bio-vcf 0.0.2 → 0.0.3

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Files changed (29) hide show
  1. checksums.yaml +4 -4
  2. data/Gemfile +1 -0
  3. data/Gemfile.lock +8 -0
  4. data/README.md +376 -11
  5. data/VERSION +1 -1
  6. data/bin/bio-vcf +172 -39
  7. data/bio-vcf.gemspec +18 -3
  8. data/features/cli.feature +32 -0
  9. data/features/multisample.feature +28 -10
  10. data/features/step_definitions/cli-feature.rb +12 -0
  11. data/features/step_definitions/multisample.rb +64 -18
  12. data/features/support/env.rb +5 -0
  13. data/lib/bio-vcf.rb +2 -0
  14. data/lib/bio-vcf/utils.rb +23 -0
  15. data/lib/bio-vcf/vcfgenotypefield.rb +73 -28
  16. data/lib/bio-vcf/vcfheader.rb +8 -0
  17. data/lib/bio-vcf/vcfline.rb +1 -0
  18. data/lib/bio-vcf/vcfrecord.rb +142 -14
  19. data/lib/bio-vcf/vcfsample.rb +88 -0
  20. data/test/data/input/dbsnp.vcf +200 -0
  21. data/test/data/input/multisample.vcf +2 -2
  22. data/test/data/regression/eval_r.info.dp.ref +150 -0
  23. data/test/data/regression/r.info.dp.ref +147 -0
  24. data/test/data/regression/rewrite.info.sample.ref +150 -0
  25. data/test/data/regression/s.dp.ref +145 -0
  26. data/test/data/regression/seval_s.dp.ref +36 -0
  27. data/test/data/regression/sfilter001.ref +145 -0
  28. data/test/performance/metrics.md +98 -0
  29. metadata +28 -2
data/test/data/input/dbsnp.vcf ADDED
@@ -0,0 +1,200 @@
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+ ##fileformat=VCFv4.0
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+ ##fileDate=20140307
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+ ##source=dbSNP
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+ ##dbSNP_BUILD_ID=138
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+ ##reference=GRCh37.p10
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+ ##phasing=partial
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+ ##variationPropertyDocumentationUrl=ftp://ftp.ncbi.nlm.nih.gov/snp/specs/dbSNP_BitField_latest.pdf
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+ ##INFO=<ID=RS,Number=1,Type=Integer,Description="dbSNP ID (i.e. rs number)">
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+ ##INFO=<ID=RSPOS,Number=1,Type=Integer,Description="Chr position reported in dbSNP">
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+ ##INFO=<ID=RV,Number=0,Type=Flag,Description="RS orientation is reversed">
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+ ##INFO=<ID=VP,Number=1,Type=String,Description="Variation Property. Documentation is at ftp://ftp.ncbi.nlm.nih.gov/snp/specs/dbSNP_BitField_latest.pdf">
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+ ##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:) and each pair is delimited by a vertical bar (|)">
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+ ##INFO=<ID=dbSNPBuildID,Number=1,Type=Integer,Description="First dbSNP Build for RS">
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+ ##INFO=<ID=SAO,Number=1,Type=Integer,Description="Variant Allele Origin: 0 - unspecified, 1 - Germline, 2 - Somatic, 3 - Both">
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+ ##INFO=<ID=SSR,Number=1,Type=Integer,Description="Variant Suspect Reason Codes (may be more than one value added together) 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other">
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+ ##INFO=<ID=WGT,Number=1,Type=Integer,Description="Weight, 00 - unmapped, 1 - weight 1, 2 - weight 2, 3 - weight 3 or more">
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+ ##INFO=<ID=VC,Number=1,Type=String,Description="Variation Class">
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+ ##INFO=<ID=PM,Number=0,Type=Flag,Description="Variant is Precious(Clinical,Pubmed Cited)">
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+ ##INFO=<ID=TPA,Number=0,Type=Flag,Description="Provisional Third Party Annotation(TPA) (currently rs from PHARMGKB who will give phenotype data)">
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+ ##INFO=<ID=PMC,Number=0,Type=Flag,Description="Links exist to PubMed Central article">
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+ ##INFO=<ID=S3D,Number=0,Type=Flag,Description="Has 3D structure - SNP3D table">
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+ ##INFO=<ID=SLO,Number=0,Type=Flag,Description="Has SubmitterLinkOut - From SNP->SubSNP->Batch.link_out">
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+ ##INFO=<ID=NSF,Number=0,Type=Flag,Description="Has non-synonymous frameshift A coding region variation where one allele in the set changes all downstream amino acids. FxnClass = 44">
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+ ##INFO=<ID=NSM,Number=0,Type=Flag,Description="Has non-synonymous missense A coding region variation where one allele in the set changes protein peptide. FxnClass = 42">
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+ ##INFO=<ID=NSN,Number=0,Type=Flag,Description="Has non-synonymous nonsense A coding region variation where one allele in the set changes to STOP codon (TER). FxnClass = 41">
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+ ##INFO=<ID=REF,Number=0,Type=Flag,Description="Has reference A coding region variation where one allele in the set is identical to the reference sequence. FxnCode = 8">
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+ ##INFO=<ID=SYN,Number=0,Type=Flag,Description="Has synonymous A coding region variation where one allele in the set does not change the encoded amino acid. FxnCode = 3">
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+ ##INFO=<ID=U3,Number=0,Type=Flag,Description="In 3' UTR Location is in an untranslated region (UTR). FxnCode = 53">
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+ ##INFO=<ID=U5,Number=0,Type=Flag,Description="In 5' UTR Location is in an untranslated region (UTR). FxnCode = 55">
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+ ##INFO=<ID=ASS,Number=0,Type=Flag,Description="In acceptor splice site FxnCode = 73">
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+ ##INFO=<ID=DSS,Number=0,Type=Flag,Description="In donor splice-site FxnCode = 75">
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+ ##INFO=<ID=INT,Number=0,Type=Flag,Description="In Intron FxnCode = 6">
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+ ##INFO=<ID=R3,Number=0,Type=Flag,Description="In 3' gene region FxnCode = 13">
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+ ##INFO=<ID=R5,Number=0,Type=Flag,Description="In 5' gene region FxnCode = 15">
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+ ##INFO=<ID=OTH,Number=0,Type=Flag,Description="Has other variant with exactly the same set of mapped positions on NCBI refernce assembly.">
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+ ##INFO=<ID=CFL,Number=0,Type=Flag,Description="Has Assembly conflict. This is for weight 1 and 2 variant that maps to different chromosomes on different assemblies.">
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+ ##INFO=<ID=ASP,Number=0,Type=Flag,Description="Is Assembly specific. This is set if the variant only maps to one assembly">
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+ ##INFO=<ID=MUT,Number=0,Type=Flag,Description="Is mutation (journal citation, explicit fact): a low frequency variation that is cited in journal and other reputable sources">
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+ ##INFO=<ID=VLD,Number=0,Type=Flag,Description="Is Validated. This bit is set if the variant has 2+ minor allele count based on frequency or genotype data.">
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+ ##INFO=<ID=G5A,Number=0,Type=Flag,Description=">5% minor allele frequency in each and all populations">
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+ ##INFO=<ID=G5,Number=0,Type=Flag,Description=">5% minor allele frequency in 1+ populations">
