclone105_dedup_realigned_recalibrated.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[/data_fedor13/sander/variant_calling/Liver_clones/.queue/scatterGather/UnifiedGenotyper_noref-1-sg/temp_001_of_500/scatter.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data_fedor13/common_data/references/H_sapiens/GATK_b37_bundle_reference/basespace/human_g1k_v37.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 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 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false 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 genotype_likelihoods_model=SNP pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 allSitePLs=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false output_mode=EMIT_VARIANTS_ONLY heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name= source=UNBOUND) comp=[] 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 onlyEmitSamples=[] debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
|
9
|
+
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
|
10
|
+
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
|
11
|
+
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
|
12
|
+
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
|
13
|
+
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
|
14
|
+
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
|
15
|
+
##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
|
16
|
+
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
|
17
|
+
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
|
18
|
+
##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">
|
19
|
+
##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">
|
20
|
+
##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">
|
21
|
+
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
|
22
|
+
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
|
23
|
+
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
|
24
|
+
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
|
25
|
+
##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
|
26
|
+
##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
|
27
|
+
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
|
28
|
+
##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
|
29
|
+
##contig=<ID=1,length=249250621,assembly=b37>
|
30
|
+
##contig=<ID=2,length=243199373,assembly=b37>
|
31
|
+
##contig=<ID=3,length=198022430,assembly=b37>
|
32
|
+
##contig=<ID=4,length=191154276,assembly=b37>
|
33
|
+
##contig=<ID=5,length=180915260,assembly=b37>
|
34
|
+
##contig=<ID=6,length=171115067,assembly=b37>
|
35
|
+
##contig=<ID=7,length=159138663,assembly=b37>
|
36
|
+
##contig=<ID=8,length=146364022,assembly=b37>
|
37
|
+
##contig=<ID=9,length=141213431,assembly=b37>
|
38
|
+
##contig=<ID=10,length=135534747,assembly=b37>
|
39
|
+
##contig=<ID=11,length=135006516,assembly=b37>
|
40
|
+
##contig=<ID=12,length=133851895,assembly=b37>
|
41
|
+
##contig=<ID=13,length=115169878,assembly=b37>
|
42
|
+
##contig=<ID=14,length=107349540,assembly=b37>
|
43
|
+
##contig=<ID=15,length=102531392,assembly=b37>
|
44
|
+
##contig=<ID=16,length=90354753,assembly=b37>
|
45
|
+
##contig=<ID=17,length=81195210,assembly=b37>
|
46
|
+
##contig=<ID=18,length=78077248,assembly=b37>
|
47
|
+
##contig=<ID=19,length=59128983,assembly=b37>
|
48
|
+
##contig=<ID=20,length=63025520,assembly=b37>
|
49
|
+
##contig=<ID=21,length=48129895,assembly=b37>
|
50
|
+
##contig=<ID=22,length=51304566,assembly=b37>
|
51
|
+
##contig=<ID=X,length=155270560,assembly=b37>
|
52
|
+
##contig=<ID=Y,length=59373566,assembly=b37>
|
53
|
+
##contig=<ID=MT,length=16569,assembly=b37>
|
54
|
+
##contig=<ID=GL000207.1,length=4262,assembly=b37>
|
55
|
+
##contig=<ID=GL000226.1,length=15008,assembly=b37>
|
56
|
+
##contig=<ID=GL000229.1,length=19913,assembly=b37>
|
57
|
+
##contig=<ID=GL000231.1,length=27386,assembly=b37>
|
58
|
+
##contig=<ID=GL000210.1,length=27682,assembly=b37>
|
59
|
+
##contig=<ID=GL000239.1,length=33824,assembly=b37>
|
60
|
+
##contig=<ID=GL000235.1,length=34474,assembly=b37>
|
61
|
+
##contig=<ID=GL000201.1,length=36148,assembly=b37>
|
62
|
+
##contig=<ID=GL000247.1,length=36422,assembly=b37>
|
63
|
+
##contig=<ID=GL000245.1,length=36651,assembly=b37>
|
64
|
+
##contig=<ID=GL000197.1,length=37175,assembly=b37>
|
65
|
+
##contig=<ID=GL000203.1,length=37498,assembly=b37>
|
66
|
+
##contig=<ID=GL000246.1,length=38154,assembly=b37>
|
67
|
+
##contig=<ID=GL000249.1,length=38502,assembly=b37>
|
68
|
+
##contig=<ID=GL000196.1,length=38914,assembly=b37>
|
69
|
+
##contig=<ID=GL000248.1,length=39786,assembly=b37>
|
70
|
+
##contig=<ID=GL000244.1,length=39929,assembly=b37>
|
71
|
+
##contig=<ID=GL000238.1,length=39939,assembly=b37>
|
72
|
+
##contig=<ID=GL000202.1,length=40103,assembly=b37>
|
73
|
+
##contig=<ID=GL000234.1,length=40531,assembly=b37>
|
74
|
+
##contig=<ID=GL000232.1,length=40652,assembly=b37>
|
75
|
+
##contig=<ID=GL000206.1,length=41001,assembly=b37>
|
76
|
+
##contig=<ID=GL000240.1,length=41933,assembly=b37>
|
77
|
+
##contig=<ID=GL000236.1,length=41934,assembly=b37>
|
78
|
+
##contig=<ID=GL000241.1,length=42152,assembly=b37>
|
79
|
+
##contig=<ID=GL000243.1,length=43341,assembly=b37>
|
80
|
+
##contig=<ID=GL000242.1,length=43523,assembly=b37>
|
81
|
+
##contig=<ID=GL000230.1,length=43691,assembly=b37>
|
82
|
+
##contig=<ID=GL000237.1,length=45867,assembly=b37>
|
83
|
+
##contig=<ID=GL000233.1,length=45941,assembly=b37>
|
84
|
+
##contig=<ID=GL000204.1,length=81310,assembly=b37>
|
85
|
+
##contig=<ID=GL000198.1,length=90085,assembly=b37>
|
86
|
+
##contig=<ID=GL000208.1,length=92689,assembly=b37>
|
87
|
+
##contig=<ID=GL000191.1,length=106433,assembly=b37>
|
88
|
+
##contig=<ID=GL000227.1,length=128374,assembly=b37>
|
89
|
+
##contig=<ID=GL000228.1,length=129120,assembly=b37>
|
90
|
+
##contig=<ID=GL000214.1,length=137718,assembly=b37>
|
91
|
+
##contig=<ID=GL000221.1,length=155397,assembly=b37>
|
92
|
+
##contig=<ID=GL000209.1,length=159169,assembly=b37>
|
93
|
+
##contig=<ID=GL000218.1,length=161147,assembly=b37>
|
94
|
+
##contig=<ID=GL000220.1,length=161802,assembly=b37>
|
95
|
+
##contig=<ID=GL000213.1,length=164239,assembly=b37>
|
96
|
+
##contig=<ID=GL000211.1,length=166566,assembly=b37>
|
97
|
+
##contig=<ID=GL000199.1,length=169874,assembly=b37>
|
98
|
+
##contig=<ID=GL000217.1,length=172149,assembly=b37>
|
99
|
+
##contig=<ID=GL000216.1,length=172294,assembly=b37>
|
100
|
+
##contig=<ID=GL000215.1,length=172545,assembly=b37>
|
101
|
+
##contig=<ID=GL000205.1,length=174588,assembly=b37>
|
102
|
+
##contig=<ID=GL000219.1,length=179198,assembly=b37>
|
103
|
+
##contig=<ID=GL000224.1,length=179693,assembly=b37>
|
104
|
+
##contig=<ID=GL000223.1,length=180455,assembly=b37>
|
105
|
+
##contig=<ID=GL000195.1,length=182896,assembly=b37>
|
106
|
+
##contig=<ID=GL000212.1,length=186858,assembly=b37>
|
107
|
+
##contig=<ID=GL000222.1,length=186861,assembly=b37>
|
108
|
+
##contig=<ID=GL000200.1,length=187035,assembly=b37>
|
109
|
+
##contig=<ID=GL000193.1,length=189789,assembly=b37>
|
110
|
+
##contig=<ID=GL000194.1,length=191469,assembly=b37>
|
111
|
+
##contig=<ID=GL000225.1,length=211173,assembly=b37>
|
112
|
+
##contig=<ID=GL000192.1,length=547496,assembly=b37>
|
113
|
+
##reference=file:human_g1k_v37.fasta
|
114
|
+
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Original s1t1 s2t1 s3t1 s1t2 s2t2 s3t2
|
115
|
+
1 10257 . A C 77.69 . AC=1;AF=0.071;AN=14;BaseQRankSum=-0.066;DP=1518;Dels=0.00;FS=24.214;HaplotypeScore=226.5209;MLEAC=1;MLEAF=0.071;MQ=25.00;MQ0=329;MQRankSum=-1.744;QD=0.37;ReadPosRankSum=1.551;sample=XXXXX GT:AD:DP:GQ:PL 0/0:151,8:159:99:0,195,2282 0/0:219,22:242:99:0,197,2445 0/0:227,22:249:90:0,90,2339 0/0:226,22:249:99:0,159,2695 0/0:166,18:186:99:0,182,1989 0/1:185,27:212:99:111,0,2387 0/0:201,15:218:24:0,24,1972
|
116
|
+
1 10291 . C T 1031.89 . AC=7;AF=0.500;AN=14;BaseQRankSum=4.367;DP=1433;Dels=0.00;FS=0.696;HaplotypeScore=101.0885;MLEAC=7;MLEAF=0.500;MQ=26.96;MQ0=225;MQRankSum=0.087;QD=0.72;ReadPosRankSum=-1.640;sample=XXXXX GT:AD:DP:GQ:PL 0/1:145,16:165:23:23,0,491 0/1:218,26:249:29:29,0,611 0/1:214,30:249:99:145,0,801 0/1:213,32:247:20:20,0,1031 0/1:122,36:161:99:347,0,182 0/1:131,27:163:99:255,0,508 0/1:156,31:189:99:252,0,372
|
117
|
+
1 10297 . C T 187.21 . AC=5;AF=0.357;AN=14;BaseQRankSum=-2.778;DP=1440;Dels=0.00;FS=0.000;HaplotypeScore=123.6373;MLEAC=5;MLEAF=0.357;MQ=27.26;MQ0=217;MQRankSum=-2.914;QD=0.18;ReadPosRankSum=1.927;sample=XXXXX GT:AD:DP:GQ:PL 0/1:155,18:182:44:44,0,654 0/1:218,23:246:21:21,0,673 0/1:219,26:250:41:41,0,898 0/0:207,30:246:39:0,39,963 0/0:137,20:165:21:0,21,363 0/1:124,27:158:65:65,0,435 0/1:151,27:183:63:63,0,485
|
118
|
+
1 10303 . C T 166.50 . AC=3;AF=0.214;AN=14;BaseQRankSum=-3.960;DP=1460;Dels=0.00;FS=2.121;HaplotypeScore=138.0883;MLEAC=2;MLEAF=0.143;MQ=27.29;MQ0=220;MQRankSum=-2.873;QD=0.27;ReadPosRankSum=1.756;sample=XXXXX GT:AD:DP:GQ:PL 0/1:169,25:198:99:195,0,609 0/1:211,31:247:1:1,0,656 0/0:214,28:248:7:0,7,982 0/0:214,32:248:25:0,25,980 0/0:146,17:172:2:0,2,353 0/1:123,23:157:17:17,0,541 0/0:156,22:182:19:0,19,413
|
119
|
+
1 10315 . C T 108.20 . AC=3;AF=0.214;AN=14;BaseQRankSum=-3.769;DP=1500;Dels=0.01;FS=1.493;HaplotypeScore=169.3933;MLEAC=3;MLEAF=0.214;MQ=26.95;MQ0=241;MQRankSum=-4.511;QD=0.19;ReadPosRankSum=2.373;sample=XXXXX GT:AD:DP:GQ:PL 0/1:181,26:212:41:41,0,618 0/0:223,17:246:99:0,102,832 0/0:219,20:242:66:0,66,924 0/0:217,23:245:99:0,109,1384 0/1:155,27:190:97:97,0,328 0/1:130,20:157:10:10,0,531 0/0:163,24:189:5:0,5,450
|
120
|
+
1 10321 . C T 106.30 . AC=5;AF=0.357;AN=14;BaseQRankSum=3.045;DP=1537;Dels=0.01;FS=5.835;HaplotypeScore=220.1531;MLEAC=5;MLEAF=0.357;MQ=26.69;MQ0=258;MQRankSum=-4.870;QD=0.10;ReadPosRankSum=0.815;sample=XXXXX GT:AD:DP:GQ:PL 0/1:189,25:218:30:30,0,810 0/0:219,22:246:24:0,24,593 0/1:218,27:248:34:34,0,1134 0/0:220,22:248:56:0,56,1207 0/1:168,23:193:19:19,0,493 0/1:139,22:164:46:46,0,689 0/1:167,26:196:20:20,0,522
|
121
|
+
1 10327 . T C 1215.15 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.585;DP=1641;Dels=0.02;FS=6.639;HaplotypeScore=237.4339;MLEAC=7;MLEAF=0.500;MQ=25.22;MQ0=321;MQRankSum=4.402;QD=0.74;ReadPosRankSum=3.957;sample=XXXXX GT:AD:DP:GQ:PL 0/1:178,56:237:99:178,0,848 0/1:178,60:238:99:320,0,575 0/1:185,40:229:99:236,0,679 0/1:184,52:237:99:358,0,544 0/1:165,43:209:57:57,0,726 0/1:151,31:183:9:9,0,780 0/1:164,46:210:96:96,0,550
|
122
|
+
1 10583 . G A 699.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-4.714;DP=129;Dels=0.00;FS=7.556;HaplotypeScore=0.6677;MLEAC=7;MLEAF=0.500;MQ=41.33;MQ0=2;MQRankSum=-2.309;QD=5.43;ReadPosRankSum=-0.296;sample=XXXXX GT:AD:DP:GQ:PL 0/1:5,3:8:58:58,0,133 0/1:12,12:24:99:231,0,287 0/1:16,4:21:38:38,0,491 0/1:19,4:23:57:57,0,494 0/1:9,6:15:99:140,0,180 0/1:11,8:19:99:173,0,235 0/1:15,4:19:42:42,0,344
|
123
|
+
1 10665 . C G 56.61 . AC=2;AF=0.250;AN=8;BaseQRankSum=2.219;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=0.250;MQ=25.41;MQ0=15;MQRankSum=0.185;QD=4.72;ReadPosRankSum=1.849;sample=XXXXX GT:AD:DP:GQ:PL ./. ./. 0/1:4,3:7:57:57,0,78 0/1:3,2:5:23:30,0,23 ./. 0/0:2,0:2:3:0,3,26 0/0:6,1:7:6:0,6,49
|
124
|
+
1 10694 . C G 85.78 . AC=4;AF=1.00;AN=4;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=17.21;MQ0=17;QD=8.58;sample=XXXXX GT:AD:DP:GQ:PL ./. ./. 1/1:2,3:5:6:74,6,0 1/1:3,2:5:3:35,3,0 ./. ./. ./.
