TB-Profiler result

Run: ERR11465510
Summary

Run ID: ERR11465510

Sample name:

Date: 2024-04-16T04:11:37.679281

Number of reads: 1066652

Percentage reads mapped: 81.96

Median coverage: 22.0

Strain: lineage4.3.4.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 1.0
lineage4 Euro-American None 1.0
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.94
lineage4.3.4 Euro-American (LAM) RD174 1.0
lineage4.3.4.2 Euro-American (LAM) RD174 0.93
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
gyrB 5611 c.372C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6140 p.Val301Leu missense_variant 0.86 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6196 c.957C>G synonymous_variant 0.24 levofloxacin
moxifloxacin
gyrA 6700 c.-602T>C upstream_gene_variant 0.3 levofloxacin
moxifloxacin
gyrA 6703 c.-599G>C upstream_gene_variant 0.27 levofloxacin
moxifloxacin
gyrA 6709 c.-593A>G upstream_gene_variant 0.3 levofloxacin
moxifloxacin
gyrA 6724 c.-578G>C upstream_gene_variant 0.3 levofloxacin
moxifloxacin
gyrA 6730 c.-572A>G upstream_gene_variant 0.27 levofloxacin
moxifloxacin
gyrA 6760 c.-542G>C upstream_gene_variant 0.22 levofloxacin
moxifloxacin
gyrA 6775 c.-527G>T upstream_gene_variant 0.2 levofloxacin
moxifloxacin
gyrB 6793 c.1554T>C synonymous_variant 0.2 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6797 p.Gly520Ser missense_variant 0.23 levofloxacin
moxifloxacin
gyrB 6808 c.1569C>G synonymous_variant 0.3 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6811 c.1572C>T synonymous_variant 0.32 levofloxacin
moxifloxacin Not assoc w R - Interim
gyrA 6838 c.-464C>A upstream_gene_variant 0.29 levofloxacin
moxifloxacin
gyrB 6841 c.1602T>C synonymous_variant 0.26 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 6844 c.-458T>C upstream_gene_variant 0.26 levofloxacin
moxifloxacin
gyrB 6856 c.1617T>C synonymous_variant 0.18 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6859 c.1620T>C synonymous_variant 0.21 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6862 c.1623C>G synonymous_variant 0.21 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8546 c.1245T>C synonymous_variant 0.18 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8552 c.1251C>G synonymous_variant 0.18 levofloxacin
moxifloxacin
gyrA 8555 c.1254G>T synonymous_variant 0.18 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrA 8561 c.1260A>C synonymous_variant 0.21 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8603 c.1302A>G synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8981 c.1680G>C synonymous_variant 0.29 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8996 c.1695T>C synonymous_variant 0.32 levofloxacin
moxifloxacin
gyrA 8998 p.Leu566Trp missense_variant 0.33 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9023 c.1722A>C synonymous_variant 0.38 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9029 c.1728T>G synonymous_variant 0.38 levofloxacin
moxifloxacin
gyrA 9032 c.1731T>C synonymous_variant 0.38 levofloxacin
moxifloxacin
gyrA 9038 c.1737C>G synonymous_variant 0.32 levofloxacin
moxifloxacin
gyrA 9050 p.Asp583Glu missense_variant 0.3 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 575767 c.420G>A synonymous_variant 0.22 ethionamide
isoniazid
mshA 575770 c.423G>C synonymous_variant 0.22 ethionamide
isoniazid
mshA 575771 p.Val142Thr missense_variant 0.21 ethionamide
isoniazid
mshA 575782 c.435G>C synonymous_variant 0.29 ethionamide
isoniazid
mshA 575821 c.474G>C synonymous_variant 0.25 ethionamide
isoniazid
mshA 575842 c.495G>C synonymous_variant 0.22 ethionamide
isoniazid
mshA 575845 c.498C>G synonymous_variant 0.22 ethionamide
isoniazid
mshA 575864 c.517T>C synonymous_variant 0.21 ethionamide
isoniazid
ccsA 620712 c.822G>C synonymous_variant 0.28 capreomycin
amikacin
kanamycin
ccsA 620718 c.828G>C synonymous_variant 0.28 capreomycin
amikacin
kanamycin
ccsA 620721 c.831G>C synonymous_variant 0.28 capreomycin
amikacin