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+ ##INFO=<ID=HD,Number=0,Type=Flag,Description="Marker is on high density genotyping kit (50K density or greater). The variant may have phenotype associations present in dbGaP.">
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+ ##INFO=<ID=GNO,Number=0,Type=Flag,Description="Genotypes available. The variant has individual genotype (in SubInd table).">
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+ ##INFO=<ID=KGValidated,Number=0,Type=Flag,Description="1000 Genome validated">
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+ ##INFO=<ID=KGPhase1,Number=0,Type=Flag,Description="1000 Genome phase 1 (incl. June Interim phase 1)">
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+ ##INFO=<ID=KGPilot123,Number=0,Type=Flag,Description="1000 Genome discovery all pilots 2010(1,2,3)">
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+ ##INFO=<ID=KGPROD,Number=0,Type=Flag,Description="Has 1000 Genome submission">
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+ ##INFO=<ID=OTHERKG,Number=0,Type=Flag,Description="non-1000 Genome submission">
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+ ##INFO=<ID=PH3,Number=0,Type=Flag,Description="HAP_MAP Phase 3 genotyped: filtered, non-redundant">
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+ ##INFO=<ID=CDA,Number=0,Type=Flag,Description="Variation is interrogated in a clinical diagnostic assay">
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+ ##INFO=<ID=LSD,Number=0,Type=Flag,Description="Submitted from a locus-specific database">
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+ ##INFO=<ID=MTP,Number=0,Type=Flag,Description="Microattribution/third-party annotation(TPA:GWAS,PAGE)">
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+ ##INFO=<ID=OM,Number=0,Type=Flag,Description="Has OMIM/OMIA">
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+ ##INFO=<ID=NOC,Number=0,Type=Flag,Description="Contig allele not present in variant allele list. The reference sequence allele at the mapped position is not present in the variant allele list, adjusted for orientation.">
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+ ##INFO=<ID=WTD,Number=0,Type=Flag,Description="Is Withdrawn by submitter If one member ss is withdrawn by submitter, then this bit is set. If all member ss' are withdrawn, then the rs is deleted to SNPHistory">
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+ ##INFO=<ID=NOV,Number=0,Type=Flag,Description="Rs cluster has non-overlapping allele sets. True when rs set has more than 2 alleles from different submissions and these sets share no alleles in common.">
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+ ##FILTER=<ID=NC,Description="Inconsistent Genotype Submission For At Least One Sample">
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+ ##INFO=<ID=CAF,Number=.,Type=String,Description="An ordered, comma delimited list of allele frequencies based on 1000Genomes, starting with the reference allele followed by alternate alleles as ordered in the ALT column. Where a 1000Genomes alternate allele is not in the dbSNPs alternate allele set, the allele is added to the ALT column. The minor allele is the second largest value in the list, and was previuosly reported in VCF as the GMAF. This is the GMAF reported on the RefSNP and EntrezSNP pages and VariationReporter">
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+ ##INFO=<ID=COMMON,Number=1,Type=Integer,Description="RS is a common SNP. A common SNP is one that has at least one 1000Genomes population with a minor allele of frequency >= 1% and for which 2 or more founders contribute to that minor allele frequency.">
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+ ##INFO=<ID=CLNHGVS,Number=.,Type=String,Description="Variant names from HGVS. The order of these variants corresponds to the order of the info in the other clinical INFO tags.">
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+ ##INFO=<ID=CLNALLE,Number=.,Type=Integer,Description="Variant alleles from REF or ALT columns. 0 is REF, 1 is the first ALT allele, etc. This is used to match alleles with other corresponding clinical (CLN) INFO tags. A value of -1 indicates that no allele was found to match a corresponding HGVS allele name.">
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+ ##INFO=<ID=CLNSRC,Number=.,Type=String,Description="Variant Clinical Chanels">
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+ ##INFO=<ID=CLNORIGIN,Number=.,Type=String,Description="Allele Origin. One or more of the following values may be added: 0 - unknown; 1 - germline; 2 - somatic; 4 - inherited; 8 - paternal; 16 - maternal; 32 - de-novo; 64 - biparental; 128 - uniparental; 256 - not-tested; 512 - tested-inconclusive; 1073741824 - other">
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+ ##INFO=<ID=CLNSRCID,Number=.,Type=String,Description="Variant Clinical Channel IDs">
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+ ##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Variant Clinical Significance, 0 - unknown, 1 - untested, 2 - non-pathogenic, 3 - probable-non-pathogenic, 4 - probable-pathogenic, 5 - pathogenic, 6 - drug-response, 7 - histocompatibility, 255 - other">
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+ ##INFO=<ID=CLNDSDB,Number=.,Type=String,Description="Variant disease database name">
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+ ##INFO=<ID=CLNDSDBID,Number=.,Type=String,Description="Variant disease database ID">
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+ ##INFO=<ID=CLNDBN,Number=.,Type=String,Description="Variant disease name">
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+ ##INFO=<ID=CLNACC,Number=.,Type=String,Description="Variant Accession and Versions">
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+ #CHROM POS ID REF ALT QUAL FILTER INFO
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+ 1 883516 rs267598747 G A . . RS=267598747;RSPOS=883516;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=NOC2L:26155;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.883516G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064926.2
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+ 1 891344 rs267598748 G A . . RS=267598748;RSPOS=891344;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=NOC2L:26155;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.891344G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064927.2
73
+ 1 906168 rs267598759 G A . . RS=267598759;RSPOS=906168;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=PLEKHN1:84069;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.906168G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064940.2
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+ 1 985955 rs199476396 G C . . RS=199476396;RSPOS=985955;dbSNPBuildID=136;SSR=0;SAO=1;VP=0x050260000000000002110100;GENEINFO=AGRN:375790;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.985955G>C;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=103320.0001;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet;CLNDSDBID=NBK1168:C1850792:254300:590;CLNDBN=Myasthenia\x2c_limb-girdle\x2c_familial;CLNACC=RCV000019902.26
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+ 1 1115553 rs267597918 C T . . RS=267597918;RSPOS=1115553;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=TTLL10:254173|TTLL10-AS1:100506376;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.1115553C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064012.2
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+ 1 1119314 rs267597921 C G . . RS=267597921;RSPOS=1119314;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=TTLL10:254173;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.1119314C>G;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064015.2
77