|
125
|
+
1 10723 . C G 73.85 . AC=4;AF=0.667;AN=6;BaseQRankSum=1.300;DP=18;Dels=0.00;FS=3.680;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.667;MQ=20.49;MQ0=11;MQRankSum=1.754;QD=8.21;ReadPosRankSum=0.000;sample=XXXXX GT:AD:DP:GQ:PL ./. ./. 1/1:2,2:4:6:66,6,0 1/1:4,1:5:3:36,3,0 ./. ./. 0/0:6,0:6:3:0,3,33
|
126
|
+
1 12783 . G A 4330.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=12.671;DP=939;Dels=0.00;FS=0.000;HaplotypeScore=1.4998;MLEAC=7;MLEAF=0.500;MQ=14.64;MQ0=602;MQRankSum=-3.992;QD=4.61;ReadPosRankSum=0.195;sample=XXXXX GT:AD:DP:GQ:PL 0/1:24,34:58:82:174,0,82 0/1:80,84:164:99:658,0,433 0/1:59,85:144:99:670,0,407 0/1:68,114:182:99:1074,0,463 0/1:58,68:126:99:437,0,310 0/1:37,66:103:99:446,0,369 0/1:62,96:158:99:911,0,417
|
127
|
+
1 13116 . T G 2592.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-5.563;DP=721;Dels=0.00;FS=381.256;HaplotypeScore=2.5606;MLEAC=7;MLEAF=0.500;MQ=23.97;MQ0=222;MQRankSum=-14.896;QD=3.60;ReadPosRankSum=3.079;sample=XXXXX GT:AD:DP:GQ:PL 0/1:20,12:32:92:92,0,300 0/1:84,47:131:99:479,0,1548 0/1:65,37:102:99:441,0,1153 0/1:94,57:152:99:584,0,1993 0/1:61,43:104:99:360,0,1199 0/1:54,33:88:99:221,0,986 0/1:62,47:109:99:455,0,1128
|
128
|
+
1 13118 . A G 2317.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-9.647;DP=703;Dels=0.00;FS=362.380;HaplotypeScore=2.3393;MLEAC=7;MLEAF=0.500;MQ=23.54;MQ0=228;MQRankSum=-14.592;QD=3.30;ReadPosRankSum=3.437;sample=XXXXX GT:AD:DP:GQ:PL 0/1:21,13:34:95:95,0,277 0/1:82,47:129:99:444,0,1445 0/1:65,36:101:99:412,0,1179 0/1:92,53:145:99:455,0,1989 0/1:58,40:99:99:312,0,1216 0/1:52,33:85:99:186,0,1000 0/1:61,47:108:99:453,0,1079
|
129
|
+
1 13178 . G A 72.69 . AC=2;AF=0.143;AN=14;BaseQRankSum=-2.194;DP=929;Dels=0.00;FS=8.154;HaplotypeScore=1.8585;MLEAC=2;MLEAF=0.143;MQ=13.49;MQ0=590;MQRankSum=-3.030;QD=0.38;ReadPosRankSum=-0.383;sample=XXXXX GT:AD:DP:GQ:PL 0/1:49,3:52:11:11,0,292 0/0:161,11:172:60:0,60,1328 0/1:122,15:137:99:99,0,936 0/0:164,8:172:99:0,112,1436 0/0:120,9:129:62:0,62,771 0/0:113,6:119:12:0,12,885 0/0:138,10:148:99:0,112,1596
|
130
|
+
1 13302 . C T 1067.42 . AC=6;AF=0.429;AN=14;BaseQRankSum=11.584;DP=692;Dels=0.00;FS=86.736;HaplotypeScore=2.8260;MLEAC=6;MLEAF=0.429;MQ=27.08;MQ0=150;MQRankSum=-14.794;QD=1.63;ReadPosRankSum=-9.193;sample=XXXXX GT:AD:DP:GQ:PL 0/0:26,10:36:41:0,41,616 0/1:91,45:136:99:183,0,2085 0/1:71,28:99:86:86,0,1557 0/1:96,50:146:99:333,0,2098 0/1:55,34:90:99:283,0,1321 0/1:47,18:65:99:157,0,943 0/1:89,28:117:67:67,0,1921
|
131
|
+
1 13757 . G A 271.89 . AC=2;AF=0.143;AN=14;BaseQRankSum=2.916;DP=1149;Dels=0.00;FS=11.172;HaplotypeScore=7.1466;MLEAC=2;MLEAF=0.143;MQ=18.17;MQ0=374;MQRankSum=3.990;QD=0.87;ReadPosRankSum=1.309;sample=XXXXX GT:AD:DP:GQ:PL 0/0:47,4:53:16:0,16,344 0/0:185,16:201:60:0,60,2690 0/1:157,24:181:99:162,0,2556 0/0:232,18:250:99:0,137,3600 0/0:139,13:152:15:0,15,2266 0/1:114,16:130:99:147,0,1525 0/0:168,14:182:2:0,2,2230
|
132
|
+
1 13868 . A G 1481.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=2.036;DP=1108;Dels=0.00;FS=4.601;HaplotypeScore=6.7136;MLEAC=7;MLEAF=0.500;MQ=13.23;MQ0=622;MQRankSum=1.659;QD=1.34;ReadPosRankSum=0.283;sample=XXXXX GT:AD:DP:GQ:PL 0/1:60,15:75:80:80,0,568 0/1:146,46:192:99:289,0,1030 0/1:146,36:182:99:203,0,1001 0/1:172,52:224:99:222,0,1150 0/1:106,36:142:99:181,0,621 0/1:79,32:111:99:126,0,467 0/1:129,38:167:99:420,0,767
|
133
|
+
1 13896 . C A 389.42 . AC=6;AF=0.429;AN=14;BaseQRankSum=-0.743;DP=830;Dels=0.00;FS=0.000;HaplotypeScore=1.6931;MLEAC=6;MLEAF=0.429;MQ=11.88;MQ0=518;MQRankSum=-1.292;QD=0.54;ReadPosRankSum=0.433;sample=XXXXX GT:AD:DP:GQ:PL 0/1:50,12:62:99:107,0,367 0/1:107,28:135:40:40,0,660 0/1:120,23:143:37:37,0,675 0/1:144,31:175:99:172,0,690 0/0:98,14:112:42:0,42,577 0/1:65,16:81:34:34,0,290 0/1:102,19:121:41:41,0,677
|
134
|
+
1 14354 . C A 109.72 . AC=3;AF=0.250;AN=12;BaseQRankSum=-2.527;DP=764;Dels=0.00;FS=0.000;HaplotypeScore=0.3231;MLEAC=3;MLEAF=0.250;MQ=5.02;MQ0=710;MQRankSum=1.079;QD=0.47;ReadPosRankSum=-0.178;sample=XXXXX GT:AD:DP:GQ:PL 0/1:36,7:43:68:68,0,75 0/0:141,17:158:9:0,9,86 0/1:103,12:115:42:42,0,72 0/0:132,13:145:21:0,21,201 ./. 0/1:62,10:72:38:38,0,117 0/0:108,11:119:9:0,9,86
|
135
|
+
1 14464 . A T 3945.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=0.104;DP=809;Dels=0.00;FS=38.588;HaplotypeScore=5.8354;MLEAC=7;MLEAF=0.500;MQ=23.21;MQ0=241;MQRankSum=6.859;QD=4.88;ReadPosRankSum=-0.294;sample=XXXXX GT:AD:DP:GQ:PL 0/1:41,10:51:99:183,0,569 0/1:107,48:155:99:829,0,1388 0/1:99,42:141:99:691,0,1103 0/1:114,36:150:99:454,0,1544 0/1:48,35:83:99:781,0,561 0/1:64,25:89:99:409,0,781 0/1:102,38:140:99:638,0,1310
|
136
|
+
1 14673 . G C 1012.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.674;DP=754;Dels=0.00;FS=115.496;HaplotypeScore=14.9167;MLEAC=7;MLEAF=0.500;MQ=23.97;MQ0=268;MQRankSum=-1.459;QD=1.34;ReadPosRankSum=-3.039;sample=XXXXX GT:AD:DP:GQ:PL 0/1:28,8:36:34:34,0,409 0/1:117,25:142:99:125,0,1964 0/1:87,30:117:99:214,0,1506 0/1:130,27:157:99:193,0,2076 0/1:77,18:95:99:114,0,1273 0/1:49,27:76:99:200,0,719 0/1:103,28:131:99:172,0,1620
|
137
|
+
1 14699 . C G 64.65 . AC=2;AF=0.143;AN=14;BaseQRankSum=6.064;DP=719;Dels=0.00;FS=29.480;HaplotypeScore=5.5900;MLEAC=2;MLEAF=0.143;MQ=24.79;MQ0=233;MQRankSum=-8.066;QD=0.27;ReadPosRankSum=-0.696;sample=XXXXX GT:AD:DP:GQ:PL 0/0:35,6:43:51:0,51,720 0/1:91,37:128:59:59,0,1859 0/0:80,29:109:99:0,101,1700 0/0:113,34:147:14:0,14,1987 0/0:72,26:98:37:0,37,1319 0/0:53,25:78:78:0,78,1035 0/1:84,30:114:44:44,0,1326
|
138
|
+
1 14907 . A G 9688.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.299;DP=1083;Dels=0.00;FS=20.983;HaplotypeScore=11.4413;MLEAC=7;MLEAF=0.500;MQ=33.27;MQ0=51;MQRankSum=1.076;QD=8.95;ReadPosRankSum=0.653;sample=XXXXX GT:AD:DP:GQ:PL 0/1:27,30:57:99:603,0,550 0/1:117,99:216:99:2024,0,2888 0/1:91,71:162:99:1489,0,1990 0/1:119,86:205:99:1876,0,2588 0/1:100,53:153:99:1001,0,2297 0/1:59,59:118:99:1240,0,1241 0/1:91,67:158:99:1495,0,2003
|
139
|
+
1 14930 . A G 8665.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-13.760;DP=1092;Dels=0.00;FS=17.240;HaplotypeScore=20.0469;MLEAC=7;MLEAF=0.500;MQ=34.72;MQ0=22;MQRankSum=1.127;QD=7.94;ReadPosRankSum=0.785;sample=XXXXX GT:AD:DP:GQ:PL 0/1:32,36:68:99:609,0,659 0/1:123,92:216:99:1636,0,3225 0/1:92,78:170:99:1449,0,2202 0/1:123,86:210:99:1748,0,3028 0/1:85,50:136:99:802,0,2117 0/1:62,63:125:99:1072,0,1437 0/1:92,71:164:99:1389,0,2055
|
140
|
+
1 14933 . G A 248.54 . AC=3;AF=0.214;AN=14;BaseQRankSum=1.588;DP=1089;Dels=0.00;FS=14.333;HaplotypeScore=19.7793;MLEAC=3;MLEAF=0.214;MQ=34.91;MQ0=18;MQRankSum=1.439;QD=0.45;ReadPosRankSum=0.752;sample=XXXXX GT:AD:DP:GQ:PL 0/0:59,9:68:1:0,1,1361 0/1:192,24:216:99:125,0,4941 0/0:160,9:169:99:0,142,4118 0/1:191,21:212:39:39,0,4848 0/0:126,6:132:99:0,210,3367 0/1:113,15:128:99:124,0,2578 0/0:154,10:164:99:0,158,3934
|
141
|
+
1 14948 . G A 570.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=9.167;DP=1050;Dels=0.00;FS=11.131;HaplotypeScore=6.4398;MLEAC=7;MLEAF=0.500;MQ=32.69;MQ0=53;MQRankSum=0.017;QD=0.54;ReadPosRankSum=-1.181;sample=XXXXX GT:AD:DP:GQ:PL 0/1:56,7:63:79:79,0,1134 0/1:168,24:192:70:70,0,3900 0/1:160,21:181:99:147,0,3515 0/1:188,23:211:57:57,0,4113 0/1:115,14:129:32:32,0,2406 0/1:103,18:121:99:173,0,2016 0/1:132,21:153:52:52,0,2861
|
142
|
+
1 14976 . G A 195.07 . AC=3;AF=0.214;AN=14;BaseQRankSum=7.340;DP=939;Dels=0.00;FS=32.492;HaplotypeScore=4.6786;MLEAC=3;MLEAF=0.214;MQ=27.87;MQ0=167;MQRankSum=1.477;QD=0.53;ReadPosRankSum=-0.560;sample=XXXXX GT:AD:DP:GQ:PL 0/1:50,6:56:12:12,0,929 0/0:152,14:166:81:0,81,3159 0/0:152,9:161:99:0,113,2885 0/1:174,22:196:99:127,0,3211 0/0:100,9:109:97:0,97,1900 0/1:103,13:116:97:97,0,1548 0/0:122,13:135:55:0,55,2246
|
143
|
+
1 15118 . A G 2503.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-5.645;DP=1004;Dels=0.00;FS=0.313;HaplotypeScore=4.1078;MLEAC=7;MLEAF=0.500;MQ=21.49;MQ0=207;MQRankSum=-0.007;QD=2.49;ReadPosRankSum=-0.291;sample=XXXXX GT:AD:DP:GQ:PL 0/1:38,8:46:50:50,0,575 0/1:148,50:198:99:671,0,2598 0/1:97,32:129:99:358,0,1911 0/1:176,53:230:99:700,0,2989 0/1:91,19:113:99:146,0,1741 0/1:92,31:126:99:347,0,1543 0/1:126,30:158:99:271,0,2193
