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reproduce_setup/pgx-main/pgx_results/CAN-NA19239-29Mar2025_S32_pgx_result/matcher.json

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{
"metadata": {
"namedAlleleMatcherVersion": "1.0.0",
"genomeBuild": "GRCh38.p13",
"inputFilename": "pharmcat.vcf",
"timestamp": "Aug 15, 2025, 2:22:38 PM"
},
"results": [
{
"alleleDefinitionVersion": "05/05/22",
"chromosome": "chr4",
"gene": "ABCG2",
"diplotypes": [
{
"name": "rs2231142 reference (G)/rs2231142 reference (G)",
"haplotype1": {
"name": "rs2231142 reference (G)",
"sequences": [
"88131171:G;"
]
},
"haplotype2": {
"name": "rs2231142 reference (G)",
"sequences": [
"88131171:G;"
]
},
"score": 2
}
],
"haplotypes": [
{
"name": "rs2231142 reference (G)",
"sequences": [
"88131171:G;"
]
}
],
"phased": true,
"variants": [
{
"position": 88131171,
"rsid": "rs2231142",
"vcfCall": "G|G"
}
],
"variantsOfInterest": [],
"matchData": {
"missingPositions": [],
"mismatchedAlleles": []
},
"uncallableHaplotypes": [],
"ignoredHaplotypes": []
},
{
"alleleDefinitionVersion": "05/05/22",
"chromosome": "chr7",
"gene": "CFTR",
"diplotypes": [
{
"name": "ivacaftor non-responsive CFTR sequence/ivacaftor non-responsive CFTR sequence",
"haplotype1": {
"name": "ivacaftor non-responsive CFTR sequence",
"sequences": [
"117509035:G;117509069:C;117509089:C;117530953:G;117530955:C;117530974:C;117530975:G;117534318:G;117534363:G;117534368:A;117535285:T;117540270:G;117540285:G;117548795:C;117587799:A;117587800:G;117587801:T;117587805:G;117587806:G;117590409:A;117594930:G;117602868:G;117603708:C;117606695:C;117611555:A;117611595:T;117611620:A;117611640:G;117611646:G;117611649:C;117611650:G;117611663:T;117614699:G;117639961:C;117642451:G;117642472:G;117642483:T;117642528:G;117664770:G;"
]
},
"haplotype2": {
"name": "ivacaftor non-responsive CFTR sequence",
"sequences": [
"117509035:G;117509069:C;117509089:C;117530953:G;117530955:C;117530974:C;117530975:G;117534318:G;117534363:G;117534368:A;117535285:T;117540270:G;117540285:G;117548795:C;117587799:A;117587800:G;117587801:T;117587805:G;117587806:G;117590409:A;117594930:G;117602868:G;117603708:C;117606695:C;117611555:A;117611595:T;117611620:A;117611640:G;117611646:G;117611649:C;117611650:G;117611663:T;117614699:G;117639961:C;117642451:G;117642472:G;117642483:T;117642528:G;117664770:G;"
]
},
"score": 78
}
],
"haplotypes": [
{
"name": "ivacaftor non-responsive CFTR sequence",
"sequences": [
"117509035:G;117509069:C;117509089:C;117530953:G;117530955:C;117530974:C;117530975:G;117534318:G;117534363:G;117534368:A;117535285:T;117540270:G;117540285:G;117548795:C;117587799:A;117587800:G;117587801:T;117587805:G;117587806:G;117590409:A;117594930:G;117602868:G;117603708:C;117606695:C;117611555:A;117611595:T;117611620:A;117611640:G;117611646:G;117611649:C;117611650:G;117611663:T;117614699:G;117639961:C;117642451:G;117642472:G;117642483:T;117642528:G;117664770:G;"
]
}
],
"phased": true,
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{
"position": 117509035,
"rsid": "rs397508256",
"vcfCall": "G|G"
},
{
"position": 117509069,
"rsid": "rs368505753",
"vcfCall": "C|C"
},
{
"position": 117509089,
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{
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{
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}
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"uncallableHaplotypes": [],
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},
{
"alleleDefinitionVersion": "08/05/22",
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{
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{
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{
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},
{
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},
{
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},
{
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{
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},
{
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},
{
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},
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],
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},
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]
},
{
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],
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},
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]
},
{
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],
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"C": "C"
},
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]
},
{
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],
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},
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]
},
{
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"G"
],
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},
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]
},
{
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"position": 40851439,
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"T"
],
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"C": "C"
},
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}
],
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},
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"*46.015",
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"*35",
"*36",
"*37",
"*38",
"*39",
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},
{
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{
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"40991224:T;40991367:A;40991369:C;40991381:A;40991388:A;40991390:C;40991391:G;40991441:A;41004015:T;41004125:G;41004158:G;41004303:T;41004377:A;41004381:G;41004406:G;41006919:C;41006923:C;41006936:G;41006968:T;41007013:T;41009350:C;41009358:A;41010006:G;41010088:C;41010108:C;41012316:T;41012339:C;41012465:C;41012693:T;41012740:G;41012803:C;41016726:A;41016778:G;41016805:A;41016810:C;"
]
},
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]
},
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}
],
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{
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]
},
{
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"40991224:T;40991367:A;40991369:C;40991381:A;40991388:A;40991390:C;40991391:G;40991441:A;41004015:T;41004125:G;41004158:G;41004303:T;41004377:A;41004381:G;41004406:G;41006919:C;41006923:C;41006936:T;41006968:T;41007013:T;41009350:C;41009358:G;41010006:G;41010088:C;41010108:C;41012316:T;41012339:C;41012465:C;41012693:T;41012740:G;41012803:C;41016726:A;41016778:G;41016805:A;41016810:C;"