+ 1 1167674 rs397514722 C T . . RS=397514722;RSPOS=1167674;RV;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=B3GALT6:126792|SDF4:51150;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.1167674C>T;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=615291.0010;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=CN178404:615349:75496;CLNDBN=Ehlers-Danlos_syndrome\x2c_progeroid_type\x2c_2;CLNACC=RCV000054399.1
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+ 1 1167851 rs397514719 A G . . RS=397514719;RSPOS=1167851;RV;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=B3GALT6:126792|SDF4:51150;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.1167851A>G;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=615291.0005;CLNSIG=5;CLNDSDB=MedGen:OMIM:SNOMED_CT;CLNDSDBID=C0432243:271640:254100000;CLNDBN=Spondyloepimetaphyseal_dysplasia_with_joint_laxity;CLNACC=RCV000054394.1
79
+ 1 1167858 rs397514720 C T . . RS=397514720;RSPOS=1167858;RV;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=B3GALT6:126792|SDF4:51150;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.1167858C>T;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=615291.0006;CLNSIG=5;CLNDSDB=MedGen:OMIM:SNOMED_CT;CLNDSDBID=C0432243:271640:254100000;CLNDBN=Spondyloepimetaphyseal_dysplasia_with_joint_laxity;CLNACC=RCV000054395.1
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+ 1 1168124 rs397514718 G A . . RS=397514718;RSPOS=1168124;RV;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=B3GALT6:126792|SDF4:51150;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.1168124G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=615291.0003;CLNSIG=5;CLNDSDB=MedGen:OMIM:SNOMED_CT;CLNDSDBID=C0432243:271640:254100000;CLNDBN=Spondyloepimetaphyseal_dysplasia_with_joint_laxity;CLNACC=RCV000054392.1
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+ 1 1168277 rs397514723 G C . . RS=397514723;RSPOS=1168277;RV;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002100100;GENEINFO=B3GALT6:126792|SDF4:51150;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.1168277G>C;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=615291.0012;CLNSIG=5;CLNDSDB=.;CLNDSDBID=.;CLNDBN=SPONDYLOEPIMETAPHYSEAL_DYSPLASIA_WITH_JOINT_LAXITY\x2c_TYPE_1\x2c_WITH_FRACTURES;CLNACC=RCV000054401.2
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+ 1 1168307 rs397514724 G A . . RS=397514724;RSPOS=1168307;RV;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002100100;GENEINFO=B3GALT6:126792|SDF4:51150;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.1168307G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=615291.0013;CLNSIG=5;CLNDSDB=.;CLNDSDBID=.;CLNDBN=SPONDYLOEPIMETAPHYSEAL_DYSPLASIA_WITH_JOINT_LAXITY\x2c_TYPE_1\x2c_WITH_FRACTURES;CLNACC=RCV000054402.1
83
+ 1 1168352 rs397514717 C T . . RS=397514717;RSPOS=1168352;RV;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=B3GALT6:126792|SDF4:51150;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.1168352C>T;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=615291.0002;CLNSIG=5;CLNDSDB=MedGen:OMIM:SNOMED_CT;CLNDSDBID=C0432243:271640:254100000;CLNDBN=Spondyloepimetaphyseal_dysplasia_with_joint_laxity;CLNACC=RCV000054391.1
84
+ 1 1168583 rs397514721 T A . . RS=397514721;RSPOS=1168583;RV;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=B3GALT6:126792|SDF4:51150;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.1168583T>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=615291.0008;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=CN178404:615349:75496;CLNDBN=Ehlers-Danlos_syndrome\x2c_progeroid_type\x2c_2;CLNACC=RCV000054397.2
85
+ 1 1245104 rs144003672 C A . . RS=144003672;RSPOS=1245104;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050268000000000002100120;GENEINFO=ACAP3:116983|PUSL1:126789;WGT=0;VC=SNV;PM;PMC;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.1245104C>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000059856.2
86
+ 1 1248974 rs267597965 T A . . RS=267597965;RSPOS=1248974;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=CPSF3L:54973;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.1248974T>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064062.2
87
+ 1 1469331 rs145324009 G A . . RS=145324009;RSPOS=1469331;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050268000000000002100120;GENEINFO=ATAD3A:55210;WGT=0;VC=SNV;PM;PMC;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.1469331G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000059865.2
88
+ 1 1635335 rs201004006 G A . . RS=201004006;RSPOS=1635335;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=CDK11A:728642;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.1635335G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064284.2
89
+ 1 1905619 rs267598251 G A . . RS=267598251;RSPOS=1905619;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=KIAA1751:85452;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.1905619G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064400.2
90
+ 1 1916905 rs267598254 G A . . RS=267598254;RSPOS=1916905;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=KIAA1751:85452;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.1916905G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064403.2
91
+ 1 1916906 rs267598255 G A . . RS=267598255;RSPOS=1916906;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=KIAA1751:85452;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.1916906G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064404.2
92
+ 1 1959075 rs121434580 A C . . RS=121434580;RSPOS=1959075;dbSNPBuildID=132;SSR=0;SAO=1;VP=0x050260000000000002110100;GENEINFO=GABRD:2563;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.1959075A>C;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=137163.0001;CLNSIG=255;CLNDSDB=MedGen;CLNDSDBID=C3150401;CLNDBN=Generalized_epilepsy_with_febrile_seizures_plus_type_5;CLNACC=RCV000017598.1
93
+ 1 1959699 rs41307846 G A . . RS=41307846;RSPOS=1959699;dbSNPBuildID=127;SSR=0;SAO=1;VP=0x050260000000040116110100;GENEINFO=GABRD:2563;WGT=0;VC=SNV;PM;S3D;VLD;GNO;KGPhase1;KGPROD;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.1959699G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=137163.0002;CLNSIG=255|255|255;CLNDSDB=MedGen|MedGen|MedGen:OMIM;CLNDSDBID=C3150401|CN043549|C2751603:613060;CLNDBN=Generalized_epilepsy_with_febrile_seizures_plus_type_5|Epilepsy\x2c_juvenile_myoclonic_7|Epilepsy\x2c_idiopathic_generalized_10;CLNACC=RCV000017599.1|RCV000017600.1|RCV000022558.1;CAF=[0.9904,0.009642];COMMON=1
94
+ 1 1961453 rs142619552 C T . . RS=142619552;RSPOS=1961453;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050068000000000002100120;GENEINFO=GABRD:2563;WGT=0;VC=SNV;PM;PMC;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.1961453C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060029.2
95
+ 1 2160299 rs387907304 C G . . RS=387907304;RSPOS=2160299;dbSNPBuildID=137;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=SKI:6497;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.2160299C>G;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=164780.0002;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=NBK1277:C1321551:182212:2462:83092002;CLNDBN=Shprintzen-Goldberg_syndrome;CLNACC=RCV000030817.20
96
+ 1 2160305 rs387907306 G A,T . . RS=387907306;RSPOS=2160305;dbSNPBuildID=137;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=SKI:6497;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1,2;CLNHGVS=NC_000001.10:g.2160305G>A,NC_000001.10:g.2160305G>T;CLNSRC=OMIM_Allelic_Variant,OMIM_Allelic_Variant;CLNORIGIN=.,.;CLNSRCID=164780.0004,164780.0005;CLNSIG=5,5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet:SNOMED_CT,GeneReviews:MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=NBK1277:C1321551:182212:2462:83092002,NBK1277:C1321551:182212:2462:83092002;CLNDBN=Shprintzen-Goldberg_syndrome,Shprintzen-Goldberg_syndrome;CLNACC=RCV000030819.24,RCV000030820.24
97
