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SimurgArray/docs/validation/V2_pgx_star_gse165845.json
T
kemal cfae926fbc PGx validation on GSE165845: WGS-derived star truth, 2-fold masks, array-resolvable concordance 
- scripts/pgx/wgs_star_truth.py: star alleles from the 1000G 30x phased panel with the DB definitions
  (wildcard-aware haplotype assignment; checked against GeT-RM on the demo CEPH individuals).
- validate_star_getrm.py: --all-genes, --individuals, --coverage (projection onto what the array can see);
  replicate_concordance.py.
- 120 individuals x 3 GSA v1 arrays: array-resolvable 1637/1710 (95.7 %), top 1223/1800 (chip lacks many
  defining variants), GeT-RM subset 28/35, replicates 99.2 % without the failed array (V2_pgx_star.md, K-029).
2026-09-29 19:00:34 +01:00

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{
"wgs_half_A": {
"individuals": 60,
"genes": {
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"top": 8,
"equivalent": 32,
"array_resolvable_n": 60,
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},
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},
"CYP2A6": {
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},
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},
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},
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},
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},
"CYP3A4": {
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"equivalent": 60,
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"array_resolvable": 60
},
"CYP3A5": {
"n": 60,
"top": 60,
"equivalent": 60,
"array_resolvable_n": 60,
"array_resolvable": 60
},
"CYP4F2": {
"n": 60,
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"array_resolvable": 46
},
"NAT2": {
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"array_resolvable": 60
},
"NUDT15": {
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"array_resolvable_n": 60,
"array_resolvable": 60
},
"SLCO1B1": {
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"array_resolvable_n": 60,
"array_resolvable": 55
},
"TPMT": {
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},
"UGT1A1": {
"n": 60,
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"equivalent": 60,
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"array_resolvable": 22
}
},
"array_resolvable_total": {
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"n": 854
},
"legacy_nomenclature_genes": [],
"total": {
"n": 900,
"top": 602,
"equivalent": 782
},
"discordant": [
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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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{
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},
{
"individual": "HG02010",
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},
{
"individual": "HG02010",
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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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"gene": "CYP1A2",
"truth": "*1/*30",
"call": "*1/*10",
"within_equivalents": true
},
{
"individual": "NA20798",
"gene": "CYP2A6",
"truth": "*1/*18",
"call": "*1/*1",
"within_equivalents": true
},
{
"individual": "NA20798",
"gene": "CYP2C9",
"truth": "*1/*2",
"call": "*1/*1",
"within_equivalents": true