|
144
|
+
1 15190 . G A 2564.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=11.094;DP=1090;Dels=0.00;FS=0.297;HaplotypeScore=4.3151;MLEAC=7;MLEAF=0.500;MQ=26.11;MQ0=187;MQRankSum=-0.724;QD=2.35;ReadPosRankSum=0.530;sample=XXXXX GT:AD:DP:GQ:PL 0/1:42,11:53:99:177,0,696 0/1:157,51:208:99:839,0,3145 0/1:142,28:170:91:91,0,2919 0/1:160,40:200:99:499,0,2815 0/1:109,17:126:99:167,0,2363 0/1:111,34:145:99:554,0,2268 0/1:141,38:179:99:277,0,2827
|
145
|
+
1 15211 . T G 14032.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-11.292;DP=992;Dels=0.00;FS=0.281;HaplotypeScore=11.0809;MLEAC=7;MLEAF=0.500;MQ=27.20;MQ0=159;MQRankSum=3.859;QD=14.15;ReadPosRankSum=-1.972;sample=XXXXX GT:AD:DP:GQ:PL 0/1:19,35:54:99:858,0,183 0/1:63,120:183:99:2771,0,960 0/1:50,111:161:99:2213,0,740 0/1:58,113:171:99:2326,0,685 0/1:39,81:120:99:1707,0,678 0/1:38,96:134:99:2126,0,499 0/1:61,107:168:99:2071,0,895
|
146
|
+
1 15274 . A G,T 8909.81 . AC=7,7;AF=0.500,0.500;AN=14;BaseQRankSum=2.416;DP=636;Dels=0.00;FS=0.000;HaplotypeScore=5.1061;MLEAC=7,7;MLEAF=0.500,0.500;MQ=22.77;MQ0=195;MQRankSum=2.299;QD=14.01;ReadPosRankSum=1.707;sample=XXXXX GT:AD:DP:GQ:PL 1/2:1,14,22:37:99:717,494,467,224,0,170 1/2:1,45,75:121:99:1922,1334,1265,588,0,441 1/2:0,31,71:102:99:1960,1563,1515,396,0,222 1/2:1,59,77:137:99:2009,1376,1298,633,0,486 1/2:0,18,52:71:62:938,789,771,149,0,62 1/2:0,29,38:67:99:1141,883,853,258,0,162 1/2:0,38,60:98:99:1464,1064,1016,399,0,285
|
147
|
+
1 15447 . A G 109.56 . AC=3;AF=0.214;AN=14;BaseQRankSum=-9.704;DP=1213;Dels=0.00;FS=0.000;HaplotypeScore=16.4636;MLEAC=3;MLEAF=0.214;MQ=19.12;MQ0=346;MQRankSum=-0.997;QD=0.20;ReadPosRankSum=-1.088;sample=XXXXX GT:AD:DP:GQ:PL 0/0:42,4:46:34:0,34,690 0/0:220,22:242:99:0,99,3639 0/0:167,16:183:42:0,42,2582 0/1:201,25:226:78:78,0,2854 0/1:121,16:137:39:39,0,1877 0/0:160,13:173:99:0,139,2724 0/1:157,18:175:34:34,0,2472
|
148
|
+
1 15688 . C T 54.29 . AC=2;AF=0.143;AN=14;BaseQRankSum=-8.686;DP=904;Dels=0.00;FS=11.971;HaplotypeScore=3.1454;MLEAC=2;MLEAF=0.143;MQ=16.75;MQ0=361;MQRankSum=-0.069;QD=0.16;ReadPosRankSum=0.355;sample=XXXXX GT:AD:DP:GQ:PL 0/0:34,3:37:15:0,15,335 0/0:166,16:182:61:0,61,2190 0/1:131,16:147:69:69,0,1563 0/1:167,17:184:22:22,0,1894 0/0:88,12:100:15:0,15,1099 0/0:88,13:101:1:0,1,1126 0/0:132,16:148:18:0,18,1706
|
149
|
+
1 16068 . T C 377.22 . AC=4;AF=0.286;AN=14;BaseQRankSum=-7.618;DP=398;Dels=0.00;FS=12.349;HaplotypeScore=1.8069;MLEAC=4;MLEAF=0.286;MQ=26.64;MQ0=64;MQRankSum=-4.589;QD=1.80;ReadPosRankSum=-0.448;sample=XXXXX GT:AD:DP:GQ:PL 0/1:18,15:33:99:182,0,404 0/0:51,6:57:31:0,31,815 0/1:52,16:68:64:64,0,1101 0/0:68,13:81:99:0,99,1505 0/0:41,8:49:51:0,51,1010 0/1:40,9:49:21:21,0,702 0/1:38,19:58:99:153,0,760
|
150
|
+
1 16103 . T G 2348.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-1.646;DP=526;Dels=0.00;FS=2.577;HaplotypeScore=0.9645;MLEAC=7;MLEAF=0.500;MQ=26.64;MQ0=82;MQRankSum=-2.736;QD=4.47;ReadPosRankSum=-2.044;sample=XXXXX GT:AD:DP:GQ:PL 0/1:21,29:50:99:504,0,450 0/1:55,24:79:99:209,0,838 0/1:49,37:86:99:456,0,1002 0/1:74,32:106:99:193,0,1519 0/1:41,19:60:99:141,0,740 0/1:38,23:61:99:257,0,548 0/1:38,46:84:99:628,0,641
|
@@ -0,0 +1,145 @@
|
|
1
|
+
##fileformat=VCFv4.1
|
2
|
+
##FILTER=<ID=LowQual,Description="Low quality">
|
3
|
+
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
|
4
|
+
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
|
5
|
+
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
|
6
|
+
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
|
7
|
+
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
|
8
|
+
##GATKCommandLine=<ID=UnifiedGenotyper,Version=2.8-1-g932cd3a,Date="Sat Jan 25 10:33:56 CET 2014",Epoch=1390642436187,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[/data_fedor12/BAM/sander/Liver_clones/BIOPSY17513D/mapping/BIOPSY17513D_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone3/mapping/clone3_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone4/mapping/clone4_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone10/mapping/clone10_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone33/mapping/subclone33_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone46/mapping/subclone46_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone105/mapping/subclone105_dedup_realigned_recalibrated.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[/data_fedor13/sander/variant_calling/Liver_clones/.queue/scatterGather/UnifiedGenotyper_noref-1-sg/temp_001_of_500/scatter.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data_fedor13/common_data/references/H_sapiens/GATK_b37_bundle_reference/basespace/human_g1k_v37.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 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 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false 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 genotype_likelihoods_model=SNP pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 allSitePLs=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false output_mode=EMIT_VARIANTS_ONLY heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name= source=UNBOUND) comp=[] 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 onlyEmitSamples=[] debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
|
9
|
+
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
|
10
|
+
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
|
11
|
+
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
|
12
|
+
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
|
13
|
+
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
|
14
|
+
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
|
15
|
+
##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
|
16
|
+
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
|
17
|
+
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
|
18
|
+
##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">
|
19
|
+
##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">
|
20
|
+
##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">
|
21
|
+
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
|
22
|
+
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
|
23
|
+
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
|
24
|
+
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
|
25
|
+
##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
|
26
|
+
##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
|
27
|
+
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
|
28
|
+
##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
|
29
|
+
##contig=<ID=1,length=249250621,assembly=b37>
|
30
|
+
##contig=<ID=2,length=243199373,assembly=b37>
|
31
|
+
##contig=<ID=3,length=198022430,assembly=b37>
|
32
|
+
##contig=<ID=4,length=191154276,assembly=b37>
|
33
|
+
##contig=<ID=5,length=180915260,assembly=b37>
|
34
|
+
##contig=<ID=6,length=171115067,assembly=b37>
|
35
|
+
##contig=<ID=7,length=159138663,assembly=b37>
|
36
|
+
##contig=<ID=8,length=146364022,assembly=b37>
|
37
|
+
##contig=<ID=9,length=141213431,assembly=b37>
|
38
|
+
##contig=<ID=10,length=135534747,assembly=b37>
|
39
|
+
##contig=<ID=11,length=135006516,assembly=b37>
|
40
|
+
##contig=<ID=12,length=133851895,assembly=b37>
|
41
|
+
##contig=<ID=13,length=115169878,assembly=b37>
|
42
|
+
##contig=<ID=14,length=107349540,assembly=b37>
|
43
|
+
##contig=<ID=15,length=102531392,assembly=b37>
|
44
|
+
##contig=<ID=16,length=90354753,assembly=b37>
|
45
|
+
##contig=<ID=17,length=81195210,assembly=b37>
|
46
|
+
##contig=<ID=18,length=78077248,assembly=b37>
|
47
|
+
##contig=<ID=19,length=59128983,assembly=b37>
|
48
|
+
##contig=<ID=20,length=63025520,assembly=b37>
|
49
|
+
##contig=<ID=21,length=48129895,assembly=b37>
|
50
|
+
##contig=<ID=22,length=51304566,assembly=b37>
|
51
|
+
##contig=<ID=X,length=155270560,assembly=b37>
|
52
|
+
##contig=<ID=Y,length=59373566,assembly=b37>
|
53
|
+
##contig=<ID=MT,length=16569,assembly=b37>