+ 1 2160306 rs387907305 G A,T . . RS=387907305;RSPOS=2160306;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=SKI:6497;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1,2;CLNHGVS=NC_000001.10:g.2160306G>A,NC_000001.10:g.2160306G>T;CLNSRC=OMIM_Allelic_Variant,OMIM_Allelic_Variant;CLNORIGIN=.,.;CLNSRCID=164780.0003,164780.0007;CLNSIG=5,5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet:SNOMED_CT,GeneReviews:MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=NBK1277:C1321551:182212:2462:83092002,NBK1277:C1321551:182212:2462:83092002;CLNDBN=Shprintzen-Goldberg_syndrome,Shprintzen-Goldberg_syndrome;CLNACC=RCV000030818.24,RCV000033005.24
98
+ 1 2160308 rs397514590 C T . . RS=397514590;RSPOS=2160308;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=SKI:6497;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.2160308C>T;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=164780.0010;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=NBK1277:C1321551:182212:2462:83092002;CLNDBN=Shprintzen-Goldberg_syndrome;CLNACC=RCV000033008.24
99
+ 1 2160309 rs397514589 C A . . RS=397514589;RSPOS=2160309;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=SKI:6497;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.2160309C>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=164780.0009;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=NBK1277:C1321551:182212:2462:83092002;CLNDBN=Shprintzen-Goldberg_syndrome;CLNACC=RCV000033007.20
100
+ 1 2160484 rs398122914 GTCCGACCGCTCC G . . RS=398122914;RSPOS=2160485;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050060000000000002110200;GENEINFO=SKI:6497;WGT=0;VC=DIV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.2160485_2160496delTCCGACCGCTCC;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=164780.0008;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=NBK1277:C1321551:182212:2462:83092002;CLNDBN=Shprintzen-Goldberg_syndrome;CLNACC=RCV000033006.20
101
+ 1 2160487 rs398122889 CGACCGCTCC C . . RS=398122889;RSPOS=2160488;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050060000000000002110200;GENEINFO=SKI:6497;WGT=0;VC=DIV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.2160488_2160496delGACCGCTCC;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=164780.0006;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=NBK1277:C1321551:182212:2462:83092002;CLNDBN=Shprintzen-Goldberg_syndrome;CLNACC=RCV000030821.20
102
+ 1 2160552 rs387907303 G A . . RS=387907303;RSPOS=2160552;dbSNPBuildID=137;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=SKI:6497;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.2160552G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=164780.0001;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=NBK1277:C1321551:182212:2462:83092002;CLNDBN=Shprintzen-Goldberg_syndrome;CLNACC=RCV000030816.24
103
+ 1 2337965 rs61752095 G C . . RS=61752095;RSPOS=2337965;RV;dbSNPBuildID=129;SSR=0;SAO=1;VP=0x050368000000000002110100;GENEINFO=PEX10:5192;WGT=0;VC=SNV;PM;PMC;S3D;SLO;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.2337965G>C;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=0;CLNSRCID=602859.0002;CLNSIG=5;CLNDSDB=MedGen:OMIM;CLNDSDBID=CN159233:614871;CLNDBN=Peroxisome_biogenesis_disorder_6B;CLNACC=RCV000007173.1
104
+ 1 2340118 rs61750434 G A . . RS=61750434;RSPOS=2340118;RV;dbSNPBuildID=129;SSR=0;SAO=1;VP=0x050168000000000002110100;GENEINFO=PEX10:5192;WGT=0;VC=SNV;PM;PMC;SLO;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.2340118G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=0;CLNSRCID=602859.0003;CLNSIG=5;CLNDSDB=MedGen:OMIM;CLNDSDBID=CN159233:614871;CLNDBN=Peroxisome_biogenesis_disorder_6B;CLNACC=RCV000007174.1
105
+ 1 2445510 rs267598457 G A . . RS=267598457;RSPOS=2445510;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=PANK4:55229;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.2445510G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064619.2
106
+ 1 2445511 rs267598458 G A . . RS=267598458;RSPOS=2445511;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=PANK4:55229;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.2445511G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064620.2
107
+ 1 2452272 rs267598460 C T . . RS=267598460;RSPOS=2452272;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=PANK4:55229;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.2452272C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064622.2
108
+ 1 2452273 rs267598461 C T . . RS=267598461;RSPOS=2452273;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=PANK4:55229;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.2452273C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064623.2
109
+ 1 2938382 rs267598541 C T . . RS=267598541;RSPOS=2938382;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=ACTRT2:140625;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.2938382C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064708.2
110
+ 1 3319357 rs267598556 G A . . RS=267598556;RSPOS=3319357;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=PRDM16:63976;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.3319357G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064723.2
111
+ 1 3319550 rs397514744 C T . . RS=397514744;RSPOS=3319550;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002100100;GENEINFO=PRDM16:63976;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.3319550C>T;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=605557.0005;CLNSIG=5;CLNDSDB=MedGen;CLNDSDBID=CN178850;CLNDBN=Dilated_cardiomyopathy_1LL;CLNACC=RCV000054522.1
112
+ 1 3328865 rs397514742 A T . . RS=397514742;RSPOS=3328865;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=PRDM16:63976;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.3328865A>T;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=605557.0001;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet:Orphanet;CLNDSDBID=CN178849:615373:154:54260;CLNDBN=Left_ventricular_noncompaction_8;CLNACC=RCV000054518.1
113
+ 1 3328870 rs267598557 C T . . RS=267598557;RSPOS=3328870;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=PRDM16:63976;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.3328870C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064724.2
114
+ 1 3329208 rs397514743 A G . . RS=397514743;RSPOS=3329208;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=PRDM16:63976;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.3329208A>G;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=605557.0003;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet:Orphanet;CLNDSDBID=CN178849:615373:154:54260;CLNDBN=Left_ventricular_noncompaction_8;CLNACC=RCV000054520.1
115
+ 1 3331180 rs202115331 T C . . RS=202115331;RSPOS=3331180;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050260000000000002100100;GENEINFO=PRDM16:63976;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.3331180T>C;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=605557.0006;CLNSIG=5;CLNDSDB=MedGen;CLNDSDBID=CN178850;CLNDBN=Dilated_cardiomyopathy_1LL;CLNACC=RCV000054523.1
116
+ 1 3334486 rs145632008 C A,T . . RS=145632008;RSPOS=3334486;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050068000000000002100120;GENEINFO=PRDM16:63976;WGT=0;VC=SNV;PM;PMC;OTHERKG;LSD;CLNALLE=2;CLNHGVS=NC_000001.10:g.3334486C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060177.2
117
+ 1 3347452 rs201654872 G A . . RS=201654872;RSPOS=3347452;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002100100;GENEINFO=PRDM16:63976;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.3347452G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=605557.0004;CLNSIG=5;CLNDSDB=MedGen;CLNDSDBID=CN178850;CLNDBN=Dilated_cardiomyopathy_1LL;CLNACC=RCV000054521.1
118
+ 1 3548169 rs267598574 G A . . RS=267598574;RSPOS=3548169;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=WRAP73:49856;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.3548169G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064742.2
119
+ 1 3624269 rs267598580 A G . . RS=267598580;RSPOS=3624269;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=TP73:7161;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.3624269A>G;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064748.2
