From 83e9c1cfd511f401716216a752feed1f5f7f8481 Mon Sep 17 00:00:00 2001 From: Jody Phelan Date: Wed, 17 Jul 2024 09:39:37 +0100 Subject: [PATCH] update db --- db/tbdb.bed | 58 +++++++++++++++++++++--------------------- db/tbdb.dr.json | 2 +- db/tbdb.variables.json | 46 ++++++++++++++++++++++++++++++++- 3 files changed, 75 insertions(+), 31 deletions(-) diff --git a/db/tbdb.bed b/db/tbdb.bed index 1797ff4..65b8112 100644 --- a/db/tbdb.bed +++ b/db/tbdb.bed @@ -2,66 +2,66 @@ Chromosome 1 1524 Rv0001 dnaA isoniazid Chromosome 4933 7267 Rv0005 gyrB levofloxacin,moxifloxacin Chromosome 7068 9818 Rv0006 gyrA levofloxacin,moxifloxacin Chromosome 13133 13911 Rv0010c Rv0010c isoniazid -Chromosome 490545 491793 Rv0407 fgd1 clofazimine,pretomanid,delamanid -Chromosome 574479 576790 Rv0486 mshA ethionamide,isoniazid -Chromosome 619500 620865 Rv0529 ccsA capreomycin,amikacin,kanamycin +Chromosome 490545 491793 Rv0407 fgd1 pretomanid,delamanid,clofazimine +Chromosome 574479 576790 Rv0486 mshA isoniazid,ethionamide +Chromosome 619500 620865 Rv0529 ccsA kanamycin,capreomycin,amikacin Chromosome 656010 657739 Rv0565c Rv0565c ethionamide Chromosome 731680 732406 Rv0635 hadA isoniazid Chromosome 733853 734970 Rv0639 nusG rifampicin +Chromosome 737268 738349 Rv0643c mmaA3 isoniazid Chromosome 759342 763325 Rv0667 rpoB rifampicin Chromosome 763127 767320 Rv0668 rpoC rifampicin -Chromosome 775586 778680 Rv0676c mmpL5 clofazimine,bedaquiline -Chromosome 778477 779624 Rv0677c mmpS5 clofazimine,bedaquiline -Chromosome 778790 779487 Rv0678 mmpR5 clofazimine,bedaquiline +Chromosome 775586 778680 Rv0676c mmpL5 bedaquiline,clofazimine +Chromosome 778477 779624 Rv0677c mmpS5 bedaquiline,clofazimine +Chromosome 778790 779487 Rv0678 mmpR5 bedaquiline,clofazimine Chromosome 781126 781934 Rv0682 rpsL streptomycin Chromosome 800106 801462 Rv0701 rplC linezolid -Chromosome 1253074 1254783 Rv1129c Rv1129c moxifloxacin,levofloxacin,rifampicin,isoniazid -Chromosome 1302606 1305501 Rv1173 fbiC clofazimine,pretomanid,delamanid +Chromosome 1253074 1254783 Rv1129c Rv1129c levofloxacin,moxifloxacin,isoniazid,rifampicin +Chromosome 1302606 1305501 Rv1173 fbiC pretomanid,delamanid,clofazimine Chromosome 1364162 1365186 Rv1221 sigE pyrazinamide -Chromosome 1406081 1407604 Rv1258c Rv1258c streptomycin,isoniazid,pyrazinamide +Chromosome 1406081 1407604 Rv1258c Rv1258c streptomycin,pyrazinamide,isoniazid Chromosome 1416181 1418048 Rv1267c embR ethambutol Chromosome 1460802 1461290 Rv1305 atpE bedaquiline -Chromosome 1471498 1473382 EBG00000313325 rrs streptomycin,kanamycin,capreomycin,amikacin +Chromosome 1471498 1473382 EBG00000313325 rrs kanamycin,capreomycin,streptomycin,amikacin Chromosome 1473408 1476795 EBG00000313339 rrl capreomycin,linezolid -Chromosome 1673148 1674183 Rv1483 fabG1 ethionamide,isoniazid -Chromosome 1673189 1675011 Rv1484 inhA ethionamide,isoniazid +Chromosome 1673148 1675011 Rv1484 inhA isoniazid,ethionamide Chromosome 1833247 1834987 Rv1630 rpsA pyrazinamide Chromosome 1853358 1854388 Rv1644 tsnR linezolid Chromosome 1917506 1918746 Rv1694 tlyA capreomycin -Chromosome 2062809 2065010 Rv1819c bacA streptomycin,kanamycin,capreomycin,amikacin -Chromosome 2101651 2103337 Rv1854c ndh ethionamide,delamanid,isoniazid +Chromosome 2062809 2065010 Rv1819c bacA kanamycin,capreomycin,streptomycin,amikacin +Chromosome 2101651 2103337 Rv1854c ndh isoniazid,delamanid,ethionamide Chromosome 2153889 2156842 Rv1908c katG isoniazid Chromosome 2167649 2170934 Rv1918c PPE35 pyrazinamide -Chromosome 2221719 2223825 Rv1979c Rv1979c clofazimine,bedaquiline +Chromosome 2221719 2223825 Rv1979c Rv1979c bedaquiline,clofazimine Chromosome 2288681 2290323 Rv2043c pncA pyrazinamide Chromosome 2517915 2519365 Rv2245 kasA isoniazid -Chromosome 2714124 2715832 Rv2416c eis amikacin,kanamycin +Chromosome 2714124 2715832 Rv2416c eis kanamycin,amikacin Chromosome 2725899 2726780 Rv2428 ahpC isoniazid Chromosome 2746135 2747798 Rv2447c folC para-aminosalicylic_acid -Chromosome 2782366 2786169 Rv2477c Rv2477c ethambutol,moxifloxacin,streptomycin,levofloxacin,kanamycin,rifampicin,amikacin -Chromosome 2859300 2860640 Rv2535c pepQ clofazimine,bedaquiline +Chromosome 2782366 2786169 Rv2477c Rv2477c kanamycin,levofloxacin,moxifloxacin,streptomycin,rifampicin,ethambutol,amikacin +Chromosome 2859300 2860640 Rv2535c pepQ bedaquiline,clofazimine Chromosome 2986639 2987615 Rv2671 ribD para-aminosalicylic_acid Chromosome 2995772 2996737 Rv2680 Rv2680 capreomycin Chromosome 2996539 2998055 Rv2681 Rv2681 capreomycin -Chromosome 3064515 3067372 Rv2752c Rv2752c ethambutol,moxifloxacin,levofloxacin,rifampicin,isoniazid +Chromosome 3064515 3067372 Rv2752c Rv2752c levofloxacin,moxifloxacin,isoniazid,rifampicin,ethambutol