},
{
"individual": "NA20798",
"gene": "CYP2D6",
"truth": "*1/*41",
"call": "*1/*2",
"within_equivalents": false
},
{
"individual": "NA20798",
"gene": "CYP3A4",
"truth": "*1/*1",
"call": "*1/*2",
"within_equivalents": false
},
{
"individual": "NA20798",
"gene": "CYP4F2",
"truth": "*1/*4",
"call": "*1/*3",
"within_equivalents": true
},
{
"individual": "NA20798",
"gene": "SLCO1B1",
"truth": "*1/*14",
"call": "*14/*37",
"within_equivalents": true
},
{
"individual": "NA20798",
"gene": "UGT1A1",
"truth": "*1/*1",
"call": "*1/*28",
"within_equivalents": true
},
{
"individual": "HG02009",
"gene": "CYP1A2",
"truth": "*30/*30",
"call": "*10/*13",
"within_equivalents": false
},
{
"individual": "HG02009",
"gene": "CYP2A13",
"truth": "*1/*8",
"call": "*1/*1",
"within_equivalents": true
},
{
"individual": "HG02009",
"gene": "CYP2D6",
"truth": "*2/*35",
"call": "*1/*2",
"within_equivalents": false
},
{
"individual": "HG02009",
"gene": "CYP4F2",
"truth": "*1/*5",
"call": "*1/*1",
"within_equivalents": false
},
{
"individual": "HG02009",
"gene": "NAT2",
"truth": "*7/*14",
"call": "*4/*7",
"within_equivalents": true
},
{
"individual": "HG02009",
"gene": "SLCO1B1",
"truth": "*1/*27",
"call": "*1/*37",
"within_equivalents": true
},
{
"individual": "HG00242",
"gene": "CYP1A2",
"truth": "*30/*30",
"call": "*10/*13",
"within_equivalents": false
},
{
"individual": "HG00242",
"gene": "SLCO1B1",
"truth": "*1/*15",
"call": "*15/*37",
"within_equivalents": true
},
{
"individual": "HG01500",
"gene": "CYP4F2",
"truth": "*4/*4",
"call": "*3/*3",
"within_equivalents": true
},
{
"individual": "HG01500",
"gene": "TPMT",
"truth": "*1/*3A",
"call": "*1/*3C",
"within_equivalents": true
},
{
"individual": "HG01500",
"gene": "UGT1A1",
"truth": "*1/*1",
"call": "*1/*28",
"within_equivalents": true
},
{
"individual": "HG02941",
"gene": "CYP1A2",
"truth": "*1/*30",
"call": "*1/*10",
"within_equivalents": true
},
{
"individual": "HG02941",
"gene": "CYP2A13",
"truth": "*1/*2",
"call": "*1/*10",
"within_equivalents": true
},
{
"individual": "HG02941",
"gene": "CYP2C9",
"truth": "*1/*8",
"call": "*1/*1",
"within_equivalents": false
},
{
"individual": "HG02941",
"gene": "CYP2D6",
"truth": "*1/*29",
"call": "*1/*2",
"within_equivalents": false
},
{
"individual": "HG02941",
"gene": "NAT2",
"truth": "*4/*14",
"call": "*4/*4",
"within_equivalents": true
},
{
"individual": "HG02941",
"gene": "UGT1A1",
"truth": "*36/*36",
"call": "*1/*28",
"within_equivalents": true
},
{
"individual": "HG01771",
"gene": "CYP1A2",
"truth": "*1/*30",
"call": "*1/*10",
"within_equivalents": true
},
{
"individual": "HG01771",
"gene": "CYP2C19",
"truth": "*1/*38",
"call": "*1/*1",
"within_equivalents": false
},
{
"individual": "HG01771",
"gene": "CYP2C9",
"truth": "*2/*3",
"call": "*1/*3",
"within_equivalents": false
},
{
"individual": "HG01771",
"gene": "CYP2D6",
"truth": "*1/*4",
"call": "*1/*2",
"within_equivalents": false
},
{
"individual": "HG01771",
"gene": "CYP4F2",
"truth": "*4/*4",
"call": "*3/*3",
"within_equivalents": true
},
{
"individual": "HG01771",
"gene": "UGT1A1",
"truth": "*1/*1",
"call": "*1/*28",
"within_equivalents": true
},
{
"individual": "HG02282",
"gene": "CYP1A2",
"truth": "*30/*30",
"call": "*10/*13",
"within_equivalents": false
},
{
"individual": "HG02282",
"gene": "CYP2A6",
"truth": "*17/*23",