120
+ 1 3672076 rs267598583 G A . . RS=267598583;RSPOS=3672076;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=CCDC27:148870;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.3672076G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064751.2
121
+ 1 3673309 rs267598584 C T . . RS=267598584;RSPOS=3673309;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=CCDC27:148870;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.3673309C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064752.2
122
+ 1 3680269 rs139984517 G A . . RS=139984517;RSPOS=3680269;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050068000000000002100120;GENEINFO=CCDC27:148870;WGT=0;VC=SNV;PM;PMC;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.3680269G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060186.2
123
+ 1 3755581 rs139901107 G A . . RS=139901107;RSPOS=3755581;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050068000000000002100120;GENEINFO=CEP104:9731;WGT=0;VC=SNV;PM;PMC;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.3755581G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060189.2
124
+ 1 3765182 rs145420390 G A . . RS=145420390;RSPOS=3765182;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050068000000000002100120;GENEINFO=CEP104:9731;WGT=0;VC=SNV;PM;PMC;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.3765182G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060190.2
125
+ 1 4832363 rs267598631 G T . . RS=267598631;RSPOS=4832363;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=AJAP1:55966;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.4832363G>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064801.2
126
+ 1 5925224 rs398124290 G A . . RS=398124290;RSPOS=5925224;RV;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050060000000000002100100;GENEINFO=NPHP4:261734;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.5925224G>A;CLNSRC=.|Emory_University;CLNORIGIN=.;CLNSRCID=.|3979;CLNSIG=0;CLNDSDB=.;CLNDSDBID=.;CLNDBN=not_provided;CLNACC=RCV000081717.1
127
+ 1 5935006 rs28940891 A G . . RS=28940891;RSPOS=5935006;RV;dbSNPBuildID=136;SSR=0;SAO=1;VP=0x050060000000000002110100;GENEINFO=NPHP4:261734;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.5935006A>G;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=607215.0004;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C1847013:606966:655;CLNDBN=Nephronophthisis_4;CLNACC=RCV000003571.1
128
+ 1 5935033 rs398124289 T TGGAGC . . RS=398124289;RSPOS=5935033;RV;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050060000000000002100200;GENEINFO=NPHP4:261734;WGT=0;VC=DIV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.5935034_5935038dupGGAGC;CLNSRC=.;CLNORIGIN=.;CLNSRCID=.;CLNSIG=5;CLNDSDB=.;CLNDSDBID=.;CLNDBN=not_provided;CLNACC=RCV000081713.1
129
+ 1 5940242 rs398124288 C T . . RS=398124288;RSPOS=5940242;RV;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050060000000000002100100;GENEINFO=NPHP4:261734;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.5940242C>T;CLNSRC=.|Emory_University;CLNORIGIN=.;CLNSRCID=.|7428;CLNSIG=0;CLNDSDB=.;CLNDSDBID=.;CLNDBN=not_provided;CLNACC=RCV000081709.1
130
+ 1 5947454 rs137852919 G A . . RS=137852919;RSPOS=5947454;RV;dbSNPBuildID=133;SSR=0;SAO=1;VP=0x050060000000000002110100;GENEINFO=NPHP4:261734;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.5947454G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=607215.0002;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C1847013:606966:655;CLNDBN=Nephronophthisis_4;CLNACC=RCV000003569.1
131
+ 1 5947463 rs137852918 C A . . RS=137852918;RSPOS=5947463;RV;dbSNPBuildID=133;SSR=0;SAO=1;VP=0x050060000000000002110100;GENEINFO=NPHP4:261734;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.5947463C>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=607215.0001;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C1847013:606966:655;CLNDBN=Nephronophthisis_4;CLNACC=RCV000003568.1
132
+ 1 5947496 rs137852922 G A . . RS=137852922;RSPOS=5947496;RV;dbSNPBuildID=133;SSR=0;SAO=1;VP=0x050060000000000002110100;GENEINFO=NPHP4:261734;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.5947496G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=607215.0006;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C1846979:606996:3156;CLNDBN=Senior-Loken_syndrome_4;CLNACC=RCV000003573.1
133
+ 1 5964776 rs137852920 G A . . RS=137852920;RSPOS=5964776;RV;dbSNPBuildID=133;SSR=0;SAO=1;VP=0x050060000000000002110100;GENEINFO=NPHP4:261734;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.5964776G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=607215.0003;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C1847013:606966:655;CLNDBN=Nephronophthisis_4;CLNACC=RCV000003570.1
134
+ 1 5964848 rs137852923 G A . . RS=137852923;RSPOS=5964848;RV;dbSNPBuildID=133;SSR=0;SAO=1;VP=0x050060000000000002110100;GENEINFO=NPHP4:261734;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.5964848G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=607215.0007;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C1846979:606996:3156;CLNDBN=Senior-Loken_syndrome_4;CLNACC=RCV000003574.1
135
+ 1 6007278 rs398124287 T C . . RS=398124287;RSPOS=6007278;RV;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050060000000000002100100;GENEINFO=NPHP4:261734;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6007278T>C;CLNSRC=.|Emory_University;CLNORIGIN=.;CLNSRCID=.|11436;CLNSIG=0;CLNDSDB=.;CLNDSDBID=.;CLNDBN=not_provided;CLNACC=RCV000081703.1
136
+ 1 6027450 rs200754878 C T . . RS=200754878;RSPOS=6027450;dbSNPBuildID=137;SSR=0;SAO=0;VP=0x050060000000000016100100;GENEINFO=NPHP4:261734;WGT=0;VC=SNV;PM;KGPhase1;KGPROD;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6027450C>T;CLNSRC=.;CLNORIGIN=.;CLNSRCID=.;CLNSIG=2;CLNDSDB=MedGen;CLNDSDBID=CN169374;CLNDBN=AllHighlyPenetrant;CLNACC=RCV000081720.1;CAF=[1,0];COMMON=0
137
+ 1 6111773 rs267598678 C T . . RS=267598678;RSPOS=6111773;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=KCNAB2:8514;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6111773C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064851.2
138
+ 1 6151338 rs267598679 C T . . RS=267598679;RSPOS=6151338;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=KCNAB2:8514;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6151338C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064852.2
139
+ 1 6170558 rs267598680 G A . . RS=267598680;RSPOS=6170558;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=CHD5:26038;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6170558G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064853.2
140
+ 1 6172231 rs150855676 G A . . RS=150855676;RSPOS=6172231;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050068000000000002100120;GENEINFO=CHD5:26038;WGT=0;VC=SNV;PM;PMC;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6172231G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060228.2
141
+ 1 6211203 rs267598681 C A . . RS=267598681;RSPOS=6211203;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=CHD5:26038;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6211203C>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064854.2
142
+ 1 6211204 rs267598682 A T . . RS=267598682;RSPOS=6211204;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=CHD5:26038;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6211204A>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064855.2
143
+ 1 6304465 rs267598684 G A . . RS=267598684;RSPOS=6304465;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=HES3:390992;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6304465G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064857.2
144
+ 1 6511986 rs121908134 A C . . RS=121908134;RSPOS=6511986;dbSNPBuildID=132;SSR=0;SAO=1;VP=0x050060000000000002110100;GENEINFO=ESPN:83715;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.6511986A>C;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=606351.0003;CLNSIG=5;CLNDSDB=.;CLNDSDBID=.;CLNDBN=Deafness\x2c_without_vestibular_involvement\x2c_autosomal_dominant;CLNACC=RCV000004670.1
