kemal
dfba22496a
fetch_sources.sh downloads PharmVar per-gene zips; pgx db build adds core alleles for genes CPIC does not define (normalised against the FASTA, *1 = reference). Masks re-derived with the new variants. GeT-RM: CYP3A4 15/15, CYP2A6 7/9; all comparable genes 154/168 (CYP1A2/CYP2C8 definitions differ from GeT-RM's).
429 lines
7.3 KiB
JSON
429 lines
7.3 KiB
JSON
{
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"individuals": 30,
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"genes": {
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"CYP1A2": {
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"n": 9,
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"top": 0,
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"equivalent": 0
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},
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"CYP2A6": {
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"n": 9,
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"top": 7,
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"equivalent": 8
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},
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"CYP2B6": {
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"n": 14,
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"top": 12,
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"equivalent": 12,
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"not_comparable": 1
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},
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"CYP2C19": {
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"n": 15,
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"top": 14,
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"equivalent": 15
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},
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"CYP2C8": {
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"n": 15,
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"top": 8,
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"equivalent": 9
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},
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"CYP2C9": {
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"n": 15,
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"top": 15,
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"equivalent": 15
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},
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"CYP2D6": {
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"n": 15,
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"top": 13,
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"equivalent": 15
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},
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"CYP3A4": {
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"n": 15,
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"top": 15,
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"equivalent": 15
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},
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"CYP3A5": {
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"n": 15,
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"top": 15,
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"equivalent": 15
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},
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"CYP4F2": {
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"n": 9,
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"top": 8,
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"equivalent": 8
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},
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"GSTM1": {
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"n": 9,
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"top": 9,
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"equivalent": 9
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},
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"GSTT1": {
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"n": 9,
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"top": 7,
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"equivalent": 7
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},
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"NAT2": {
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"n": 9,
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"top": 8,
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"equivalent": 8
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},
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"NUDT15": {
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"n": 1,
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"top": 1,
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"equivalent": 1
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},
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"SLCO1B1": {
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"n": 15,
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"top": 9,
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"equivalent": 9
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},
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"TPMT": {
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"n": 16,
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"top": 15,
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"equivalent": 15
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},
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"UGT1A1": {
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"n": 9,
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"top": 0,
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"equivalent": 1
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},
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"UGT2B17": {
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"n": 2,
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"top": 2,
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"equivalent": 2
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},
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"VKORC1": {
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"n": 15,
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"top": 13,
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"equivalent": 13
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}
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},
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"legacy_nomenclature_genes": [
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"CYP1A2",
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"CYP2C8",
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"SLCO1B1",
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"UGT1A1"
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],
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"total": {
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"n": 168,
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"top": 154,
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"equivalent": 158
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},
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"discordant": [
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{
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"individual": "NA12156",
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"gene": "CYP1A2",
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"truth": "*1A/*1F",
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"call": "*1/*15",
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"within_equivalents": false
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},
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{
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"individual": "NA12156",
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"gene": "CYP2C8",
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"truth": "*1/*15",
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"call": "*1/*1",
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"within_equivalents": true
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},
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{
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"individual": "NA12156",
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"gene": "CYP4F2",
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"truth": "(*2)/*3",
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"call": "*1/*3",
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"within_equivalents": false
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},
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{
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"individual": "NA12156",
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"gene": "SLCO1B1",
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"truth": "*1/*21",
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"call": "*1/*37",
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"within_equivalents": false
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},
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{
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"individual": "NA12156",
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"gene": "UGT1A1",
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"truth": "*60/*28",
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"call": "*28/*80",
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"within_equivalents": false
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},
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{
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"individual": "NA12044",
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"gene": "TPMT",
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"truth": "*1/*21",
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"call": "*1/*1",
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"within_equivalents": false
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},
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{
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"individual": "NA07019",
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"gene": "CYP1A2",
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"truth": "*1A/*1F",
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"call": "*1/*15",
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"within_equivalents": false
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},
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{
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"individual": "NA07019",
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"gene": "CYP2C8",
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"truth": "*1/*1",
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"call": "*1/*19",
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"within_equivalents": false
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},
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{
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"individual": "NA07019",
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"gene": "UGT1A1",
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"truth": "*1/*60",
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"call": "*1/*1",
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"within_equivalents": false
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},
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{
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"individual": "NA06991",
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"gene": "CYP1A2",
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"truth": "*1F/*1F",
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"call": "*15/*24",
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"within_equivalents": false
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},
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{
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"individual": "NA06991",
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"gene": "UGT1A1",
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"truth": "*60/*60",
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"call": "*1/*1",
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"within_equivalents": false
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},
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{
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"individual": "NA06991",
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"gene": "VKORC1",
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"truth": "AA",
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"call": "rs9923231 T/T",
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"within_equivalents": false
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},
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{
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"individual": "NA12878",
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"gene": "CYP1A2",
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"truth": "*1F/*1F",
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"call": "*15/*24",
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"within_equivalents": false
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},
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{
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"individual": "NA12878",
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"gene": "UGT1A1",
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"truth": "*60/*28",
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"call": "*28/*80",
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"within_equivalents": false
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},
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{
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"individual": "NA11993",
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"gene": "CYP1A2",
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"truth": "*1F/*1F",
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"call": "*15/*24",
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"within_equivalents": false
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},