"call": "*1/*17",
"within_equivalents": true
},
{
"individual": "HG02282",
"gene": "CYP2D6",
"truth": "*10/*17",
"call": "*1/*17",
"within_equivalents": true
},
{
"individual": "HG02282",
"gene": "CYP4F2",
"truth": "*1/*4",
"call": "*1/*3",
"within_equivalents": true
},
{
"individual": "HG02282",
"gene": "NAT2",
"truth": "*4/*33",
"call": "*4/*5",
"within_equivalents": false
},
{
"individual": "HG02282",
"gene": "SLCO1B1",
"truth": "*20/*27",
"call": "*20/*37",
"within_equivalents": false
},
{
"individual": "HG02282",
"gene": "UGT1A1",
"truth": "*1/*36",
"call": "*1/*28",
"within_equivalents": true
},
{
"individual": "NA20359",
"gene": "CYP2A6",
"truth": "*9/*26",
"call": "*1/*15",
"within_equivalents": false
},
{
"individual": "NA20359",
"gene": "CYP2C9",
"truth": "*1/*2",
"call": "*1/*1",
"within_equivalents": true
},
{
"individual": "NA20359",
"gene": "CYP2D6",
"truth": "*2/*4",
"call": "*1/*2",
"within_equivalents": false
},
{
"individual": "NA20359",
"gene": "CYP4F2",
"truth": "*2/*4",
"call": "*1/*3",
"within_equivalents": false
},
{
"individual": "NA20359",
"gene": "UGT1A1",
"truth": "*36/*80+*28",
"call": "*1/*80",
"within_equivalents": true
},
{
"individual": "NA20822",
"gene": "CYP1A2",
"truth": "*30/*30",
"call": "*10/*13",
"within_equivalents": false
},
{
"individual": "NA20822",
"gene": "CYP2D6",
"truth": "*4/*41",
"call": "*41/*41",
"within_equivalents": false
},
{
"individual": "NA20822",
"gene": "TPMT",
"truth": "*1/*2",
"call": "*1/*1",
"within_equivalents": true
},
{
"individual": "HG00101",
"gene": "CYP1A2",
"truth": "*1/*30",
"call": "*1/*10",
"within_equivalents": true
},
{
"individual": "HG00101",
"gene": "CYP2D6",
"truth": "*2/*41",
"call": "*1/*2",
"within_equivalents": false
},
{
"individual": "HG00101",
"gene": "SLCO1B1",
"truth": "*1/*15",
"call": "*15/*37",
"within_equivalents": true
},
{
"individual": "HG00101",
"gene": "UGT1A1",
"truth": "*1/*1",
"call": "*1/*28",
"within_equivalents": true
},
{
"individual": "HG00108",
"gene": "CYP1A2",
"truth": "*30/*30",
"call": "*10/*13",
"within_equivalents": false
},
{
"individual": "HG00108",
"gene": "SLCO1B1",
"truth": "*1/*1",
"call": "*1/*37",
"within_equivalents": true
},
{
"individual": "HG00108",
"gene": "TPMT",
"truth": "*1/*3A",
"call": "*1/*3C",
"within_equivalents": true
},
{
"individual": "HG00108",
"gene": "UGT1A1",
"truth": "*1/*1",
"call": "*1/*28",
"within_equivalents": true
},
{
"individual": "HG01781",
"gene": "CYP1A2",
"truth": "*30/*30",
"call": "*10/*13",
"within_equivalents": false
},
{
"individual": "HG01781",
"gene": "CYP2D6",
"truth": "*2/*35",
"call": "*1/*2",
"within_equivalents": false
},
{
"individual": "HG01781",
"gene": "CYP4F2",
"truth": "*1/*4",
"call": "*1/*3",
"within_equivalents": true
},
{
"individual": "HG01781",
"gene": "SLCO1B1",
"truth": "*1/*1",
"call": "*1/*37",
"within_equivalents": true
},
{
"individual": "NA12878",
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"truth": "*30/*30",
"call": "*10/*13",
"within_equivalents": false
},
{
"individual": "NA12878",
"gene": "CYP2C9",
"truth": "*1/*2",
"call": "*1/*1",
"within_equivalents": true
},
{
"individual": "NA12878",
"gene": "CYP2D6",
"truth": "*3/*4",
"call": "*1/*2",
"within_equivalents": false
},
{
"individual": "NA12878",
"gene": "SLCO1B1",
"truth": "*1/*15",
"call": "*15/*37",