145
+ 1 6512061 rs121908135 G A . . RS=121908135;RSPOS=6512061;dbSNPBuildID=132;SSR=0;SAO=1;VP=0x050060000000000002110100;GENEINFO=ESPN:83715;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.6512061G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=606351.0004;CLNSIG=5;CLNDSDB=.;CLNDSDBID=.;CLNDBN=Deafness\x2c_without_vestibular_involvement\x2c_autosomal_dominant;CLNACC=RCV000004671.1
146
+ 1 6512152 rs121908136 G A . . RS=121908136;RSPOS=6512152;dbSNPBuildID=132;SSR=0;SAO=1;VP=0x050060000000000002110100;GENEINFO=ESPN:83715;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.6512152G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=606351.0005;CLNSIG=5;CLNDSDB=.;CLNDSDBID=.;CLNDBN=Deafness\x2c_without_vestibular_involvement\x2c_autosomal_dominant;CLNACC=RCV000004672.1
147
+ 1 6528438 rs202191898 C G,T . . RS=202191898;RSPOS=6528438;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000016110100;GENEINFO=PLEKHG5:57449;WGT=0;VC=SNV;PM;KGPhase1;KGPROD;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.6528438C>G;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=611101.0005;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C3150897:613641:254334;CLNDBN=Charcot-Marie-Tooth_disease\x2c_recessive_intermediate_B;CLNACC=RCV000054546.1;CAF=[0.9995,.,0.0004591];COMMON=0
148
+ 1 6529456 rs397515456 G A . . RS=397515456;RSPOS=6529456;RV;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=PLEKHG5:57449;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.6529456G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=611101.0004;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C3150897:613641:254334;CLNDBN=Charcot-Marie-Tooth_disease\x2c_recessive_intermediate_B;CLNACC=RCV000054547.1
149
+ 1 6529504 rs63750315 A G . . RS=63750315;RSPOS=6529504;RV;dbSNPBuildID=130;SSR=0;SAO=1;VP=0x050268000000000002110100;GENEINFO=PLEKHG5:57449;WGT=0;VC=SNV;PM;PMC;S3D;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.6529504A>G;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=611101.0001;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C1970211:611067:206580;CLNDBN=Distal_spinal_muscular_atrophy\x2c_autosomal_recessive_4;CLNACC=RCV000001074.2
150
+ 1 6530327 rs267598689 C T . . RS=267598689;RSPOS=6530327;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=PLEKHG5:57449;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6530327C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064862.2
151
+ 1 6530355 rs267598690 C T . . RS=267598690;RSPOS=6530355;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=PLEKHG5:57449;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6530355C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064863.2
152
+ 1 6531604 rs267598691 C T . . RS=267598691;RSPOS=6531604;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=PLEKHG5:57449;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6531604C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064864.2
153
+ 1 6533111 rs397515455 C CGTCTTCA . . RS=397515455;RSPOS=6533111;RV;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110200;GENEINFO=PLEKHG5:57449;WGT=0;VC=DIV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.6533112_6533118dupGTCTTCA;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=611101.0003;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C3150897:613641:254334;CLNDBN=Charcot-Marie-Tooth_disease\x2c_recessive_intermediate_B;CLNACC=RCV000054545.1
154
+ 1 6537593 rs397515454 TG T . . RS=397515454;RSPOS=6537594;RV;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110200;GENEINFO=PLEKHG5:57449;WGT=0;VC=DIV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.6537594delG;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=611101.0002;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C3150897:613641:254334;CLNDBN=Charcot-Marie-Tooth_disease\x2c_recessive_intermediate_B;CLNACC=RCV000054544.1
155
+ 1 6589228 rs145449783 G A . . RS=145449783;RSPOS=6589228;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050068000000000002100120;GENEINFO=NOL9:79707;WGT=0;VC=SNV;PM;PMC;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6589228G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060234.2
156
+ 1 6637073 rs148829212 C T . . RS=148829212;RSPOS=6637073;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050268000000000002100120;GENEINFO=TAS1R1:80835;WGT=0;VC=SNV;PM;PMC;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6637073C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060235.2
157
+ 1 6653500 rs137992292 G A . . RS=137992292;RSPOS=6653500;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=KLHL21:9903;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6653500G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064865.2
158
+ 1 6706031 rs150959272 T A . . RS=150959272;RSPOS=6706031;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050068000000000002100120;GENEINFO=DNAJC11:55735;WGT=0;VC=SNV;PM;PMC;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6706031T>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060237.2
159
+ 1 6727837 rs267598695 G A . . RS=267598695;RSPOS=6727837;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=DNAJC11:55735;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6727837G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064869.2
160
+ 1 7723700 rs267598725 G A . . RS=267598725;RSPOS=7723700;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=CAMTA1:23261;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.7723700G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064902.2
161
+ 1 7798488 rs267598727 C T . . RS=267598727;RSPOS=7798488;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=CAMTA1:23261;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.7798488C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064904.2
162
+ 1 7811268 rs267598728 T C . . RS=267598728;RSPOS=7811268;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=CAMTA1:23261;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.7811268T>C;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064905.2
163
+ 1 7887271 rs139934930 C T . . RS=139934930;RSPOS=7887271;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050068000000000002100120;GENEINFO=PER3:8863;WGT=0;VC=SNV;PM;PMC;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.7887271C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060248.2
164
+ 1 7887619 rs137949562 C T . . RS=137949562;RSPOS=7887619;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=PER3:8863;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.7887619C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064906.2
165
+ 1 7895998 rs267598729 C T . . RS=267598729;RSPOS=7895998;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=PER3:8863;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.7895998C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064907.2
166
+ 1 8022923 rs74315351 G A . . RS=74315351;RSPOS=8022923;dbSNPBuildID=133;SSR=0;SAO=1;VP=0x050260000000000002110100;GENEINFO=PARK7:11315;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.8022923G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=0;CLNSRCID=602533.0003;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet;CLNDSDBID=NBK1223:C1853445:606324:2828;CLNDBN=Parkinson_disease_7;CLNACC=RCV000007481.1
167
+ 1 8025408 rs137853051 G T . . RS=137853051;RSPOS=8025408;dbSNPBuildID=133;SSR=0;SAO=1;VP=0x050260000000000002110100;GENEINFO=PARK7:11315;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.8025408G>T;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=602533.0007;CLNSIG=5;CLNDSDB=GeneReviews:MedGen;CLNDSDBID=NBK1223:C2751533;CLNDBN=Parkinson_disease\x2c_autosomal_recessive_early-onset\x2c_digenic\x2c_PINK1/DJ1;CLNACC=RCV000007485.1
168