Chromosome 3067193 3068161 Rv2754c thyX para-aminosalicylic_acid Chromosome 3073680 3074671 Rv2764c thyA para-aminosalicylic_acid Chromosome 3086620 3087935 Rv2780 ald cycloserine -Chromosome 3338868 3339762 Rv2983 fbiD clofazimine,pretomanid,delamanid +Chromosome 3338868 3339762 Rv2983 fbiD pretomanid,delamanid,clofazimine Chromosome 3448253 3449991 Rv3083 Rv3083 ethionamide -Chromosome 3568401 3569280 Rv3197A whiB7 streptomycin,amikacin,kanamycin +Chromosome 3568401 3569280 Rv3197A whiB7 kanamycin,amikacin,streptomycin Chromosome 3611959 3613847 Rv3236c Rv3236c pyrazinamide -Chromosome 3623159 3625110 Rv3244c lpqB bedaquiline,rifampicin -Chromosome 3624910 3626860 Rv3245c mtrB bedaquiline,rifampicin -Chromosome 3626663 3627924 Rv3246c mtrA bedaquiline,rifampicin -Chromosome 3640207 3641538 Rv3261 fbiA clofazimine,pretomanid,delamanid -Chromosome 3641335 3642881 Rv3262 fbiB clofazimine,pretomanid,delamanid +Chromosome 3623159 3625110 Rv3244c lpqB rifampicin,bedaquiline +Chromosome 3624910 3626860 Rv3245c mtrB rifampicin,bedaquiline +Chromosome 3626663 3627924 Rv3246c mtrA rifampicin,bedaquiline +Chromosome 3640207 3641538 Rv3261 fbiA pretomanid,delamanid,clofazimine +Chromosome 3641335 3642881 Rv3262 fbiB pretomanid,delamanid,clofazimine Chromosome 3840194 3841620 Rv3423c alr cycloserine Chromosome 3877464 3879240 Rv3457c rpoA rifampicin -Chromosome 3986612 3987299 Rv3547 ddn delamanid,pretomanid +Chromosome 3986612 3987299 Rv3547 ddn pretomanid,delamanid Chromosome 4038158 4041013 Rv3596c clpC1 pyrazinamide Chromosome 4043862 4046428 Rv3601c panD pyrazinamide -Chromosome 4138202 4140002 Rv3696c glpK ethambutol,moxifloxacin,streptomycin,levofloxacin,rifampicin,isoniazid +Chromosome 4138202 4140002 Rv3696c glpK levofloxacin,moxifloxacin,isoniazid,streptomycin,rifampicin,ethambutol Chromosome 4237683 4243147 Rv3793 embC ethambutol Chromosome 4242947 4246517 Rv3794 embA ethambutol Chromosome 4246314 4249810 Rv3795 embB ethambutol @@ -69,5 +69,5 @@ Chromosome 4266953 4269124 Rv3805c aftB ethambutol Chromosome 4268925 4270084 Rv3806c ubiA ethambutol Chromosome 4326004 4330174 Rv3854c ethA ethionamide Chromosome 4327328 4328199 Rv3855 ethR ethionamide -Chromosome 4338171 4338961 Rv3862c whiB6 capreomycin,amikacin,kanamycin +Chromosome 4338171 4338961 Rv3862c whiB6 kanamycin,capreomycin,amikacin Chromosome 4407528 4408481 Rv3919c gid streptomycin diff --git a/db/tbdb.dr.json b/db/tbdb.dr.json index c331c96..0af4a55 100644 --- a/db/tbdb.dr.json +++ b/db/tbdb.dr.json @@ -1 +1 @@ -{"Rv1819c": {"c.102G>A": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.102G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.102G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2064627], "chromosome": "Chromosome"}, "c.1044G>A": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1044G>A", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.1044G>A", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.1044G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "streptomycin", "original_mutation": "c.1044G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063685], "chromosome": "Chromosome"}, "c.105C>G": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.105C>G", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.105C>G", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.105C>G", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2064624], "chromosome": "Chromosome"}, "c.1065T>G": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1065T>G", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.1065T>G", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.1065T>G", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "streptomycin", "original_mutation": "c.1065T>G", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063664], "chromosome": "Chromosome"}, "c.1080G>A": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1080G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.1080G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.1080G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "streptomycin", "original_mutation": "c.1080G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063649], "chromosome": "Chromosome"}, "c.1140G>A": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1140G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.1140G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.1140G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063589], "chromosome": "Chromosome"}, "c.1170G>A": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1170G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.1170G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.1170G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "streptomycin", "original