"within_equivalents": true
},
{
"individual": "HG00268",
"gene": "CYP1A2",
"truth": "*1/*30",
"call": "*1/*10",
"within_equivalents": true
}
]
},
"getrm_half_B": {
"individuals": 60,
"genes": {
"CYP1A2": {
"n": 2,
"top": 0,
"equivalent": 0
},
"CYP2A6": {
"n": 2,
"top": 2,
"equivalent": 2,
"array_resolvable_n": 2,
"array_resolvable": 2
},
"CYP2B6": {
"n": 2,
"top": 2,
"equivalent": 2,
"array_resolvable_n": 2,
"array_resolvable": 2
},
"CYP2C19": {
"n": 2,
"top": 2,
"equivalent": 2,
"array_resolvable_n": 2,
"array_resolvable": 2
},
"CYP2C8": {
"n": 2,
"top": 2,
"equivalent": 2,
"array_resolvable_n": 2,
"array_resolvable": 2
},
"CYP2C9": {
"n": 2,
"top": 1,
"equivalent": 2,
"array_resolvable_n": 2,
"array_resolvable": 2
},
"CYP2D6": {
"n": 4,
"top": 0,
"equivalent": 0,
"array_resolvable_n": 3,
"array_resolvable": 3
},
"CYP3A4": {
"n": 2,
"top": 2,
"equivalent": 2,
"array_resolvable_n": 1,
"array_resolvable": 1
},
"CYP3A5": {
"n": 2,
"top": 2,
"equivalent": 2,
"array_resolvable_n": 2,
"array_resolvable": 2
},
"CYP4F2": {
"n": 2,
"top": 2,
"equivalent": 2,
"array_resolvable_n": 2,
"array_resolvable": 2
},
"NAT2": {
"n": 2,
"top": 1,
"equivalent": 1,
"array_resolvable_n": 2,
"array_resolvable": 1
},
"SLCO1B1": {
"n": 2,
"top": 0,
"equivalent": 2,
"array_resolvable_n": 2,
"array_resolvable": 2
},
"TPMT": {
"n": 3,
"top": 2,
"equivalent": 2,
"array_resolvable_n": 3,
"array_resolvable": 3
},
"UGT1A1": {
"n": 2,
"top": 0,
"equivalent": 1,
"array_resolvable_n": 1,
"array_resolvable": 0
},
"VKORC1": {
"n": 2,
"top": 2,
"equivalent": 2
}
},
"array_resolvable_total": {
"concordant": 20,
"n": 21
},
"legacy_nomenclature_genes": [
"CYP1A2",
"CYP2C8",
"SLCO1B1",
"UGT1A1"
],
"total": {
"n": 25,
"top": 18,
"equivalent": 19
},
"discordant": [
{
"individual": "NA20803",
"gene": "CYP2D6",
"truth": "*2/*22",
"call": "*1/*22",
"within_equivalents": false
},
{
"individual": "HG00111",
"gene": "CYP2D6",
"truth": "*3/*3",
"call": "*1/*2",
"within_equivalents": false
},
{
"individual": "HG03521",
"gene": "TPMT",
"truth": "*1/*46",
"call": "*1/*1",
"within_equivalents": false
},
{
"individual": "NA12878",
"gene": "CYP1A2",
"truth": "*1F/*1F",
"call": "*10/*13",
"within_equivalents": false
},
{
"individual": "NA12878",
"gene": "CYP2C9",
"truth": "*1/*2",
"call": "*1/*1",
"within_equivalents": true
},
{
"individual": "NA12878",
"gene": "CYP2D6",
"truth": "*3/(*68)+*4",
"call": "*1/*2",
"within_equivalents": false
},
{
"individual": "NA12878",
"gene": "SLCO1B1",
"truth": "*1/*15",
"call": "*15/*37",
"within_equivalents": true
},
{
"individual": "NA12878",
"gene": "UGT1A1",
"truth": "*60/*28",
"call": "*1/*80",
"within_equivalents": false
},
{
"individual": "NA19239",
"gene": "CYP1A2",
"truth": "*1A/*1L,*1C/*1F",
"call": "*1/*10",
"within_equivalents": false
},
{
"individual": "NA19239",
"gene": "CYP2D6",
"truth": "*15/*17",
"call": "*1/*17",
"within_equivalents": false
},
{
"individual": "NA19239",
"gene": "NAT2",
"truth": "(*4)/*14",
"call": "*1/*4",
"within_equivalents": false
},
{
"individual": "NA19239",
"gene": "SLCO1B1",
"truth": "*1/*1",
"call": "*1/*37",
"within_equivalents": true
},
{
"individual": "NA19239",
"gene": "UGT1A1",
"truth": "(*28 + *60)/(*37 + *60)",
"call": "*80/*80",
"within_equivalents": true
}
]
},
"replicates_half_B": {
"pairs_by_gene": {
"ABCG2": {
"concordant": 180,