]
}
],
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},
{
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},
{
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},
{
"position": 40991381,
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},
{
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},
{
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},
{
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},
{
"position": 40991441,
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},
{
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},
{
"position": 41004125,
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},
{
"position": 41004158,
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},
{
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},
{
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},
{
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},
{
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},
{
"position": 41006919,
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},
{
"position": 41006923,
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},
{
"position": 41006936,
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},
{
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},
{
"position": 41007013,
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},
{
"position": 41009350,
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},
{
"position": 41009358,
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},
{
"position": 41010006,
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},
{
"position": 41010088,
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},
{
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},
{
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},
{
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},
{
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},
{
"position": 41012693,
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},
{
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},
{
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},
{
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},
{
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},
{
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},
{
"position": 41016810,
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}
],
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},
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},
{
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{
"name": "*13/*17",
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"94761900:C;94762706:A;94762712:C;94762715:T;94762755:T;94762760:A;94762788:A;94762856:A;94775106:C;94775121:C;94775160:G;94775185:A;94775367:A;94775416:T;94775423:A;94775453:G;94775489:G;94775507:G;94780574:G;94780579:G;94780653:G;94781858:C;94781859:G;94781944:G;94781999:T;94842861:G;94842866:G;94842879:G;94842995:G;94849995:T;94852738:C;94852765:C;94852785:C;94852914:A;"
]
},
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"94761900:T;94762706:A;94762712:C;94762715:T;94762755:T;94762760:A;94762788:A;94762856:A;94775106:C;94775121:C;94775160:G;94775185:A;94775367:A;94775416:T;94775423:A;94775453:G;94775489:G;94775507:G;94780574:G;94780579:G;94780653:G;94781858:C;94781859:G;94781944:G;94781999:T;94842861:G;94842866:G;94842879:G;94842995:G;94849995:C;94852738:C;94852765:C;94852785:C;94852914:A;"
]
},
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}
],
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{
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]
},
{
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"94761900:T;94762706:A;94762712:C;94762715:T;94762755:T;94762760:A;94762788:A;94762856:A;94775106:C;94775121:C;94775160:G;94775185:A;94775367:A;94775416:T;94775423:A;94775453:G;94775489:G;94775507:G;94780574:G;94780579:G;94780653:G;94781858:C;94781859:G;94781944:G;94781999:T;94842861:G;94842866:G;94842879:G;94842995:G;94849995:C;94852738:C;94852765:C;94852785:C;94852914:A;"
]
}
],
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{
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},
{
"position": 94762706,
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},
{
"position": 94762712,
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},
{
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},
{
"position": 94762755,
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},
{
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},
{
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},
{
"position": 94762856,
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},
{
"position": 94775106,
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},
{
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},
{
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},
{
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{
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},
{
"position": 94775416,
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},
{
"position": 94775423,
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},
{
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},
{
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},
{
"position": 94775507,
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},
{
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},
{
"position": 94780579,
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},
{
"position": 94780653,
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},
{
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},
{
"position": 94781859,
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},
{
"position": 94781944,
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},
{
"position": 94781999,
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},
{
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},
{
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},
{
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},
{
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},
{
"position": 94849995,
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},
{
"position": 94852738,
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},
{
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},
{
"position": 94852785,
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},
{