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{
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"individual": "NA11993",
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"gene": "CYP2A6",
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"truth": "*9/*17",
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"call": "*15/*17",
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"within_equivalents": true
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},
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{
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"individual": "NA11993",
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"gene": "SLCO1B1",
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"truth": "*1/*17",
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"call": "*1/*15",
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"within_equivalents": false
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},
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{
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"individual": "NA11993",
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"gene": "UGT1A1",
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"truth": "(*28 + *60)/*60",
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"call": "*28/*80",
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"within_equivalents": false
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},
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{
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"individual": "NA12003",
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"gene": "CYP1A2",
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"truth": "*1A/*1F",
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"call": "*15/*24",
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"within_equivalents": false
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},
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{
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"individual": "NA12003",
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"gene": "CYP2A6",
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"truth": "*1/(*8)",
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"call": "*1/*1",
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"within_equivalents": false
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},
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{
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"individual": "NA12003",
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"gene": "UGT1A1",
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"truth": "*60/*28",
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"call": "*28/*80",
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"within_equivalents": false
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},
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{
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"individual": "NA12003",
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"gene": "VKORC1",
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"truth": "AA",
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"call": "rs9923231 T/T",
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"within_equivalents": false
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},
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{
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"individual": "NA12003",
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"gene": "GSTT1",
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"truth": "(*A/*A)",
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"call": "*1/*0",
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"within_equivalents": false
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},
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{
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"individual": "NA07029",
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"gene": "CYP1A2",
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"truth": "*1A/*1F",
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"call": "*1/*15",
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"within_equivalents": false
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},
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{
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"individual": "NA07029",
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"gene": "CYP2B6",
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"truth": "*6/(*27)",
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"call": "*1/*6",
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"within_equivalents": false
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},
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{
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"individual": "NA07029",
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"gene": "CYP2C19",
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"truth": "*8/*17",
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"call": "*1/*17",
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"within_equivalents": true
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},
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{
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"individual": "NA07029",
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"gene": "CYP2C8",
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"truth": "*1/*3",
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"call": "*19/*3",
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"within_equivalents": false
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},
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{
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"individual": "NA07029",
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"gene": "UGT1A1",
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"truth": "*1/*1",
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"call": "*1/*28",
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"within_equivalents": true
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},
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{
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"individual": "NA12892",
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"gene": "CYP2B6",
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"truth": "*1/*1",
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"call": "*1/*5",
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"within_equivalents": false
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},
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{
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"individual": "NA10846",
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"gene": "CYP2C8",
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"truth": "*1/*1",
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"call": "*1/*19",
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"within_equivalents": false
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},
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{
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"individual": "NA07000",
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"gene": "CYP2C8",
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"truth": "*1/*1",
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"call": "*1/*19",
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"within_equivalents": false
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},
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{
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"individual": "NA11832",
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"gene": "CYP1A2",
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"truth": "*1F/*1F",
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"call": "*15/*24",
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"within_equivalents": false
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},
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{
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"individual": "NA11832",
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"gene": "NAT2",
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"truth": "*5/(*12)",
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"call": "*1/*5",
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"within_equivalents": false
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},
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{
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"individual": "NA11832",
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"gene": "SLCO1B1",
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"truth": "*1/*1",
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"call": "*14/*20",
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"within_equivalents": false
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},
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{
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"individual": "NA11832",
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"gene": "UGT1A1",
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"truth": "(*28 + *60)/*60",
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"call": "*28/*80",
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"within_equivalents": false
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},
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{
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"individual": "NA10838",
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"gene": "CYP2D6",
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"truth": "*2/*4",
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"call": "*1/*4;*2/*4",
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"within_equivalents": true
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},
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{
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"individual": "NA10838",
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"gene": "SLCO1B1",
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"truth": "*1/*1",
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"call": "*1/*14",
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"within_equivalents": false
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},
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{
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"individual": "NA12813",
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"gene": "CYP1A2",
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"truth": "*1F/*1L",
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"call": "*15/*24",
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"within_equivalents": false
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},
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{
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"individual": "NA12813",
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"gene": "CYP2C8",
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"truth": "*1/*1",
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"call": "*1/*19",
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"within_equivalents": false
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},
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{
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"individual": "NA12813",
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"gene": "CYP2D6",
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"truth": "*2/*4",
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"call": "*1/*4;*2/*4",
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"within_equivalents": true
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},
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{
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"individual": "NA12813",
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"gene": "SLCO1B1",
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"truth": "*1/*21",
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"call": "*1/*20",
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"within_equivalents": false
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},
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{
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"individual": "NA12813",
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"gene": "UGT1A1",
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"truth": "(*28 + *60)/(*28 + *60)",
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"call": "*80/*80",
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"within_equivalents": false
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},
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{
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"individual": "NA12813",
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"gene": "GSTT1",
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"truth": "(*A/*A)",
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"call": "*1/*0",
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"within_equivalents": false
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},
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{
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"individual": "NA11881",
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"gene": "CYP2C8",
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"truth": "*1/*1",
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"call": "*1/*19",
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"within_equivalents": false
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},
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{
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"individual": "NA11881",
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"gene": "SLCO1B1",
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"truth": "*1/(*15)",
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"call": "*14/*15",
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"within_equivalents": false
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}
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]
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} |