"pairs": 180
},
"ACE": {
"concordant": 180,
"pairs": 180
},
"ADD1": {
"concordant": 180,
"pairs": 180
},
"ADH1B": {
"concordant": 162,
"pairs": 180
},
"ADRB2": {
"concordant": 180,
"pairs": 180
},
"ALDH2": {
"concordant": 180,
"pairs": 180
},
"ANKK1": {
"concordant": 180,
"pairs": 180
},
"APOE": {
"concordant": 180,
"pairs": 180
},
"ATIC": {
"concordant": 180,
"pairs": 180
},
"ATM": {
"concordant": 180,
"pairs": 180
},
"BDNF": {
"concordant": 178,
"pairs": 180
},
"CACNA1C": {
"concordant": 180,
"pairs": 180
},
"CACNA1S": {
"concordant": 180,
"pairs": 180
},
"CES1": {
"concordant": 180,
"pairs": 180
},
"CFTR": {
"concordant": 180,
"pairs": 180
},
"CHRNA5": {
"concordant": 180,
"pairs": 180
},
"COMT": {
"concordant": 178,
"pairs": 180
},
"CYP1A2": {
"concordant": 180,
"pairs": 180
},
"CYP2A13": {
"concordant": 180,
"pairs": 180
},
"CYP2A6": {
"concordant": 180,
"pairs": 180
},
"CYP2B6": {
"concordant": 178,
"pairs": 180
},
"CYP2C19": {
"concordant": 158,
"pairs": 180
},
"CYP2C8": {
"concordant": 180,
"pairs": 180
},
"CYP2C9": {
"concordant": 176,
"pairs": 180
},
"CYP2D6": {
"concordant": 170,
"pairs": 180
},
"CYP3A4": {
"concordant": 164,
"pairs": 180
},
"CYP3A5": {
"concordant": 180,
"pairs": 180
},
"CYP4F2": {
"concordant": 180,
"pairs": 180
},
"DPYD": {
"concordant": 180,
"pairs": 180
},
"DRD2": {
"concordant": 172,
"pairs": 180
},
"EGFR": {
"concordant": 180,
"pairs": 180
},
"F13A1": {
"concordant": 180,
"pairs": 180
},
"F2": {
"concordant": 180,
"pairs": 180
},
"F5": {
"concordant": 180,
"pairs": 180
},
"FCGR3A": {
"concordant": 180,
"pairs": 180
},
"FKBP5": {
"concordant": 180,
"pairs": 180
},
"G6PD": {
"concordant": 180,
"pairs": 180
},
"GRIK1": {
"concordant": 180,
"pairs": 180
},
"GRIK4": {
"concordant": 180,
"pairs": 180
},
"GRIN2B": {
"concordant": 180,
"pairs": 180
},
"HLA-A": {
"concordant": 180,
"pairs": 180
},
"HLA-B": {
"concordant": 180,
"pairs": 180
},
"HMGCR": {
"concordant": 178,
"pairs": 180
},
"HTR2A": {
"concordant": 180,
"pairs": 180
},
"HTR2C": {
"concordant": 180,
"pairs": 180
},
"IFNL3": {
"concordant": 180,
"pairs": 180
},
"IFNL4": {
"concordant": 180,
"pairs": 180
},
"IL6": {
"concordant": 180,
"pairs": 180
},
"ITGB3": {
"concordant": 180,
"pairs": 180
},
"ITPA": {
"concordant": 180,
"pairs": 180
},
"KIF6": {
"concordant": 180,
"pairs": 180
},
"LPA": {
"concordant": 180,
"pairs": 180
},
"MT-RNR1": {
"concordant": 180,
"pairs": 180
},
"MTHFR": {
"concordant": 180,
"pairs": 180
},
"NAT2": {
"concordant": 180,
"pairs": 180
},
"NUDT15": {
"concordant": 180,
"pairs": 180
},
"OPRD1": {
"concordant": 178,
"pairs": 180
},
"OPRK1": {
"concordant": 180,
"pairs": 180
},
"OPRM1": {
"concordant": 180,
"pairs": 180
},
"RYR1": {
"concordant": 180,
"pairs": 180
},
"SCN1A": {
"concordant": 180,
"pairs": 180
},
"SLC19A1": {
"concordant": 180,
"pairs": 180
},
"SLC28A3": {
"concordant": 180,
"pairs": 180
},
"SLCO1B1": {
"concordant": 180,
"pairs": 180
},
"TNF": {
"concordant": 180,
"pairs": 180
},
"TPMT": {
"concordant": 171,
"pairs": 180
},
"UGT1A1": {
"concordant": 180,
"pairs": 180
},
"VKORC1": {
"concordant": 180,
"pairs": 180
},
"XRCC1": {
"concordant": 180,
"pairs": 180
},
"YEATS4": {
"concordant": 180,
"pairs": 180
}
},
"total": {
"concordant": 12503,
"pairs": 12600,
"rate": 0.9923
}
}
}
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