kanamycin
ccsA 620733 c.843G>C synonymous_variant 0.26 capreomycin
amikacin
kanamycin
ccsA 620736 c.846G>C synonymous_variant 0.26 capreomycin
amikacin
kanamycin
ccsA 620739 c.849A>G synonymous_variant 0.26 capreomycin
amikacin
kanamycin
ccsA 620745 c.855G>C synonymous_variant 0.26 capreomycin
amikacin
kanamycin
ccsA 620748 c.858T>G synonymous_variant 0.26 capreomycin
amikacin
kanamycin
ccsA 620769 c.879C>G synonymous_variant 0.24 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
ccsA 620778 c.888T>C synonymous_variant 0.23 capreomycin
amikacin
kanamycin
ccsA 620781 c.891C>G synonymous_variant 0.23 capreomycin
amikacin
kanamycin
ccsA 620787 c.897C>G synonymous_variant 0.21 capreomycin
amikacin
kanamycin
ccsA 620791 c.901_903delGTGinsAC frameshift_variant&missense_variant 0.23 capreomycin
amikacin
kanamycin
ccsA 620796 c.906C>G synonymous_variant 0.23 capreomycin
amikacin
kanamycin
ccsA 620802 c.912C>G synonymous_variant 0.19 capreomycin
amikacin
kanamycin
ccsA 620808 c.918T>C synonymous_variant 0.19 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
nusG 734910 c.657C>G synonymous_variant 0.29 rifampicin
nusG 734913 c.660C>G synonymous_variant 0.3 rifampicin
rpoB 760106 c.300G>C synonymous_variant 0.17 rifampicin
rpoB 760112 c.306T>C synonymous_variant 0.22 rifampicin
rpoB 760118 c.312T>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760121 c.315T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760130 p.Asp108Glu missense_variant 0.2 rifampicin Uncertain significance
rpoB 760181 c.375T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 760184 c.378A>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 760199 c.393C>G synonymous_variant 0.15 rifampicin
rpoB 760235 c.429T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 760244 c.438G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760316 c.510C>G synonymous_variant 0.16 rifampicin
rpoB 760591 p.Val262Ala missense_variant 0.3 rifampicin
rpoB 760611 c.805_807delTTGinsCC frameshift_variant&missense_variant 0.41 rifampicin
rpoB 760625 c.819C>G synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoB 760646 c.840C>G synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoB 760655 c.849A>G synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoB 760661 c.855A>C synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoB 760670 c.864G>C synonymous_variant 0.38 rifampicin
rpoB 760674 c.868T>C synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoB 760679 c.873A>G synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoB 760683 c.877T>C synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoB 761612 c.1806G>T synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoB 761615 c.1809A>C synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoB 761690 c.1884G>C synonymous_variant 0.24 rifampicin
rpoB 761693 c.1887G>T synonymous_variant 0.23 rifampicin
rpoB 761930 c.2124G>C synonymous_variant 0.22 rifampicin
rpoB 762047 c.2241G>A synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762053 c.2247T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 762065 c.2259T>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 762068 c.2262C>T synonymous_variant 0.25 rifampicin
rpoB 762083 c.2277T>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 762086 c.2280G>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 762101 c.2295C>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 762114 p.Ile770Val missense_variant 0.22 rifampicin Uncertain significance
rpoB 762131 c.2325C>G synonymous_variant 0.17 rifampicin
rpoB 762995 c.3189G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 763040 c.3234C>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 763058 c.-312C>G upstream_gene_variant 0.21 rifampicin
rpoB 763070 c.3264T>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 763082 c.-288C>G upstream_gene_variant 0.24 rifampicin
rpoC 763103 c.-267G>C upstream_gene_variant 0.26 rifampicin