+ 1 8025485 rs74315353 G C . . RS=74315353;RSPOS=8025485;dbSNPBuildID=133;SSR=0;SAO=1;VP=0x050260000000000002110100;GENEINFO=PARK7:11315;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.8025485G>C;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=0;CLNSRCID=602533.0005;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet;CLNDSDBID=NBK1223:C1853445:606324:2828;CLNDBN=Parkinson_disease_7;CLNACC=RCV000007483.1
169
+ 1 8044990 rs74315352 A C . . RS=74315352;RSPOS=8044990;dbSNPBuildID=133;SSR=0;SAO=1;VP=0x050260000000040016110100;GENEINFO=PARK7:11315;WGT=0;VC=SNV;PM;S3D;VLD;KGPhase1;KGPROD;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.8044990A>C;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=602533.0004;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet;CLNDSDBID=NBK1223:C1853445:606324:2828;CLNDBN=Parkinson_disease_7;CLNACC=RCV000007482.1;CAF=[0.9977,0.002296];COMMON=1
170
+ 1 8045031 rs74315354 G A . . RS=74315354;RSPOS=8045031;dbSNPBuildID=131;SSR=0;SAO=1;VP=0x050260000000000002110100;GENEINFO=PARK7:11315;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.8045031G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=0;CLNSRCID=602533.0006;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet;CLNDSDBID=NBK1223:C1853445:606324:2828;CLNDBN=Parkinson_disease_7;CLNACC=RCV000007484.1
171
+ 1 8045041 rs28938172 T C . . RS=28938172;RSPOS=8045041;dbSNPBuildID=133;SSR=0;SAO=1;VP=0x050260000000000002110100;GENEINFO=PARK7:11315;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.8045041T>C;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=602533.0002;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet;CLNDSDBID=NBK1223:C1853445:606324:2828;CLNDBN=Parkinson_disease_7;CLNACC=RCV000007480.1
172
+ 1 8390585 rs138991605 C T . . RS=138991605;RSPOS=8390585;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050068000000000002100120;GENEINFO=SLC45A1:50651;WGT=0;VC=SNV;PM;PMC;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.8390585C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060251.2
173
+ 1 8390726 rs267598735 C T . . RS=267598735;RSPOS=8390726;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=SLC45A1:50651;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.8390726C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064913.2
174
+ 1 8418710 rs115986998 G A . . RS=115986998;RSPOS=8418710;dbSNPBuildID=132;SSR=0;SAO=3;VP=0x050060000000150416100120;GENEINFO=RERE:473;WGT=0;VC=SNV;PM;VLD;G5;HD;KGPhase1;KGPROD;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.8418710G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064914.2;CAF=[0.9789,0.02112];COMMON=1
175
+ 1 8424311 rs267598736 G A . . RS=267598736;RSPOS=8424311;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=RERE:473;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.8424311G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064915.2
176
+ 1 8525931 rs267598738 G A . . RS=267598738;RSPOS=8525931;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=RERE:473;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.8525931G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064917.2
177
+ 1 8924024 rs267598749 G A . . RS=267598749;RSPOS=8924024;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=ENO1:2023;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.8924024G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064928.2
178
+ 1 8924025 rs267598750 G A . . RS=267598750;RSPOS=8924025;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=ENO1:2023;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.8924025G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064929.2
179
+ 1 9030973 rs267598758 C T . . RS=267598758;RSPOS=9030973;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=CA6:765;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.9030973C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064939.2
180
+ 1 9078340 rs267598762 G A . . RS=267598762;RSPOS=9078340;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=SLC2A7:155184;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.9078340G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064943.2
181
+ 1 9078399 rs267598763 C T . . RS=267598763;RSPOS=9078399;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=SLC2A7:155184;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.9078399C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064944.2
182
+ 1 9097813 rs267598764 G A . . RS=267598764;RSPOS=9097813;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=SLC2A5:6518;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.9097813G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064945.2
183
+ 1 9305316 rs398122818 AC A . . RS=398122818;RSPOS=9305318;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050060000000000002110200;GENEINFO=H6PD:9563;WGT=0;VC=DIV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.9305318delC;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=138090.0006;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=C1291245:604931:168588:124138004;CLNDBN=Deficiency_of_(R)-20-hydroxysteroid_dehydrogenase;CLNACC=RCV000024293.26
184
+ 1 9322320 rs398122817 C G . . RS=398122817;RSPOS=9322320;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=H6PD:9563;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.9322320C>G;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=138090.0005;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=C1291245:604931:168588:124138004;CLNDBN=Deficiency_of_(R)-20-hydroxysteroid_dehydrogenase;CLNACC=RCV000024292.26
185
+ 1 9322332 rs398122816 G A . . RS=398122816;RSPOS=9322332;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=H6PD:9563;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.9322332G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=138090.0003;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=C1291245:604931:168588:124138004;CLNDBN=Deficiency_of_(R)-20-hydroxysteroid_dehydrogenase;CLNACC=RCV000024290.26
186
+ 1 9323628 rs387907167 G A . . RS=387907167;RSPOS=9323628;dbSNPBuildID=137;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=H6PD:9563;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.9323628G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=138090.0004;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=C1291245:604931:168588:124138004;CLNDBN=Deficiency_of_(R)-20-hydroxysteroid_dehydrogenase;CLNACC=RCV000024291.26
187
+ 1 9323910 rs6688832 G A . . RS=6688832;RSPOS=9323910;dbSNPBuildID=116;SSR=0;SAO=1;VP=0x05036800000015051f110101;GENEINFO=H6PD:9563;WGT=0;VC=SNV;PM;PMC;S3D;SLO;VLD;G5;HD;GNO;KGPhase1;KGPilot123;KGPROD;OTHERKG;PH3;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.9323910G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=0;CLNSRCID=138090.0002;CLNSIG=0;CLNDSDB=.;CLNDSDBID=.;CLNDBN=Reclassified_-_variant_of_unknown_significance;CLNACC=RCV000017511.1;CAF=[0.6364,0.3636];COMMON=1
188
+ 1 9324187 rs267598769 C T . . RS=267598769;RSPOS=9324187;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=H6PD:9563;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.9324187C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064951.2
189
+ 1 9780198 rs141809100 G A . . RS=141809100;RSPOS=9780198;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050268000000000002100120;GENEINFO=PIK3CD:5293;WGT=0;VC=SNV;PM;PMC;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.9780198G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060269.2
190
+ 1 9780199 rs147135836 G A . . RS=147135836;RSPOS=9780199;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050268000000000002100120;GENEINFO=PIK3CD:5293;WGT=0;VC=SNV;PM;PMC;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.9780199G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060270.2
191
+ 1 9787030 rs397518423 G A . . RS=397518423;RSPOS=9787030;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050060000000000002100100;GENEINFO=PIK3CD:5293;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.9787030G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=602839.0001;CLNSIG=5|5;CLNDSDB=MedGen|OMIM;CLNDSDBID=CN181202|615513;CLNDBN=Activated_PI3K-Delta_Syndrome_(APDS)|ACTIVATED_PI3K-DELTA_SYNDROME;CLNACC=RCV000074362.1|RCV000076908.2