_mutation": "c.1170G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063559], "chromosome": "Chromosome"}, "c.1194C>T": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1194C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.1194C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.1194C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "streptomycin", "original_mutation": "c.1194C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063535], "chromosome": "Chromosome"}, "c.1210C>T": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1210C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.1210C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.1210C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063519], "chromosome": "Chromosome"}, "c.1212G>A": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1212G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.1212G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.1212G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063517], "chromosome": "Chromosome"}, "c.1212G>C": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1212G>C", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.1212G>C", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.1212G>C", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063517], "chromosome": "Chromosome"}, "c.1242G>A": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1242G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.1242G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.1242G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "streptomycin", "original_mutation": "c.1242G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063487], "chromosome": "Chromosome"}, "c.129T>C": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.129T>C", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.129T>C", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.129T>C", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "streptomycin", "original_mutation": "c.129T>C", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2064600], "chromosome": "Chromosome"}, "c.1317C>T": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1317C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.1317C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "streptomycin", "original_mutation": "c.1317C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063412], "chromosome": "Chromosome"}, "c.1323G>C": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1323G>C", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.1323G>C", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063406], "chromosome": "Chromosome"}, "c.1348C>T": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1348C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.1348C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.1348C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "streptomycin", "original_mutation": "c.1348C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063381], "chromosome": "Chromosome"}, "c.135G>A": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.135G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.135G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2064594], "chromosome": "Chromosome"}, "c.1371G>A": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1371G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.1371G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "streptomycin", "original_mutation": "c.1371G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063358], "chromosome": "Chromosome"}, "c.1374C>T": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1374C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.1374C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "streptomycin", "original_mutation": "c.1374C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063355], "chromosome": "Chromosome"}, "c.138C>G": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.138C>G", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.138C>G", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.138C>G", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2064591], "chromosome": "Chromosome"}, "c.1405C>T": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1405C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.1405C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.1405C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063324], "chromosome": "Chromosome"}, "c.1426C>T": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1426C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": 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"Chromosome"}, "p.Glu368Gln": {"annotations": [{"type": "drug_resistance", "drug": "ethambutol", "original_mutation": "p.Glu368Gln", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [4247615, 