|
54
|
+
##contig=<ID=GL000207.1,length=4262,assembly=b37>
|
55
|
+
##contig=<ID=GL000226.1,length=15008,assembly=b37>
|
56
|
+
##contig=<ID=GL000229.1,length=19913,assembly=b37>
|
57
|
+
##contig=<ID=GL000231.1,length=27386,assembly=b37>
|
58
|
+
##contig=<ID=GL000210.1,length=27682,assembly=b37>
|
59
|
+
##contig=<ID=GL000239.1,length=33824,assembly=b37>
|
60
|
+
##contig=<ID=GL000235.1,length=34474,assembly=b37>
|
61
|
+
##contig=<ID=GL000201.1,length=36148,assembly=b37>
|
62
|
+
##contig=<ID=GL000247.1,length=36422,assembly=b37>
|
63
|
+
##contig=<ID=GL000245.1,length=36651,assembly=b37>
|
64
|
+
##contig=<ID=GL000197.1,length=37175,assembly=b37>
|
65
|
+
##contig=<ID=GL000203.1,length=37498,assembly=b37>
|
66
|
+
##contig=<ID=GL000246.1,length=38154,assembly=b37>
|
67
|
+
##contig=<ID=GL000249.1,length=38502,assembly=b37>
|
68
|
+
##contig=<ID=GL000196.1,length=38914,assembly=b37>
|
69
|
+
##contig=<ID=GL000248.1,length=39786,assembly=b37>
|
70
|
+
##contig=<ID=GL000244.1,length=39929,assembly=b37>
|
71
|
+
##contig=<ID=GL000238.1,length=39939,assembly=b37>
|
72
|
+
##contig=<ID=GL000202.1,length=40103,assembly=b37>
|
73
|
+
##contig=<ID=GL000234.1,length=40531,assembly=b37>
|
74
|
+
##contig=<ID=GL000232.1,length=40652,assembly=b37>
|
75
|
+
##contig=<ID=GL000206.1,length=41001,assembly=b37>
|
76
|
+
##contig=<ID=GL000240.1,length=41933,assembly=b37>
|
77
|
+
##contig=<ID=GL000236.1,length=41934,assembly=b37>
|
78
|
+
##contig=<ID=GL000241.1,length=42152,assembly=b37>
|
79
|
+
##contig=<ID=GL000243.1,length=43341,assembly=b37>
|
80
|
+
##contig=<ID=GL000242.1,length=43523,assembly=b37>
|
81
|
+
##contig=<ID=GL000230.1,length=43691,assembly=b37>
|
82
|
+
##contig=<ID=GL000237.1,length=45867,assembly=b37>
|
83
|
+
##contig=<ID=GL000233.1,length=45941,assembly=b37>
|
84
|
+
##contig=<ID=GL000204.1,length=81310,assembly=b37>
|
85
|
+
##contig=<ID=GL000198.1,length=90085,assembly=b37>
|
86
|
+
##contig=<ID=GL000208.1,length=92689,assembly=b37>
|
87
|
+
##contig=<ID=GL000191.1,length=106433,assembly=b37>
|
88
|
+
##contig=<ID=GL000227.1,length=128374,assembly=b37>
|
89
|
+
##contig=<ID=GL000228.1,length=129120,assembly=b37>
|
90
|
+
##contig=<ID=GL000214.1,length=137718,assembly=b37>
|
91
|
+
##contig=<ID=GL000221.1,length=155397,assembly=b37>
|
92
|
+
##contig=<ID=GL000209.1,length=159169,assembly=b37>
|
93
|
+
##contig=<ID=GL000218.1,length=161147,assembly=b37>
|
94
|
+
##contig=<ID=GL000220.1,length=161802,assembly=b37>
|
95
|
+
##contig=<ID=GL000213.1,length=164239,assembly=b37>
|
96
|
+
##contig=<ID=GL000211.1,length=166566,assembly=b37>
|
97
|
+
##contig=<ID=GL000199.1,length=169874,assembly=b37>
|
98
|
+
##contig=<ID=GL000217.1,length=172149,assembly=b37>
|
99
|
+
##contig=<ID=GL000216.1,length=172294,assembly=b37>
|
100
|
+
##contig=<ID=GL000215.1,length=172545,assembly=b37>
|
101
|
+
##contig=<ID=GL000205.1,length=174588,assembly=b37>
|
102
|
+
##contig=<ID=GL000219.1,length=179198,assembly=b37>
|
103
|
+
##contig=<ID=GL000224.1,length=179693,assembly=b37>
|
104
|
+
##contig=<ID=GL000223.1,length=180455,assembly=b37>
|
105
|
+
##contig=<ID=GL000195.1,length=182896,assembly=b37>
|
106
|
+
##contig=<ID=GL000212.1,length=186858,assembly=b37>
|
107
|
+
##contig=<ID=GL000222.1,length=186861,assembly=b37>
|
108
|
+
##contig=<ID=GL000200.1,length=187035,assembly=b37>
|
109
|
+
##contig=<ID=GL000193.1,length=189789,assembly=b37>
|
110
|
+
##contig=<ID=GL000194.1,length=191469,assembly=b37>
|
111
|
+
##contig=<ID=GL000225.1,length=211173,assembly=b37>
|
112
|
+
##contig=<ID=GL000192.1,length=547496,assembly=b37>
|
113
|
+
##reference=file:human_g1k_v37.fasta
|
114
|
+
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Original s1t1 s2t1 s3t1 s1t2 s2t2 s3t2
|
115
|
+
1 10257 . A C 77.69 . AC=1;AF=0.071;AN=14;BaseQRankSum=-0.066;DP=1518;Dels=0.00;FS=24.214;HaplotypeScore=226.5209;MLEAC=1;MLEAF=0.071;MQ=25.00;MQ0=329;MQRankSum=-1.744;QD=0.37;ReadPosRankSum=1.551 GT:AD:DP:GQ:PL 0/0:151,8:159:99:0,195,2282 0/0:219,22:242:99:0,197,2445 0/0:227,22:249:90:0,90,2339 0/0:226,22:249:99:0,159,2695 0/0:166,18:186:99:0,182,1989 0/1:185,27:212:99:111,0,2387 0/0:201,15:218:24:0,24,1972
|
116
|
+
1 10291 . C T 1031.89 . AC=7;AF=0.500;AN=14;BaseQRankSum=4.367;DP=1433;Dels=0.00;FS=0.696;HaplotypeScore=101.0885;MLEAC=7;MLEAF=0.500;MQ=26.96;MQ0=225;MQRankSum=0.087;QD=0.72;ReadPosRankSum=-1.640 GT:AD:DP:GQ:PL 0/1:145,16:165:23:23,0,491 0/1:218,26:249:29:29,0,611 0/1:214,30:249:99:145,0,801 0/1:213,32:247:20:20,0,1031 0/1:122,36:161:99:347,0,182 0/1:131,27:163:99:255,0,508 0/1:156,31:189:99:252,0,372
|
117
|
+
1 10297 . C T 187.21 . AC=5;AF=0.357;AN=14;BaseQRankSum=-2.778;DP=1440;Dels=0.00;FS=0.000;HaplotypeScore=123.6373;MLEAC=5;MLEAF=0.357;MQ=27.26;MQ0=217;MQRankSum=-2.914;QD=0.18;ReadPosRankSum=1.927 GT:AD:DP:GQ:PL 0/1:155,18:182:44:44,0,654 0/1:218,23:246:21:21,0,673 0/1:219,26:250:41:41,0,898 0/0:207,30:246:39:0,39,963 0/0:137,20:165:21:0,21,363 0/1:124,27:158:65:65,0,435 0/1:151,27:183:63:63,0,485
|
118
|
+
1 10303 . C T 166.50 . AC=3;AF=0.214;AN=14;BaseQRankSum=-3.960;DP=1460;Dels=0.00;FS=2.121;HaplotypeScore=138.0883;MLEAC=2;MLEAF=0.143;MQ=27.29;MQ0=220;MQRankSum=-2.873;QD=0.27;ReadPosRankSum=1.756 GT:AD:DP:GQ:PL 0/1:169,25:198:99:195,0,609 0/1:211,31:247:1:1,0,656 0/0:214,28:248:7:0,7,982 0/0:214,32:248:25:0,25,980 0/0:146,17:172:2:0,2,353 0/1:123,23:157:17:17,0,541 0/0:156,22:182:19:0,19,413
|
119
|
+
1 10315 . C T 108.20 . AC=3;AF=0.214;AN=14;BaseQRankSum=-3.769;DP=1500;Dels=0.01;FS=1.493;HaplotypeScore=169.3933;MLEAC=3;MLEAF=0.214;MQ=26.95;MQ0=241;MQRankSum=-4.511;QD=0.19;ReadPosRankSum=2.373 GT:AD:DP:GQ:PL 0/1:181,26:212:41:41,0,618 0/0:223,17:246:99:0,102,832 0/0:219,20:242:66:0,66,924 0/0:217,23:245:99:0,109,1384 0/1:155,27:190:97:97,0,328 0/1:130,20:157:10:10,0,531 0/0:163,24:189:5:0,5,450
|
120
|
+
1 10321 . C T 106.30 . AC=5;AF=0.357;AN=14;BaseQRankSum=3.045;DP=1537;Dels=0.01;FS=5.835;HaplotypeScore=220.1531;MLEAC=5;MLEAF=0.357;MQ=26.69;MQ0=258;MQRankSum=-4.870;QD=0.10;ReadPosRankSum=0.815 GT:AD:DP:GQ:PL 0/1:189,25:218:30:30,0,810 0/0:219,22:246:24:0,24,593 0/1:218,27:248:34:34,0,1134 0/0:220,22:248:56:0,56,1207 0/1:168,23:193:19:19,0,493 0/1:139,22:164:46:46,0,689 0/1:167,26:196:20:20,0,522
|
121
|
+
1 10327 . T C 1215.15 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.585;DP=1641;Dels=0.02;FS=6.639;HaplotypeScore=237.4339;MLEAC=7;MLEAF=0.500;MQ=25.22;MQ0=321;MQRankSum=4.402;QD=0.74;ReadPosRankSum=3.957 GT:AD:DP:GQ:PL 0/1:178,56:237:99:178,0,848 0/1:178,60:238:99:320,0,575 0/1:185,40:229:99:236,0,679 0/1:184,52:237:99:358,0,544 0/1:165,43:209:57:57,0,726 0/1:151,31:183:9:9,0,780 0/1:164,46:210:96:96,0,550
|
122
|
+
1 12783 . G A 4330.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=12.671;DP=939;Dels=0.00;FS=0.000;HaplotypeScore=1.4998;MLEAC=7;MLEAF=0.500;MQ=14.64;MQ0=602;MQRankSum=-3.992;QD=4.61;ReadPosRankSum=0.195 GT:AD:DP:GQ:PL 0/1:24,34:58:82:174,0,82 0/1:80,84:164:99:658,0,433 0/1:59,85:144:99:670,0,407 0/1:68,114:182:99:1074,0,463 0/1:58,68:126:99:437,0,310 0/1:37,66:103:99:446,0,369 0/1:62,96:158:99:911,0,417
|
123
|
+
1 13116 . T G 2592.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-5.563;DP=721;Dels=0.00;FS=381.256;HaplotypeScore=2.5606;MLEAC=7;MLEAF=0.500;MQ=23.97;MQ0=222;MQRankSum=-14.896;QD=3.60;ReadPosRankSum=3.079 GT:AD:DP:GQ:PL 0/1:20,12:32:92:92,0,300 0/1:84,47:131:99:479,0,1548 0/1:65,37:102:99:441,0,1153 0/1:94,57:152:99:584,0,1993 0/1:61,43:104:99:360,0,1199 0/1:54,33:88:99:221,0,986 0/1:62,47:109:99:455,0,1128
|
124
|
+
1 13118 . A G 2317.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-9.647;DP=703;Dels=0.00;FS=362.380;HaplotypeScore=2.3393;MLEAC=7;MLEAF=0.500;MQ=23.54;MQ0=228;MQRankSum=-14.592;QD=3.30;ReadPosRankSum=3.437 GT:AD:DP:GQ:PL 0/1:21,13:34:95:95,0,277 0/1:82,47:129:99:444,0,1445 0/1:65,36:101:99:412,0,1179 0/1:92,53:145:99:455,0,1989 0/1:58,40:99:99:312,0,1216 0/1:52,33:85:99:186,0,1000 0/1:61,47:108:99:453,0,1079
|
125
|
+