192
+ 1 9804551 rs267598783 G A . . RS=267598783;RSPOS=9804551;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.9804551G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064965.2
193
+ 1 9804656 rs140324308 G A . . RS=140324308;RSPOS=9804656;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050068000000000002100120;WGT=0;VC=SNV;PM;PMC;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.9804656G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060271.2
194
+ 1 9809643 rs267598784 G A . . RS=267598784;RSPOS=9809643;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.9809643G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064966.2
195
+ 1 10032156 rs387907294 G A . . RS=387907294;RSPOS=10032156;dbSNPBuildID=137;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=NMNAT1:64802;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.10032156G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=608700.0009;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet;CLNDSDBID=NBK1298:C1837873:608553:65;CLNDBN=Leber_congenital_amaurosis_9;CLNACC=RCV000030771.1
196
+ 1 10042370 rs387907292 G T . . RS=387907292;RSPOS=10042370;dbSNPBuildID=137;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=NMNAT1:64802;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.10042370G>T;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=608700.0004;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet;CLNDSDBID=NBK1298:C1837873:608553:65;CLNDBN=Leber_congenital_amaurosis_9;CLNACC=RCV000030767.1
197
+ 1 10042376 rs387907293 C G . . RS=387907293;RSPOS=10042376;dbSNPBuildID=137;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=NMNAT1:64802;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.10042376C>G;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=608700.0008;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet;CLNDSDBID=NBK1298:C1837873:608553:65;CLNDBN=Leber_congenital_amaurosis_9;CLNACC=RCV000030770.1
198
+ 1 10042538 rs142968179 C T . . RS=142968179;RSPOS=10042538;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050260000000000002110100;GENEINFO=NMNAT1:64802;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.10042538C>T;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=608700.0005;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet;CLNDSDBID=NBK1298:C1837873:608553:65;CLNDBN=Leber_congenital_amaurosis_9;CLNACC=RCV000030764.1
199
+ 1 10042614 rs267598792 G A . . RS=267598792;RSPOS=10042614;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=NMNAT1:64802;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.10042614G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064974.2
200
+ 1 10042629 rs368062092 G T . . RS=368062092;RSPOS=10042629;dbSNPBuildID=137;SSR=0;SAO=0;VP=0x050260000000000002110100;GENEINFO=NMNAT1:64802;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.10042629G>T;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=608700.0007;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet;CLNDSDBID=NBK1298:C1837873:608553:65;CLNDBN=Leber_congenital_amaurosis_9;CLNACC=RCV000030769.1
data/test/data/input/multisample.vcf CHANGED
@@ -110,8 +110,8 @@
110
110
  ##contig=<ID=GL000194.1,length=191469,assembly=b37>
111
111
  ##contig=<ID=GL000225.1,length=211173,assembly=b37>
112
112
  ##contig=<ID=GL000192.1,length=547496,assembly=b37>
113
- ##reference=file:///data_fedor13/common_data/references/H_sapiens/GATK_b37_bundle_reference/basespace/human_g1k_v37.fasta
114
- #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BIOPSY17513D clone10 clone3 clone4 subclone105 subclone33 subclone46
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
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
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
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
data/test/data/regression/eval_r.info.dp.ref ADDED
@@ -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>
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+ ##contig=<ID=3,length=198022430,assembly=b37>
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+ ##contig=<ID=4,length=191154276,assembly=b37>
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+ ##contig=<ID=7,length=159138663,assembly=b37>
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+ ##contig=<ID=8,length=146364022,assembly=b37>
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+ ##contig=<ID=9,length=141213431,assembly=b37>
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+ ##contig=<ID=10,length=135534747,assembly=b37>
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+ ##contig=<ID=11,length=135006516,assembly=b37>
40
+ ##contig=<ID=12,length=133851895,assembly=b37>
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+ ##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>
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+ ##contig=<ID=Y,length=59373566,assembly=b37>
53
+ ##contig=<ID=MT,length=16569,assembly=b37>
54
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87
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88
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+ ##contig=<ID=GL000228.1,length=129120,assembly=b37>
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92
+ ##contig=<ID=GL000209.1,length=159169,assembly=b37>
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+ ##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
+ 1518
116
+ 1433
117
+ 1440
118
+ 1460
119
+ 1500
120
+ 1537
121
+ 1641
122
+ 129
123
+ 28
124
+ 22
125
+ 18
126
+ 939
127
+ 721
128
+ 703
129
+ 929
130
+ 692
131
+ 1149
132
+ 1108
133
+ 830
134
+ 764
135
+ 809
136
+ 754
137
+ 719
138
+ 1083
139
+ 1092
140
+ 1089
141
+ 1050
142
+ 939
143
+ 1004
144
+ 1090
145
+ 992
146
+ 636
147
+ 1213
148
+ 904
149
+ 398
150
+ 526
data/test/data/regression/r.info.dp.ref ADDED
@@ -0,0 +1,147 @@
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>
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+ ##contig=<ID=4,length=191154276,assembly=b37>
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+ ##contig=<ID=6,length=171115067,assembly=b37>
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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 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 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 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
124
+ 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
125
+ 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
126
+ 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
127
+ 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
128
+ 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
129
+ 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
130
+ 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
131
+ 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 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
132
+ 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
133
+ 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
134
+ 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
135
+ 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
136
+ 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
137
+ 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
138
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139
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140
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141
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142
+ 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
143
+ 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
144
+ 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
145
+ 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
146
+ 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
147
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