rpoB 763115 c.3309T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 763127 c.3321G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763142 c.-228C>G upstream_gene_variant 0.19 rifampicin
rpoC 763160 c.-210G>T upstream_gene_variant 0.25 rifampicin
rpoB 763166 c.3360A>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 763217 c.-153G>C upstream_gene_variant 0.2 rifampicin
rpoC 763226 c.-144A>G upstream_gene_variant 0.17 rifampicin
rpoB 763227 p.Leu1141Met missense_variant 0.16 rifampicin
rpoC 763232 c.-138C>T upstream_gene_variant 0.17 rifampicin
rpoB 763235 p.Glu1143Asp missense_variant 0.17 rifampicin
rpoB 763241 p.Glu1145Asp missense_variant 0.17 rifampicin
rpoC 763251 c.-119C>T upstream_gene_variant 0.18 rifampicin
rpoC 763259 c.-111G>T upstream_gene_variant 0.16 rifampicin
rpoB 763265 c.3459G>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763274 c.-96G>C upstream_gene_variant 0.19 rifampicin
rpoC 763375 c.6C>A synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763402 c.33C>G synonymous_variant 0.14 rifampicin
rpoC 763408 c.39T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763411 c.42T>C synonymous_variant 0.16 rifampicin
rpoC 763414 c.45T>C synonymous_variant 0.15 rifampicin
rpoC 763420 c.51G>C synonymous_variant 0.15 rifampicin
rpoC 763423 p.Glu18Asp missense_variant 0.15 rifampicin Uncertain significance
rpoC 763429 c.60C>T synonymous_variant 0.15 rifampicin
rpoC 763430 c.61_63delAGGinsCT frameshift_variant&missense_variant 0.15 rifampicin
rpoC 763435 c.66A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763444 c.75T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763447 c.78C>T synonymous_variant 0.19 rifampicin
rpoC 763456 c.87A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763468 c.99G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763486 c.117T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 763621 c.252C>T synonymous_variant 0.4 rifampicin
rpoC 763660 c.291T>G synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoC 763666 c.297G>A synonymous_variant 0.45 rifampicin
rpoC 763675 c.306C>G synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoC 763702 c.333C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763709 c.340C>T synonymous_variant 0.2 rifampicin
rpoC 763714 c.345G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763723 c.354G>C synonymous_variant 0.15 rifampicin
rpoC 763741 c.372C>T synonymous_variant 0.22 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.2 rifampicin
rpoC 763978 c.609C>G synonymous_variant 0.4 rifampicin
rpoC 763987 c.618C>T synonymous_variant 0.33 rifampicin
rpoC 763991 p.Ile208Leu missense_variant 0.33 rifampicin
rpoC 763996 c.627T>A synonymous_variant 0.35 rifampicin
rpoC 764002 c.633C>G synonymous_variant 0.32 rifampicin
rpoC 764005 c.636G>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 764131 c.762T>C synonymous_variant 0.3 rifampicin
rpoC 764153 p.Gln262Lys missense_variant 0.31 rifampicin
rpoC 764161 c.792G>C synonymous_variant 0.32 rifampicin
rpoC 764752 c.1383G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764758 c.1389C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.93 rifampicin Not assoc w R
rpoC 765466 c.2097C>T synonymous_variant 0.41 rifampicin
rpoC 765478 c.2109T>C synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoC 765480 p.Tyr704Phe missense_variant 0.31 rifampicin Uncertain significance
rpoC 765493 c.2124G>C synonymous_variant 0.37 rifampicin
rpoC 765499 c.2130C>A synonymous_variant 0.38 rifampicin
rpoC 766429 c.3060C>G synonymous_variant 0.32 rifampicin
rpoC 766447 c.3078T>C synonymous_variant 0.36 rifampicin
rpoC 766459 c.3090G>C synonymous_variant 0.29 rifampicin
rpoC 766471 c.3102G>C synonymous_variant 0.39 rifampicin
rpoC 766483 c.3114G>C synonymous_variant 0.32 rifampicin
rpoC 766486 c.3117A>G synonymous_variant 0.32 rifampicin
rpoC 766492 c.3123T>G synonymous_variant 0.32 rifampicin