1 13178 . G A 72.69 . AC=2;AF=0.143;AN=14;BaseQRankSum=-2.194;DP=929;Dels=0.00;FS=8.154;HaplotypeScore=1.8585;MLEAC=2;MLEAF=0.143;MQ=13.49;MQ0=590;MQRankSum=-3.030;QD=0.38;ReadPosRankSum=-0.383 GT:AD:DP:GQ:PL 0/1:49,3:52:11:11,0,292 0/0:161,11:172:60:0,60,1328 0/1:122,15:137:99:99,0,936 0/0:164,8:172:99:0,112,1436 0/0:120,9:129:62:0,62,771 0/0:113,6:119:12:0,12,885 0/0:138,10:148:99:0,112,1596
|
126
|
+
1 13302 . C T 1067.42 . AC=6;AF=0.429;AN=14;BaseQRankSum=11.584;DP=692;Dels=0.00;FS=86.736;HaplotypeScore=2.8260;MLEAC=6;MLEAF=0.429;MQ=27.08;MQ0=150;MQRankSum=-14.794;QD=1.63;ReadPosRankSum=-9.193 GT:AD:DP:GQ:PL 0/0:26,10:36:41:0,41,616 0/1:91,45:136:99:183,0,2085 0/1:71,28:99:86:86,0,1557 0/1:96,50:146:99:333,0,2098 0/1:55,34:90:99:283,0,1321 0/1:47,18:65:99:157,0,943 0/1:89,28:117:67:67,0,1921
|
127
|
+
1 13757 . G A 271.89 . AC=2;AF=0.143;AN=14;BaseQRankSum=2.916;DP=1149;Dels=0.00;FS=11.172;HaplotypeScore=7.1466;MLEAC=2;MLEAF=0.143;MQ=18.17;MQ0=374;MQRankSum=3.990;QD=0.87;ReadPosRankSum=1.309 GT:AD:DP:GQ:PL 0/0:47,4:53:16:0,16,344 0/0:185,16:201:60:0,60,2690 0/1:157,24:181:99:162,0,2556 0/0:232,18:250:99:0,137,3600 0/0:139,13:152:15:0,15,2266 0/1:114,16:130:99:147,0,1525 0/0:168,14:182:2:0,2,2230
|
128
|
+
1 13868 . A G 1481.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=2.036;DP=1108;Dels=0.00;FS=4.601;HaplotypeScore=6.7136;MLEAC=7;MLEAF=0.500;MQ=13.23;MQ0=622;MQRankSum=1.659;QD=1.34;ReadPosRankSum=0.283 GT:AD:DP:GQ:PL 0/1:60,15:75:80:80,0,568 0/1:146,46:192:99:289,0,1030 0/1:146,36:182:99:203,0,1001 0/1:172,52:224:99:222,0,1150 0/1:106,36:142:99:181,0,621 0/1:79,32:111:99:126,0,467 0/1:129,38:167:99:420,0,767
|
129
|
+
1 13896 . C A 389.42 . AC=6;AF=0.429;AN=14;BaseQRankSum=-0.743;DP=830;Dels=0.00;FS=0.000;HaplotypeScore=1.6931;MLEAC=6;MLEAF=0.429;MQ=11.88;MQ0=518;MQRankSum=-1.292;QD=0.54;ReadPosRankSum=0.433 GT:AD:DP:GQ:PL 0/1:50,12:62:99:107,0,367 0/1:107,28:135:40:40,0,660 0/1:120,23:143:37:37,0,675 0/1:144,31:175:99:172,0,690 0/0:98,14:112:42:0,42,577 0/1:65,16:81:34:34,0,290 0/1:102,19:121:41:41,0,677
|
130
|
+
1 14464 . A T 3945.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=0.104;DP=809;Dels=0.00;FS=38.588;HaplotypeScore=5.8354;MLEAC=7;MLEAF=0.500;MQ=23.21;MQ0=241;MQRankSum=6.859;QD=4.88;ReadPosRankSum=-0.294 GT:AD:DP:GQ:PL 0/1:41,10:51:99:183,0,569 0/1:107,48:155:99:829,0,1388 0/1:99,42:141:99:691,0,1103 0/1:114,36:150:99:454,0,1544 0/1:48,35:83:99:781,0,561 0/1:64,25:89:99:409,0,781 0/1:102,38:140:99:638,0,1310
|
131
|
+
1 14673 . G C 1012.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.674;DP=754;Dels=0.00;FS=115.496;HaplotypeScore=14.9167;MLEAC=7;MLEAF=0.500;MQ=23.97;MQ0=268;MQRankSum=-1.459;QD=1.34;ReadPosRankSum=-3.039 GT:AD:DP:GQ:PL 0/1:28,8:36:34:34,0,409 0/1:117,25:142:99:125,0,1964 0/1:87,30:117:99:214,0,1506 0/1:130,27:157:99:193,0,2076 0/1:77,18:95:99:114,0,1273 0/1:49,27:76:99:200,0,719 0/1:103,28:131:99:172,0,1620
|
132
|
+
1 14699 . C G 64.65 . AC=2;AF=0.143;AN=14;BaseQRankSum=6.064;DP=719;Dels=0.00;FS=29.480;HaplotypeScore=5.5900;MLEAC=2;MLEAF=0.143;MQ=24.79;MQ0=233;MQRankSum=-8.066;QD=0.27;ReadPosRankSum=-0.696 GT:AD:DP:GQ:PL 0/0:35,6:43:51:0,51,720 0/1:91,37:128:59:59,0,1859 0/0:80,29:109:99:0,101,1700 0/0:113,34:147:14:0,14,1987 0/0:72,26:98:37:0,37,1319 0/0:53,25:78:78:0,78,1035 0/1:84,30:114:44:44,0,1326
|
133
|
+
1 14907 . A G 9688.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.299;DP=1083;Dels=0.00;FS=20.983;HaplotypeScore=11.4413;MLEAC=7;MLEAF=0.500;MQ=33.27;MQ0=51;MQRankSum=1.076;QD=8.95;ReadPosRankSum=0.653 GT:AD:DP:GQ:PL 0/1:27,30:57:99:603,0,550 0/1:117,99:216:99:2024,0,2888 0/1:91,71:162:99:1489,0,1990 0/1:119,86:205:99:1876,0,2588 0/1:100,53:153:99:1001,0,2297 0/1:59,59:118:99:1240,0,1241 0/1:91,67:158:99:1495,0,2003
|
134
|
+
1 14930 . A G 8665.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-13.760;DP=1092;Dels=0.00;FS=17.240;HaplotypeScore=20.0469;MLEAC=7;MLEAF=0.500;MQ=34.72;MQ0=22;MQRankSum=1.127;QD=7.94;ReadPosRankSum=0.785 GT:AD:DP:GQ:PL 0/1:32,36:68:99:609,0,659 0/1:123,92:216:99:1636,0,3225 0/1:92,78:170:99:1449,0,2202 0/1:123,86:210:99:1748,0,3028 0/1:85,50:136:99:802,0,2117 0/1:62,63:125:99:1072,0,1437 0/1:92,71:164:99:1389,0,2055
|
135
|
+
1 14933 . G A 248.54 . AC=3;AF=0.214;AN=14;BaseQRankSum=1.588;DP=1089;Dels=0.00;FS=14.333;HaplotypeScore=19.7793;MLEAC=3;MLEAF=0.214;MQ=34.91;MQ0=18;MQRankSum=1.439;QD=0.45;ReadPosRankSum=0.752 GT:AD:DP:GQ:PL 0/0:59,9:68:1:0,1,1361 0/1:192,24:216:99:125,0,4941 0/0:160,9:169:99:0,142,4118 0/1:191,21:212:39:39,0,4848 0/0:126,6:132:99:0,210,3367 0/1:113,15:128:99:124,0,2578 0/0:154,10:164:99:0,158,3934
|
136
|
+
1 14948 . G A 570.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=9.167;DP=1050;Dels=0.00;FS=11.131;HaplotypeScore=6.4398;MLEAC=7;MLEAF=0.500;MQ=32.69;MQ0=53;MQRankSum=0.017;QD=0.54;ReadPosRankSum=-1.181 GT:AD:DP:GQ:PL 0/1:56,7:63:79:79,0,1134 0/1:168,24:192:70:70,0,3900 0/1:160,21:181:99:147,0,3515 0/1:188,23:211:57:57,0,4113 0/1:115,14:129:32:32,0,2406 0/1:103,18:121:99:173,0,2016 0/1:132,21:153:52:52,0,2861
|
137
|
+
1 14976 . G A 195.07 . AC=3;AF=0.214;AN=14;BaseQRankSum=7.340;DP=939;Dels=0.00;FS=32.492;HaplotypeScore=4.6786;MLEAC=3;MLEAF=0.214;MQ=27.87;MQ0=167;MQRankSum=1.477;QD=0.53;ReadPosRankSum=-0.560 GT:AD:DP:GQ:PL 0/1:50,6:56:12:12,0,929 0/0:152,14:166:81:0,81,3159 0/0:152,9:161:99:0,113,2885 0/1:174,22:196:99:127,0,3211 0/0:100,9:109:97:0,97,1900 0/1:103,13:116:97:97,0,1548 0/0:122,13:135:55:0,55,2246
|
138
|
+
1 15118 . A G 2503.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-5.645;DP=1004;Dels=0.00;FS=0.313;HaplotypeScore=4.1078;MLEAC=7;MLEAF=0.500;MQ=21.49;MQ0=207;MQRankSum=-0.007;QD=2.49;ReadPosRankSum=-0.291 GT:AD:DP:GQ:PL 0/1:38,8:46:50:50,0,575 0/1:148,50:198:99:671,0,2598 0/1:97,32:129:99:358,0,1911 0/1:176,53:230:99:700,0,2989 0/1:91,19:113:99:146,0,1741 0/1:92,31:126:99:347,0,1543 0/1:126,30:158:99:271,0,2193
|
139
|
+
1 15190 . G A 2564.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=11.094;DP=1090;Dels=0.00;FS=0.297;HaplotypeScore=4.3151;MLEAC=7;MLEAF=0.500;MQ=26.11;MQ0=187;MQRankSum=-0.724;QD=2.35;ReadPosRankSum=0.530 GT:AD:DP:GQ:PL 0/1:42,11:53:99:177,0,696 0/1:157,51:208:99:839,0,3145 0/1:142,28:170:91:91,0,2919 0/1:160,40:200:99:499,0,2815 0/1:109,17:126:99:167,0,2363 0/1:111,34:145:99:554,0,2268 0/1:141,38:179:99:277,0,2827
|
140
|
+
1 15211 . T G 14032.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-11.292;DP=992;Dels=0.00;FS=0.281;HaplotypeScore=11.0809;MLEAC=7;MLEAF=0.500;MQ=27.20;MQ0=159;MQRankSum=3.859;QD=14.15;ReadPosRankSum=-1.972 GT:AD:DP:GQ:PL 0/1:19,35:54:99:858,0,183 0/1:63,120:183:99:2771,0,960 0/1:50,111:161:99:2213,0,740 0/1:58,113:171:99:2326,0,685 0/1:39,81:120:99:1707,0,678 0/1:38,96:134:99:2126,0,499 0/1:61,107:168:99:2071,0,895
|
141
|
+
1 15274 . A G,T 8909.81 . AC=7,7;AF=0.500,0.500;AN=14;BaseQRankSum=2.416;DP=636;Dels=0.00;FS=0.000;HaplotypeScore=5.1061;MLEAC=7,7;MLEAF=0.500,0.500;MQ=22.77;MQ0=195;MQRankSum=2.299;QD=14.01;ReadPosRankSum=1.707 GT:AD:DP:GQ:PL 1/2:1,14,22:37:99:717,494,467,224,0,170 1/2:1,45,75:121:99:1922,1334,1265,588,0,441 1/2:0,31,71:102:99:1960,1563,1515,396,0,222 1/2:1,59,77:137:99:2009,1376,1298,633,0,486 1/2:0,18,52:71:62:938,789,771,149,0,62 1/2:0,29,38:67:99:1141,883,853,258,0,162 1/2:0,38,60:98:99:1464,1064,1016,399,0,285
|
142
|
+
1 15447 . A G 109.56 . AC=3;AF=0.214;AN=14;BaseQRankSum=-9.704;DP=1213;Dels=0.00;FS=0.000;HaplotypeScore=16.4636;MLEAC=3;MLEAF=0.214;MQ=19.12;MQ0=346;MQRankSum=-0.997;QD=0.20;ReadPosRankSum=-1.088 GT:AD:DP:GQ:PL 0/0:42,4:46:34:0,34,690 0/0:220,22:242:99:0,99,3639 0/0:167,16:183:42:0,42,2582 0/1:201,25:226:78:78,0,2854 0/1:121,16:137:39:39,0,1877 0/0:160,13:173:99:0,139,2724 0/1:157,18:175:34:34,0,2472
|
143
|
+
1 15688 . C T 54.29 . AC=2;AF=0.143;AN=14;BaseQRankSum=-8.686;DP=904;Dels=0.00;FS=11.971;HaplotypeScore=3.1454;MLEAC=2;MLEAF=0.143;MQ=16.75;MQ0=361;MQRankSum=-0.069;QD=0.16;ReadPosRankSum=0.355 GT:AD:DP:GQ:PL 0/0:34,3:37:15:0,15,335 0/0:166,16:182:61:0,61,2190 0/1:131,16:147:69:69,0,1563 0/1:167,17:184:22:22,0,1894 0/0:88,12:100:15:0,15,1099 0/0:88,13:101:1:0,1,1126 0/0:132,16:148:18:0,18,1706