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],
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},
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},
{
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{
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"95037039:G;95037074:T;95037104:G;95037216:TCAA;95038958:G;95038992:T;95042890:C;95042958:G;95042980:G;95043047:A;95045835:G;95045951:C;95058349:T;95058362:G;95058414:T;95058424:T;95058442:C;95058485:A;95064886:G;95064901:C;95064931:C;95067209:C;95067213:GT;95067273:C;95069408:C;95069488:T;95069524:T;95069535:T;95069649:A;95069673:G;95069772:A;95069813:G;"
]
},
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"95037039:G;95037074:T;95037104:G;95037216:TCAA;95038958:G;95038992:T;95042890:C;95042958:G;95042980:G;95043047:A;95045835:G;95045951:C;95058349:T;95058362:G;95058414:T;95058424:T;95058442:C;95058485:A;95064886:G;95064901:C;95064931:C;95067209:C;95067213:GT;95067273:C;95069408:C;95069488:T;95069524:T;95069535:T;95069649:A;95069673:G;95069772:A;95069813:G;"
]
},
"score": 64
}
],
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{
"name": "*1.001",
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]
}
],
"phased": true,
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{
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},
{
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{
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{
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{
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{
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{
"position": 95042890,
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},
{
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},
{
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},
{
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},
{
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},
{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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},
{
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{
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],
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},
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},
{
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{
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]
},
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},
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],
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{
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]
},
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},
{
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{
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{
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{
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{
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{
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{
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{
"name": "Reference/Reference",
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"38440802:T;38440829:C;38444211:C;38444212:G;38446710:G;38448673:C;38448712:G;38451842:C;38451850:C;38455359:A;38455463:G;38455471:C;38455472:G;38455528:C;38457545:C;38457546:G;38494564:C;38494565:G;38494579:G;38496283:C;38499223:G;38499644:TGGA;38499655:G;38499670:C;38499731:G;38499975:G;38499993:G;38499997:G;38500636:C;38500642:C;38500643:G;38500654:C;38500655:G;38500898:C;38500899:G;38512321:G;38543832:G;38580004:A;38580094:C;38580114:C;38580370:C;38580403:G;38580440:G;38584989:T;"
]
},
"haplotype2": {
"name": "Reference",
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"38440802:T;38440829:C;38444211:C;38444212:G;38446710:G;38448673:C;38448712:G;38451842:C;38451850:C;38455359:A;38455463:G;38455471:C;38455472:G;38455528:C;38457545:C;38457546:G;38494564:C;38494565:G;38494579:G;38496283:C;38499223:G;38499644:TGGA;38499655:G;38499670:C;38499731:G;38499975:G;38499993:G;38499997:G;38500636:C;38500642:C;38500643:G;38500654:C;38500655:G;38500898:C;38500899:G;38512321:G;38543832:G;38580004:A;38580094:C;38580114:C;38580370:C;38580403:G;38580440:G;38584989:T;"
]
},
"score": 88
}
],
"haplotypes": [
{
"name": "Reference",
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"38440802:T;38440829:C;38444211:C;38444212:G;38446710:G;38448673:C;38448712:G;38451842:C;38451850:C;38455359:A;38455463:G;38455471:C;38455472:G;38455528:C;38457545:C;38457546:G;38494564:C;38494565:G;38494579:G;38496283:C;38499223:G;38499644:TGGA;38499655:G;38499670:C;38499731:G;38499975:G;38499993:G;38499997:G;38500636:C;38500642:C;38500643:G;38500654:C;38500655:G;38500898:C;38500899:G;38512321:G;38543832:G;38580004:A;38580094:C;38580114:C;38580370:C;38580403:G;38580440:G;38584989:T;"
]
}
],
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{
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"vcfCall": "T|T"
},
{
"position": 38440829,
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},
{
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},
{
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},
{
"position": 38446710,
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},
{
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},
{
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},
{
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},
{
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},
{
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},
{
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},
{
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},
{
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},
{
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},
{
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},
{
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},
{
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},
{
"position": 38494565,
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},
{
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},
{
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},
{
"position": 38499223,
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},
{
"position": 38499644,
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},
{
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},
{
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},
{
"position": 38499731,
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},
{
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},