4247616, 4247617], "chromosome": "Chromosome"}, "p.Ala388Gly": {"annotations": [{"type": "drug_resistance", "drug": "ethambutol", "original_mutation": "p.Ala388Gly", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [4247675, 4247676, 4247677], "chromosome": "Chromosome"}, "p.Pro397Gln": {"annotations": [{"type": "drug_resistance", "drug": "ethambutol", "original_mutation": "p.Pro397Gln", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [4247702, 4247703, 4247704], "chromosome": "Chromosome"}, "p.Trp395Arg": {"annotations": [{"type": "drug_resistance", "drug": "ethambutol", "original_mutation": "p.Trp395Arg", "confidence": "", "source": "tbdb", "comment": 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"drug_resistance", "drug": "ethambutol", "original_mutation": "p.Ser380Asn", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [4247651, 4247652, 4247653], "chromosome": "Chromosome"}, "p.Gly331Arg": {"annotations": [{"type": "drug_resistance", "drug": "ethambutol", "original_mutation": "p.Gly331Arg", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [4247504, 4247505, 4247506], "chromosome": "Chromosome"}, "p.Tyr333His": {"annotations": [{"type": "drug_resistance", "drug": "ethambutol", "original_mutation": "p.Tyr333His", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [4247510, 4247511, 4247512], "chromosome": "Chromosome"}, "p.Asn399His": {"annotations": [{"type": "drug_resistance", "drug": "ethambutol", "original_mutation": "p.Asn399His", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [4247708, 4247709, 4247710], "chromosome": "Chromosome"}, "p.Gly314Ala": {"annotations": [{"type": "drug_resistance", "drug": "ethambutol", "original_mutation": "p.Gly314Ala", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [4247453, 4247454, 4247455], "chromosome": "Chromosome"}, "p.Ser297Leu": {"annotations": [{"type": "drug_resistance", "drug": "ethambutol", "original_mutation": "p.Ser297Leu", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [4247402, 4247403, 4247404], "chromosome": "Chromosome"}, "p.Val377Gly": {"annotations": [{"type": "drug_resistance", "drug": "ethambutol", "original_mutation": "p.Val377Gly", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [4247642, 4247643, 4247644], "chromosome": "Chromosome"}, "p.Pro461Ser": {"annotations": [{"type": "drug_resistance", "drug": "ethambutol", "original_mutation": "p.Pro461Ser", 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{"annotations": [{"type": "drug_resistance", "drug": "ethambutol", "original_mutation": "p.Asn318Ser", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [4247465, 4247466, 4247467], "chromosome": "Chromosome"}, "p.Asn400Lys": {"annotations": [{"type": "drug_resistance", "drug": "ethambutol", "original_mutation": "p.Asn400Lys", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [4247711, 4247712, 4247713], "chromosome": "Chromosome"}, "p.Val282Gly": {"annotations": [{"type": "drug_resistance", "drug": "ethambutol", "original_mutation": "p.Val282Gly", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [4247357, 4247358, 4247359], "chromosome": "Chromosome"}, "p.Gly745Asp": {"annotations": [{"type": "drug_resistance", "drug": "ethambutol", "original_mutation": "p.Gly745Asp", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], 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"Chromosome"}, "c.-1002C>T": {"annotations": [{"type": "who_confidence", "drug": "ethambutol", "original_mutation": "c.-1002C>T", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [4238861], "chromosome": "Chromosome"}, "c.-1004G>A": {"annotations": [{"type": "who_confidence", "drug": "ethambutol", "original_mutation": "c.-1004G>A", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [4238859], "chromosome": "Chromosome"}, "c.-100C>T": {"annotations": [{"type": "who_confidence", "drug": "ethambutol", "original_mutation": "c.-100C>T", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [4239763], "chromosome": "Chromosome"}, "c.-1016C>T": {"annotations": [{"type": "who_confidence", "drug": "ethambutol", "original_mutation": "c.-1016C>T", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": ""}], 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+0100", + "db-schema-version": "1.0.0" + }, + "amplicon": false, + "files": { + "ref": "tbdb.fasta", + "gff": "tbdb.gff", + "bed": "tbdb.bed", + "json_db": "tbdb.dr.json", + "variables": "tbdb.variables.json", + "spoligotype_spacers": "tbdb.spoligotype_spacers.txt", + "spoligotype_annotations": "tbdb.spoligotype_list.csv", + "bedmask": "tbdb.mask.bed", + "barcode": "tbdb.barcode.bed", + "rules": "tbdb.rules.txt" + } +}