|
144
|
+
1 16068 . T C 377.22 . AC=4;AF=0.286;AN=14;BaseQRankSum=-7.618;DP=398;Dels=0.00;FS=12.349;HaplotypeScore=1.8069;MLEAC=4;MLEAF=0.286;MQ=26.64;MQ0=64;MQRankSum=-4.589;QD=1.80;ReadPosRankSum=-0.448 GT:AD:DP:GQ:PL 0/1:18,15:33:99:182,0,404 0/0:51,6:57:31:0,31,815 0/1:52,16:68:64:64,0,1101 0/0:68,13:81:99:0,99,1505 0/0:41,8:49:51:0,51,1010 0/1:40,9:49:21:21,0,702 0/1:38,19:58:99:153,0,760
|
145
|
+
1 16103 . T G 2348.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-1.646;DP=526;Dels=0.00;FS=2.577;HaplotypeScore=0.9645;MLEAC=7;MLEAF=0.500;MQ=26.64;MQ0=82;MQRankSum=-2.736;QD=4.47;ReadPosRankSum=-2.044 GT:AD:DP:GQ:PL 0/1:21,29:50:99:504,0,450 0/1:55,24:79:99:209,0,838 0/1:49,37:86:99:456,0,1002 0/1:74,32:106:99:193,0,1519 0/1:41,19:60:99:141,0,740 0/1:38,23:61:99:257,0,548 0/1:38,46:84:99:628,0,641
|
@@ -0,0 +1,36 @@
|
|
1
|
+
1 10257 159 242 249 249 186 212 218
|
2
|
+
1 10291 165 249 249 247 161 163 189
|
3
|
+
1 10297 182 246 250 246 165 158 183
|
4
|
+
1 10303 198 247 248 248 172 157 182
|
5
|
+
1 10315 212 246 242 245 190 157 189
|
6
|
+
1 10321 218 246 248 248 193 164 196
|
7
|
+
1 10327 237 238 229 237 209 183 210
|
8
|
+
1 10583 8 24 21 23 15 19 19
|
9
|
+
1 10665 7 5 2 7
|
10
|
+
1 10694 5 5
|
11
|
+
1 10723 4 5 6
|
12
|
+
1 12783 58 164 144 182 126 103 158
|
13
|
+
1 13116 32 131 102 152 104 88 109
|
14
|
+
1 13118 34 129 101 145 99 85 108
|
15
|
+
1 13178 52 172 137 172 129 119 148
|
16
|
+
1 13302 36 136 99 146 90 65 117
|
17
|
+
1 13757 53 201 181 250 152 130 182
|
18
|
+
1 13868 75 192 182 224 142 111 167
|
19
|
+
1 13896 62 135 143 175 112 81 121
|
20
|
+
1 14354 43 158 115 145 72 119
|
21
|
+
1 14464 51 155 141 150 83 89 140
|
22
|
+
1 14673 36 142 117 157 95 76 131
|
23
|
+
1 14699 43 128 109 147 98 78 114
|
24
|
+
1 14907 57 216 162 205 153 118 158
|
25
|
+
1 14930 68 216 170 210 136 125 164
|
26
|
+
1 14933 68 216 169 212 132 128 164
|
27
|
+
1 14948 63 192 181 211 129 121 153
|
28
|
+
1 14976 56 166 161 196 109 116 135
|
29
|
+
1 15118 46 198 129 230 113 126 158
|
30
|
+
1 15190 53 208 170 200 126 145 179
|
31
|
+
1 15211 54 183 161 171 120 134 168
|
32
|
+
1 15274 37 121 102 137 71 67 98
|
33
|
+
1 15447 46 242 183 226 137 173 175
|
34
|
+
1 15688 37 182 147 184 100 101 148
|
35
|
+
1 16068 33 57 68 81 49 49 58
|
36
|
+
1 16103 50 79 86 106 60 61 84
|
@@ -0,0 +1,145 @@
|
|
1
|
+
##fileformat=VCFv4.1
|
2
|
+
##FILTER=<ID=LowQual,Description="Low quality">
|
3
|
+
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
|
4
|
+
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
|
5
|
+
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
|
6
|
+
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
|
7
|
+
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
|
8
|
+
##GATKCommandLine=<ID=UnifiedGenotyper,Version=2.8-1-g932cd3a,Date="Sat Jan 25 10:33:56 CET 2014",Epoch=1390642436187,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[/data_fedor12/BAM/sander/Liver_clones/BIOPSY17513D/mapping/BIOPSY17513D_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone3/mapping/clone3_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone4/mapping/clone4_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone10/mapping/clone10_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone33/mapping/subclone33_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone46/mapping/subclone46_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone105/mapping/subclone105_dedup_realigned_recalibrated.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[/data_fedor13/sander/variant_calling/Liver_clones/.queue/scatterGather/UnifiedGenotyper_noref-1-sg/temp_001_of_500/scatter.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data_fedor13/common_data/references/H_sapiens/GATK_b37_bundle_reference/basespace/human_g1k_v37.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 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 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false 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 genotype_likelihoods_model=SNP pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 allSitePLs=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false output_mode=EMIT_VARIANTS_ONLY heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name= source=UNBOUND) comp=[] 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 onlyEmitSamples=[] debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
|
9
|
+
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
|
10
|
+
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
|
11
|
+
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
|
12
|
+
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
|
13
|
+
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
|
14
|
+
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
|
15
|
+
##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
|
16
|
+
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
|
17
|
+
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
|
18
|
+
##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">
|
19
|
+
##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">
|
20
|
+
##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">
|
21
|
+
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
|
22
|
+
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
|
23
|
+
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
|
24
|
+
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
|
25
|
+
##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
|
26
|
+
##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
|
27
|
+
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
|
28
|
+
##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
|
29
|
+
##contig=<ID=1,length=249250621,assembly=b37>
|
30
|
+
##contig=<ID=2,length=243199373,assembly=b37>
|
31
|
+
##contig=<ID=3,length=198022430,assembly=b37>
|
32
|
+
##contig=<ID=4,length=191154276,assembly=b37>
|
33
|
+
##contig=<ID=5,length=180915260,assembly=b37>
|
34
|
+
##contig=<ID=6,length=171115067,assembly=b37>
|
35
|
+
##contig=<ID=7,length=159138663,assembly=b37>
|
36
|
+
##contig=<ID=8,length=146364022,assembly=b37>
|
37
|
+
##contig=<ID=9,length=141213431,assembly=b37>
|
38
|
+
##contig=<ID=10,length=135534747,assembly=b37>
|
39
|
+
##contig=<ID=11,length=135006516,assembly=b37>
|
40
|
+
##contig=<ID=12,length=133851895,assembly=b37>
|
41
|
+
##contig=<ID=13,length=115169878,assembly=b37>
|
42
|
+
##contig=<ID=14,length=107349540,assembly=b37>
|
43
|
+
##contig=<ID=15,length=102531392,assembly=b37>
|
44
|
+
##contig=<ID=16,length=90354753,assembly=b37>
|
45
|
+
##contig=<ID=17,length=81195210,assembly=b37>
|
46
|
+
##contig=<ID=18,length=78077248,assembly=b37>
|
47
|
+
##contig=<ID=19,length=59128983,assembly=b37>
|
48
|
+
##contig=<ID=20,length=63025520,assembly=b37>
|
49
|
+
##contig=<ID=21,length=48129895,assembly=b37>
|
50
|
+
##contig=<ID=22,length=51304566,assembly=b37>
|
51
|
+
##contig=<ID=X,length=155270560,assembly=b37>
|
52
|
+
##contig=<ID=Y,length=59373566,assembly=b37>
|
53
|
+
##contig=<ID=MT,length=16569,assembly=b37>
|
54
|
+
##contig=<ID=GL000207.1,length=4262,assembly=b37>
|
55
|
+
##contig=<ID=GL000226.1,length=15008,assembly=b37>
|
56
|
+
##contig=<ID=GL000229.1,length=19913,assembly=b37>
|
57
|
+
##contig=<ID=GL000231.1,length=27386,assembly=b37>
|
58
|
+
##contig=<ID=GL000210.1,length=27682,assembly=b37>
|
59
|
+
##contig=<ID=GL000239.1,length=33824,assembly=b37>
|
60
|
+
##contig=<ID=GL000235.1,length=34474,assembly=b37>
|
61
|
+
##contig=<ID=GL000201.1,length=36148,assembly=b37>
|
62
|
+
##contig=<ID=GL000247.1,length=36422,assembly=b37>
|
63
|
+
##contig=<ID=GL000245.1,length=36651,assembly=b37>
|
64
|
+
##contig=<ID=GL000197.1,length=37175,assembly=b37>
|
65
|
+
##contig=<ID=GL000203.1,length=37498,assembly=b37>
|
66
|
+
##contig=<ID=GL000246.1,length=38154,assembly=b37>
|
67
|
+
##contig=<ID=GL000249.1,length=38502,assembly=b37>
|
68
|
+