{
"position": 38499993,
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},
{
"position": 38499997,
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},
{
"position": 38500636,
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},
{
"position": 38500642,
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},
{
"position": 38500643,
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},
{
"position": 38500654,
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},
{
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},
{
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},
{
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},
{
"position": 38512321,
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},
{
"position": 38543832,
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},
{
"position": 38580004,
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},
{
"position": 38580094,
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},
{
"position": 38580114,
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},
{
"position": 38580370,
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},
{
"position": 38580403,
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},
{
"position": 38580440,
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},
{
"position": 38584989,
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}
],
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},
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},
{
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"chromosome": "chr12",
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{
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]
},
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"21172734:C;21172776:G;21172782:T;21174595:T;21176804:A;21176868:A;21176871:G;21176879:C;21176883:A;21176898:G;21178612:A;21178615:T;21178957:A;21196951:A;21196975:C;21196976:G;21200544:C;21200595:T;21202553:T;21202555:C;21202649:A;21202664:G;21205921:A;21205999:G;21206031:A;21222355:C;21239042:A;21239077:A;21239113:A;21239145:C;21239158:C;"
]
},
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}
],
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{
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]
}
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{
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},
{
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{
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{
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{
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{
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},
{
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{
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{
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{
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{
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{
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},
{
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},
{
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{
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},
{
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{
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{
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{
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{
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{
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{
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{
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{
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},
{
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{
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{
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},
{
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},
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},
{
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{
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]
},
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},
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]
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{
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{
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{
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{
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},
{
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},
{
"position": 18149032,
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{
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},
{
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},
{
"position": 18149127,
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}
],
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},
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},
{
"alleleDefinitionVersion": "05/05/22",
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"gene": "UGT1A1",
"diplotypes": [
{
"name": "*80/*80",
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]
},
"haplotype2": {
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]
},
"score": 2
}
],
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{
"name": "*80",
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]
}
],
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{
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{
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},
{
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}
],
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"mismatchedAlleles": []
},
"uncallableHaplotypes": [],
"ignoredHaplotypes": []
},
{
"alleleDefinitionVersion": "05/05/22",
"chromosome": "chr16",
"gene": "VKORC1",
"diplotypes": [
{
"name": "rs9923231 reference (C)/rs9923231 reference (C)",
"haplotype1": {
"name": "rs9923231 reference (C)",
"sequences": [
"31096368:C;"
]
},
"haplotype2": {
"name": "rs9923231 reference (C)",
"sequences": [
"31096368:C;"
]
},
"score": 2
}
],
"haplotypes": [
{
"name": "rs9923231 reference (C)",
"sequences": [
"31096368:C;"
]
}
],
"phased": true,
"variants": [
{
"position": 31096368,
"rsid": "rs9923231",
"vcfCall": "C|C"
}
],
"variantsOfInterest": [],
"matchData": {
"missingPositions": [],
"mismatchedAlleles": []
},
"uncallableHaplotypes": [],
"ignoredHaplotypes": []
}
],
"vcfWarnings": {
"chr8:18400806": [
"Invalid allelic depth (AD) field: 323,332,.,."
]
}
}
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