##contig=<ID=GL000196.1,length=38914,assembly=b37>
|
69
|
+
##contig=<ID=GL000248.1,length=39786,assembly=b37>
|
70
|
+
##contig=<ID=GL000244.1,length=39929,assembly=b37>
|
71
|
+
##contig=<ID=GL000238.1,length=39939,assembly=b37>
|
72
|
+
##contig=<ID=GL000202.1,length=40103,assembly=b37>
|
73
|
+
##contig=<ID=GL000234.1,length=40531,assembly=b37>
|
74
|
+
##contig=<ID=GL000232.1,length=40652,assembly=b37>
|
75
|
+
##contig=<ID=GL000206.1,length=41001,assembly=b37>
|
76
|
+
##contig=<ID=GL000240.1,length=41933,assembly=b37>
|
77
|
+
##contig=<ID=GL000236.1,length=41934,assembly=b37>
|
78
|
+
##contig=<ID=GL000241.1,length=42152,assembly=b37>
|
79
|
+
##contig=<ID=GL000243.1,length=43341,assembly=b37>
|
80
|
+
##contig=<ID=GL000242.1,length=43523,assembly=b37>
|
81
|
+
##contig=<ID=GL000230.1,length=43691,assembly=b37>
|
82
|
+
##contig=<ID=GL000237.1,length=45867,assembly=b37>
|
83
|
+
##contig=<ID=GL000233.1,length=45941,assembly=b37>
|
84
|
+
##contig=<ID=GL000204.1,length=81310,assembly=b37>
|
85
|
+
##contig=<ID=GL000198.1,length=90085,assembly=b37>
|
86
|
+
##contig=<ID=GL000208.1,length=92689,assembly=b37>
|
87
|
+
##contig=<ID=GL000191.1,length=106433,assembly=b37>
|
88
|
+
##contig=<ID=GL000227.1,length=128374,assembly=b37>
|
89
|
+
##contig=<ID=GL000228.1,length=129120,assembly=b37>
|
90
|
+
##contig=<ID=GL000214.1,length=137718,assembly=b37>
|
91
|
+
##contig=<ID=GL000221.1,length=155397,assembly=b37>
|
92
|
+
##contig=<ID=GL000209.1,length=159169,assembly=b37>
|
93
|
+
##contig=<ID=GL000218.1,length=161147,assembly=b37>
|
94
|
+
##contig=<ID=GL000220.1,length=161802,assembly=b37>
|
95
|
+
##contig=<ID=GL000213.1,length=164239,assembly=b37>
|
96
|
+
##contig=<ID=GL000211.1,length=166566,assembly=b37>
|
97
|
+
##contig=<ID=GL000199.1,length=169874,assembly=b37>
|
98
|
+
##contig=<ID=GL000217.1,length=172149,assembly=b37>
|
99
|
+
##contig=<ID=GL000216.1,length=172294,assembly=b37>
|
100
|
+
##contig=<ID=GL000215.1,length=172545,assembly=b37>
|
101
|
+
##contig=<ID=GL000205.1,length=174588,assembly=b37>
|
102
|
+
##contig=<ID=GL000219.1,length=179198,assembly=b37>
|
103
|
+
##contig=<ID=GL000224.1,length=179693,assembly=b37>
|
104
|
+
##contig=<ID=GL000223.1,length=180455,assembly=b37>
|
105
|
+
##contig=<ID=GL000195.1,length=182896,assembly=b37>
|
106
|
+
##contig=<ID=GL000212.1,length=186858,assembly=b37>
|
107
|
+
##contig=<ID=GL000222.1,length=186861,assembly=b37>
|
108
|
+
##contig=<ID=GL000200.1,length=187035,assembly=b37>
|
109
|
+
##contig=<ID=GL000193.1,length=189789,assembly=b37>
|
110
|
+
##contig=<ID=GL000194.1,length=191469,assembly=b37>
|
111
|
+
##contig=<ID=GL000225.1,length=211173,assembly=b37>
|
112
|
+
##contig=<ID=GL000192.1,length=547496,assembly=b37>
|
113
|
+
##reference=file:human_g1k_v37.fasta
|
114
|
+
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Original s1t1 s2t1 s3t1 s1t2 s2t2 s3t2
|
115
|
+
1 10257 . A C 77.69 . AC=1;AF=0.071;AN=14;BaseQRankSum=-0.066;DP=1518;Dels=0.00;FS=24.214;HaplotypeScore=226.5209;MLEAC=1;MLEAF=0.071;MQ=25.00;MQ0=329;MQRankSum=-1.744;QD=0.37;ReadPosRankSum=1.551 GT:AD:DP:GQ:PL 0/0:151,8:159:99:0,195,2282 0/0:219,22:242:99:0,197,2445 0/0:227,22:249:90:0,90,2339 0/0:226,22:249:99:0,159,2695 0/0:166,18:186:99:0,182,1989 0/1:185,27:212:99:111,0,2387 0/0:201,15:218:24:0,24,1972
|
116
|
+
1 10291 . C T 1031.89 . AC=7;AF=0.500;AN=14;BaseQRankSum=4.367;DP=1433;Dels=0.00;FS=0.696;HaplotypeScore=101.0885;MLEAC=7;MLEAF=0.500;MQ=26.96;MQ0=225;MQRankSum=0.087;QD=0.72;ReadPosRankSum=-1.640 GT:AD:DP:GQ:PL 0/1:145,16:165:23:23,0,491 0/1:218,26:249:29:29,0,611 0/1:214,30:249:99:145,0,801 0/1:213,32:247:20:20,0,1031 0/1:122,36:161:99:347,0,182 0/1:131,27:163:99:255,0,508 0/1:156,31:189:99:252,0,372
|
117
|
+
1 10297 . C T 187.21 . AC=5;AF=0.357;AN=14;BaseQRankSum=-2.778;DP=1440;Dels=0.00;FS=0.000;HaplotypeScore=123.6373;MLEAC=5;MLEAF=0.357;MQ=27.26;MQ0=217;MQRankSum=-2.914;QD=0.18;ReadPosRankSum=1.927 GT:AD:DP:GQ:PL 0/1:155,18:182:44:44,0,654 0/1:218,23:246:21:21,0,673 0/1:219,26:250:41:41,0,898 0/0:207,30:246:39:0,39,963 0/0:137,20:165:21:0,21,363 0/1:124,27:158:65:65,0,435 0/1:151,27:183:63:63,0,485
|
118
|
+
1 10303 . C T 166.50 . AC=3;AF=0.214;AN=14;BaseQRankSum=-3.960;DP=1460;Dels=0.00;FS=2.121;HaplotypeScore=138.0883;MLEAC=2;MLEAF=0.143;MQ=27.29;MQ0=220;MQRankSum=-2.873;QD=0.27;ReadPosRankSum=1.756 GT:AD:DP:GQ:PL 0/1:169,25:198:99:195,0,609 0/1:211,31:247:1:1,0,656 0/0:214,28:248:7:0,7,982 0/0:214,32:248:25:0,25,980 0/0:146,17:172:2:0,2,353 0/1:123,23:157:17:17,0,541 0/0:156,22:182:19:0,19,413
|
119
|
+
1 10315 . C T 108.20 . AC=3;AF=0.214;AN=14;BaseQRankSum=-3.769;DP=1500;Dels=0.01;FS=1.493;HaplotypeScore=169.3933;MLEAC=3;MLEAF=0.214;MQ=26.95;MQ0=241;MQRankSum=-4.511;QD=0.19;ReadPosRankSum=2.373 GT:AD:DP:GQ:PL 0/1:181,26:212:41:41,0,618 0/0:223,17:246:99:0,102,832 0/0:219,20:242:66:0,66,924 0/0:217,23:245:99:0,109,1384 0/1:155,27:190:97:97,0,328 0/1:130,20:157:10:10,0,531 0/0:163,24:189:5:0,5,450
|
120
|
+
1 10321 . C T 106.30 . AC=5;AF=0.357;AN=14;BaseQRankSum=3.045;DP=1537;Dels=0.01;FS=5.835;HaplotypeScore=220.1531;MLEAC=5;MLEAF=0.357;MQ=26.69;MQ0=258;MQRankSum=-4.870;QD=0.10;ReadPosRankSum=0.815 GT:AD:DP:GQ:PL 0/1:189,25:218:30:30,0,810 0/0:219,22:246:24:0,24,593 0/1:218,27:248:34:34,0,1134 0/0:220,22:248:56:0,56,1207 0/1:168,23:193:19:19,0,493 0/1:139,22:164:46:46,0,689 0/1:167,26:196:20:20,0,522
|
121
|
+
1 10327 . T C 1215.15 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.585;DP=1641;Dels=0.02;FS=6.639;HaplotypeScore=237.4339;MLEAC=7;MLEAF=0.500;MQ=25.22;MQ0=321;MQRankSum=4.402;QD=0.74;ReadPosRankSum=3.957 GT:AD:DP:GQ:PL 0/1:178,56:237:99:178,0,848 0/1:178,60:238:99:320,0,575 0/1:185,40:229:99:236,0,679 0/1:184,52:237:99:358,0,544 0/1:165,43:209:57:57,0,726 0/1:151,31:183:9:9,0,780 0/1:164,46:210:96:96,0,550
|
122
|
+
1 12783 . G A 4330.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=12.671;DP=939;Dels=0.00;FS=0.000;HaplotypeScore=1.4998;MLEAC=7;MLEAF=0.500;MQ=14.64;MQ0=602;MQRankSum=-3.992;QD=4.61;ReadPosRankSum=0.195 GT:AD:DP:GQ:PL 0/1:24,34:58:82:174,0,82 0/1:80,84:164:99:658,0,433 0/1:59,85:144:99:670,0,407 0/1:68,114:182:99:1074,0,463 0/1:58,68:126:99:437,0,310 0/1:37,66:103:99:446,0,369 0/1:62,96:158:99:911,0,417
|
123
|
+
1 13116 . T G 2592.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-5.563;DP=721;Dels=0.00;FS=381.256;HaplotypeScore=2.5606;MLEAC=7;MLEAF=0.500;MQ=23.97;MQ0=222;MQRankSum=-14.896;QD=3.60;ReadPosRankSum=3.079 GT:AD:DP:GQ:PL 0/1:20,12:32:92:92,0,300 0/1:84,47:131:99:479,0,1548 0/1:65,37:102:99:441,0,1153 0/1:94,57:152:99:584,0,1993 0/1:61,43:104:99:360,0,1199 0/1:54,33:88:99:221,0,986 0/1:62,47:109:99:455,0,1128
|
124
|
+
1 13118 . A G 2317.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-9.647;DP=703;Dels=0.00;FS=362.380;HaplotypeScore=2.3393;MLEAC=7;MLEAF=0.500;MQ=23.54;MQ0=228;MQRankSum=-14.592;QD=3.30;ReadPosRankSum=3.437 GT:AD:DP:GQ:PL 0/1:21,13:34:95:95,0,277 0/1:82,47:129:99:444,0,1445 0/1:65,36:101:99:412,0,1179 0/1:92,53:145:99:455,0,1989 0/1:58,40:99:99:312,0,1216 0/1:52,33:85:99:186,0,1000 0/1:61,47:108:99:453,0,1079
|
125
|
+
1 13178 . G A 72.69 . AC=2;AF=0.143;AN=14;BaseQRankSum=-2.194;DP=929;Dels=0.00;FS=8.154;HaplotypeScore=1.8585;MLEAC=2;MLEAF=0.143;MQ=13.49;MQ0=590;MQRankSum=-3.030;QD=0.38;ReadPosRankSum=-0.383 GT:AD:DP:GQ:PL 0/1:49,3:52:11:11,0,292 0/0:161,11:172:60:0,60,1328 0/1:122,15:137:99:99,0,936 0/0:164,8:172:99:0,112,1436 0/0:120,9:129:62:0,62,771 0/0:113,6:119:12:0,12,885 0/0:138,10:148:99:0,112,1596
|
126
|
+
1 13302 . C T 1067.42 . AC=6;AF=0.429;AN=14;BaseQRankSum=11.584;DP=692;Dels=0.00;FS=86.736;HaplotypeScore=2.8260;MLEAC=6;MLEAF=0.429;MQ=27.08;MQ0=150;MQRankSum=-14.794;QD=1.63;ReadPosRankSum=-9.193 GT:AD:DP:GQ:PL 0/0:26,10:36:41:0,41,616 0/1:91,45:136:99:183,0,2085 0/1:71,28:99:86:86,0,1557 0/1:96,50:146:99:333,0,2098 0/1:55,34:90:99:283,0,1321 0/1:47,18:65:99:157,0,943 0/1:89,28:117:67:67,0,1921
|
127
|
+
1 13757 . G A 271.89 . AC=2;AF=0.143;AN=14;BaseQRankSum=2.916;DP=1149;Dels=0.00;FS=11.172;HaplotypeScore=7.1466;MLEAC=2;MLEAF=0.143;MQ=18.17;MQ0=374;MQRankSum=3.990;QD=0.87;ReadPosRankSum=1.309 GT:AD:DP:GQ:PL 0/0:47,4:53:16:0,16,344 0/0:185,16:201:60:0,60,2690 0/1:157,24:181:99:162,0,2556 0/0:232,18:250:99:0,137,3600 0/0:139,13:152:15:0,15,2266 0/1:114,16:130:99:147,0,1525 0/0:168,14:182:2:0,2,2230
|
128
|
+
1 13868 . A G 1481.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=2.036;DP=1108;Dels=0.00;FS=4.601;HaplotypeScore=6.7136;MLEAC=7;MLEAF=0.500;MQ=13.23;MQ0=622;MQRankSum=1.659;QD=1.34;ReadPosRankSum=0.283 GT:AD:DP:GQ:PL 0/1:60,15:75:80:80,0,568 0/1:146,46:192:99:289,0,1030 0/1:146,36:182:99:203,0,1001 0/1:172,52:224:99:222,0,1150 0/1:106,36:142:99:181,0,621 0/1:79,32:111:99:126,0,467 0/1:129,38:167:99:420,0,767
|
129
|
+
1 13896 . C A 389.42 . AC=6;AF=0.429;AN=14;BaseQRankSum=-0.743;DP=830;Dels=0.00;FS=0.000;HaplotypeScore=1.6931;MLEAC=6;MLEAF=0.429;MQ=11.88;MQ0=518;MQRankSum=-1.292;QD=0.54;ReadPosRankSum=0.433 GT:AD:DP:GQ:PL 0/1:50,12:62:99:107,0,367 0/1:107,28:135:40:40,0,660 0/1:120,23:143:37:37,0,675 0/1:144,31:175:99:172,0,690 0/0:98,14:112:42:0,42,577 0/1:65,16:81:34:34,0,290 0/1:102,19:121:41:41,0,677
|
130
|
+
1 14464 . A T 3945.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=0.104;DP=809;Dels=0.00;FS=38.588;HaplotypeScore=5.8354;MLEAC=7;MLEAF=0.500;MQ=23.21;MQ0=241;MQRankSum=6.859;QD=4.88;ReadPosRankSum=-0.294 GT:AD:DP:GQ:PL 0/1:41,10:51:99:183,0,569 0/1:107,48:155:99:829,0,1388 0/1:99,42:141:99:691,0,1103 0/1:114,36:150:99:454,0,1544 0/1:48,35:83:99:781,0,561 0/1:64,25:89:99:409,0,781 0/1:102,38:140:99:638,0,1310
|
131
|
+
1 14673 . G C 1012.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.674;DP=754;Dels=0.00;FS=115.496;HaplotypeScore=14.9167;MLEAC=7;MLEAF=0.500;MQ=23.97;MQ0=268;MQRankSum=-1.459;QD=1.34;ReadPosRankSum=-3.039 GT:AD:DP:GQ:PL 0/1:28,8:36:34:34,0,409 0/1:117,25:142:99:125,0,1964 0/1:87,30:117:99:214,0,1506 0/1:130,27:157:99:193,0,2076 0/1:77,18:95:99:114,0,1273 0/1:49,27:76:99:200,0,719 0/1:103,28:131:99:172,0,1620
|
132
|
+
1 14699 . C G 64.65 . AC=2;AF=0.143;AN=14;BaseQRankSum=6.064;DP=719;Dels=0.00;FS=29.480;HaplotypeScore=5.5900;MLEAC=2;MLEAF=0.143;MQ=24.79;MQ0=233;MQRankSum=-8.066;QD=0.27;ReadPosRankSum=-0.696 GT:AD:DP:GQ:PL 0/0:35,6:43:51:0,51,720 0/1:91,37:128:59:59,0,1859 0/0:80,29:109:99:0,101,1700 0/0:113,34:147:14:0,14,1987 0/0:72,26:98:37:0,37,1319 0/0:53,25:78:78:0,78,1035 0/1:84,30:114:44:44,0,1326
|
133
|
+
1 14907 . A G 9688.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.299;DP=1083;Dels=0.00;FS=20.983;HaplotypeScore=11.4413;MLEAC=7;MLEAF=0.500;MQ=33.27;MQ0=51;MQRankSum=1.076;QD=8.95;ReadPosRankSum=0.653 GT:AD:DP:GQ:PL 0/1:27,30:57:99:603,0,550 0/1:117,99:216:99:2024,0,2888 0/1:91,71:162:99:1489,0,1990 0/1:119,86:205:99:1876,0,2588 0/1:100,53:153:99:1001,0,2297 0/1:59,59:118:99:1240,0,1241 0/1:91,67:158:99:1495,0,2003
|
134
|
+
1 14930 . A G 8665.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-13.760;DP=1092;Dels=0.00;FS=17.240;HaplotypeScore=20.0469;MLEAC=7;MLEAF=0.500;MQ=34.72;MQ0=22;MQRankSum=1.127;QD=7.94;ReadPosRankSum=0.785 GT:AD:DP:GQ:PL 0/1:32,36:68:99:609,0,659 0/1:123,92:216:99:1636,0,3225 0/1:92,78:170:99:1449,0,2202 0/1:123,86:210:99:1748,0,3028 0/1:85,50:136:99:802,0,2117 0/1:62,63:125:99:1072,0,1437 0/1:92,71:164:99:1389,0,2055
|
135
|
+
1 14933 . G A 248.54 . AC=3;AF=0.214;AN=14;BaseQRankSum=1.588;DP=1089;Dels=0.00;FS=14.333;HaplotypeScore=19.7793;MLEAC=3;MLEAF=0.214;MQ=34.91;MQ0=18;MQRankSum=1.439;QD=0.45;ReadPosRankSum=0.752 GT:AD:DP:GQ:PL 0/0:59,9:68:1:0,1,1361 0/1:192,24:216:99:125,0,4941 0/0:160,9:169:99:0,142,4118 0/1:191,21:212:39:39,0,4848 0/0:126,6:132:99:0,210,3367 0/1:113,15:128:99:124,0,2578 0/0:154,10:164:99:0,158,3934
|
136
|
+
1 14948 . G A 570.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=9.167;DP=1050;Dels=0.00;FS=11.131;HaplotypeScore=6.4398;MLEAC=7;MLEAF=0.500;MQ=32.69;MQ0=53;MQRankSum=0.017;QD=0.54;ReadPosRankSum=-1.181 GT:AD:DP:GQ:PL 0/1:56,7:63:79:79,0,1134 0/1:168,24:192:70:70,0,3900 0/1:160,21:181:99:147,0,3515 0/1:188,23:211:57:57,0,4113 0/1:115,14:129:32:32,0,2406 0/1:103,18:121:99:173,0,2016 0/1:132,21:153:52:52,0,2861
|
137
|
+
1 14976 . G A 195.07 . AC=3;AF=0.214;AN=14;BaseQRankSum=7.340;DP=939;Dels=0.00;FS=32.492;HaplotypeScore=4.6786;MLEAC=3;MLEAF=0.214;MQ=27.87;MQ0=167;MQRankSum=1.477;QD=0.53;ReadPosRankSum=-0.560 GT:AD:DP:GQ:PL 0/1:50,6:56:12:12,0,929 0/0:152,14:166:81:0,81,3159 0/0:152,9:161:99:0,113,2885 0/1:174,22:196:99:127,0,3211 0/0:100,9:109:97:0,97,1900 0/1:103,13:116:97:97,0,1548 0/0:122,13:135:55:0,55,2246
|
138
|
+
1 15118 . A G 2503.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-5.645;DP=1004;Dels=0.00;FS=0.313;HaplotypeScore=4.1078;MLEAC=7;MLEAF=0.500;MQ=21.49;MQ0=207;MQRankSum=-0.007;QD=2.49;ReadPosRankSum=-0.291 GT:AD:DP:GQ:PL 0/1:38,8:46:50:50,0,575 0/1:148,50:198:99:671,0,2598 0/1:97,32:129:99:358,0,1911 0/1:176,53:230:99:700,0,2989 0/1:91,19:113:99:146,0,1741 0/1:92,31:126:99:347,0,1543 0/1:126,30:158:99:271,0,2193
|
139
|
+
1 15190 . G A 2564.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=11.094;DP=1090;Dels=0.00;FS=0.297;HaplotypeScore=4.3151;MLEAC=7;MLEAF=0.500;MQ=26.11;MQ0=187;MQRankSum=-0.724;QD=2.35;ReadPosRankSum=0.530 GT:AD:DP:GQ:PL 0/1:42,11:53:99:177,0,696 0/1:157,51:208:99:839,0,3145 0/1:142,28:170:91:91,0,2919 0/1:160,40:200:99:499,0,2815 0/1:109,17:126:99:167,0,2363 0/1:111,34:145:99:554,0,2268 0/1:141,38:179:99:277,0,2827
|
140
|
+
1 15211 . T G 14032.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-11.292;DP=992;Dels=0.00;FS=0.281;HaplotypeScore=11.0809;MLEAC=7;MLEAF=0.500;MQ=27.20;MQ0=159;MQRankSum=3.859;QD=14.15;ReadPosRankSum=-1.972 GT:AD:DP:GQ:PL 0/1:19,35:54:99:858,0,183 0/1:63,120:183:99:2771,0,960 0/1:50,111:161:99:2213,0,740 0/1:58,113:171:99:2326,0,685 0/1:39,81:120:99:1707,0,678 0/1:38,96:134:99:2126,0,499 0/1:61,107:168:99:2071,0,895
|
141
|
+
1 15274 . A G,T 8909.81 . AC=7,7;AF=0.500,0.500;AN=14;BaseQRankSum=2.416;DP=636;Dels=0.00;FS=0.000;HaplotypeScore=5.1061;MLEAC=7,7;MLEAF=0.500,0.500;MQ=22.77;MQ0=195;MQRankSum=2.299;QD=14.01;ReadPosRankSum=1.707 GT:AD:DP:GQ:PL 1/2:1,14,22:37:99:717,494,467,224,0,170 1/2:1,45,75:121:99:1922,1334,1265,588,0,441 1/2:0,31,71:102:99:1960,1563,1515,396,0,222 1/2:1,59,77:137:99:2009,1376,1298,633,0,486 1/2:0,18,52:71:62:938,789,771,149,0,62 1/2:0,29,38:67:99:1141,883,853,258,0,162 1/2:0,38,60:98:99:1464,1064,1016,399,0,285
|
142
|
+
1 15447 . A G 109.56 . AC=3;AF=0.214;AN=14;BaseQRankSum=-9.704;DP=1213;Dels=0.00;FS=0.000;HaplotypeScore=16.4636;MLEAC=3;MLEAF=0.214;MQ=19.12;MQ0=346;MQRankSum=-0.997;QD=0.20;ReadPosRankSum=-1.088 GT:AD:DP:GQ:PL 0/0:42,4:46:34:0,34,690 0/0:220,22:242:99:0,99,3639 0/0:167,16:183:42:0,42,2582 0/1:201,25:226:78:78,0,2854 0/1:121,16:137:39:39,0,1877 0/0:160,13:173:99:0,139,2724 0/1:157,18:175:34:34,0,2472
|
143
|
+
1 15688 . C T 54.29 . AC=2;AF=0.143;AN=14;BaseQRankSum=-8.686;DP=904;Dels=0.00;FS=11.971;HaplotypeScore=3.1454;MLEAC=2;MLEAF=0.143;MQ=16.75;MQ0=361;MQRankSum=-0.069;QD=0.16;ReadPosRankSum=0.355 GT:AD:DP:GQ:PL 0/0:34,3:37:15:0,15,335 0/0:166,16:182:61:0,61,2190 0/1:131,16:147:69:69,0,1563 0/1:167,17:184:22:22,0,1894 0/0:88,12:100:15:0,15,1099 0/0:88,13:101:1:0,1,1126 0/0:132,16:148:18:0,18,1706
|
144
|
+
1 16068 . T C 377.22 . AC=4;AF=0.286;AN=14;BaseQRankSum=-7.618;DP=398;Dels=0.00;FS=12.349;HaplotypeScore=1.8069;MLEAC=4;MLEAF=0.286;MQ=26.64;MQ0=64;MQRankSum=-4.589;QD=1.80;ReadPosRankSum=-0.448 GT:AD:DP:GQ:PL 0/1:18,15:33:99:182,0,404 0/0:51,6:57:31:0,31,815 0/1:52,16:68:64:64,0,1101 0/0:68,13:81:99:0,99,1505 0/0:41,8:49:51:0,51,1010 0/1:40,9:49:21:21,0,702 0/1:38,19:58:99:153,0,760
|
145
|
+
1 16103 . T G 2348.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-1.646;DP=526;Dels=0.00;FS=2.577;HaplotypeScore=0.9645;MLEAC=7;MLEAF=0.500;MQ=26.64;MQ0=82;MQRankSum=-2.736;QD=4.47;ReadPosRankSum=-2.044 GT:AD:DP:GQ:PL 0/1:21,29:50:99:504,0,450 0/1:55,24:79:99:209,0,838 0/1:49,37:86:99:456,0,1002 0/1:74,32:106:99:193,0,1519 0/1:41,19:60:99:141,0,740 0/1:38,23:61:99:257,0,548 0/1:38,46:84:99:628,0,641
|