rpoC 766493 p.Gly1042Asn missense_variant 0.32 rifampicin
rpoC 766517 p.Thr1050Ser missense_variant 0.35 rifampicin
rpoC 766525 c.3156G>T synonymous_variant 0.39 rifampicin
rpoC 766528 c.3159T>G synonymous_variant 0.39 rifampicin
rpoC 766530 p.Arg1054Gln missense_variant 0.41 rifampicin
rpoC 766540 p.Asp1057Glu missense_variant 0.42 rifampicin
rpoC 766543 c.3174C>T synonymous_variant 0.42 rifampicin
rpoC 766549 c.3180G>C synonymous_variant 0.45 rifampicin
rpoC 766570 c.3201T>C synonymous_variant 0.42 rifampicin
rpoC 766573 c.3204T>G synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoC 766582 c.3213C>T synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoC 766585 c.3216T>C synonymous_variant 0.33 rifampicin
rpoC 766607 p.Ile1080Leu missense_variant 0.32 rifampicin
rpoC 766618 c.3249G>T synonymous_variant 0.34 rifampicin
rpoC 766624 c.3255G>C synonymous_variant 0.24 rifampicin
rpoC 766630 c.3261G>T synonymous_variant 0.24 rifampicin
rpoC 766634 p.Phe1089Ile missense_variant 0.24 rifampicin
rpoC 766702 c.3333G>C synonymous_variant 0.27 rifampicin
rpoC 766708 c.3339A>G synonymous_variant 0.32 rifampicin
rpoC 766711 c.3342C>T synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 766732 c.3363G>T synonymous_variant 0.36 rifampicin
rpoC 766738 c.3369G>T synonymous_variant 0.39 rifampicin
rpoC 766747 c.3378C>T synonymous_variant 0.35 rifampicin
rpoC 766750 c.3381C>G synonymous_variant 0.35 rifampicin
rpoC 766753 c.3384C>T synonymous_variant 0.35 rifampicin
rpoC 766765 c.3396A>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 766774 c.3405T>C synonymous_variant 0.38 rifampicin
rpoC 766776 p.Arg1136His missense_variant 0.38 rifampicin
rpoC 766798 c.3429C>G synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 767023 c.3654C>T synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 767191 c.3822C>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 767281 c.3912C>G synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 767284 c.3915C>G synonymous_variant 0.26 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 775916 c.2565T>C synonymous_variant 0.31 clofazimine
bedaquiline
mmpL5 775922 c.2559G>C synonymous_variant 0.22 clofazimine
bedaquiline
mmpL5 775946 c.2535C>G synonymous_variant 0.34 clofazimine
bedaquiline
mmpL5 775951 c.2530C>T synonymous_variant 0.44 clofazimine
bedaquiline
mmpL5 775966 p.Ala839Ser missense_variant 0.35 clofazimine
bedaquiline
mmpL5 775975 p.Leu836Met missense_variant 0.48 clofazimine
bedaquiline
mmpL5 775981 p.Leu834Met missense_variant 0.36 clofazimine
bedaquiline
mmpL5 775991 c.2490G>A synonymous_variant 0.35 clofazimine
bedaquiline
mmpL5 775997 c.2484T>G synonymous_variant 0.34 clofazimine
bedaquiline
mmpL5 776000 c.2479_2481delCTGinsAC frameshift_variant&missense_variant 0.34 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 776009 c.2472A>G synonymous_variant 0.39 clofazimine
bedaquiline
mmpL5 776021 c.2460G>A synonymous_variant 0.38 clofazimine
bedaquiline
mmpL5 776024 c.2457G>C synonymous_variant 0.41 clofazimine
bedaquiline
mmpL5 776030 c.2451G>C synonymous_variant 0.41 clofazimine
bedaquiline
mmpL5 776060 c.2421C>G synonymous_variant 0.24 clofazimine
bedaquiline
mmpL5 776072 c.2409C>G synonymous_variant 0.19 clofazimine
bedaquiline
mmpL5 776075 c.2406C>G synonymous_variant 0.19 clofazimine
bedaquiline
mmpL5 776080 p.Ala801Ser missense_variant 0.21 clofazimine
bedaquiline
mmpL5 776084 c.2397C>G synonymous_variant 0.22 clofazimine
bedaquiline
mmpL5 776087 c.2394C>G synonymous_variant 0.22 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781628 c.69T>C synonymous_variant 0.2 streptomycin Not assoc w R - Interim
rpsL 781631 c.72G>C synonymous_variant 0.19 streptomycin
rpsL 781655 c.96T>C synonymous_variant 0.2 streptomycin
rpsL 781658 c.99A>G synonymous_variant 0.21 streptomycin
rpsL 781676 c.117C>G synonymous_variant 0.21 streptomycin
rpsL 781682 c.123T>C synonymous_variant 0.22 streptomycin
rpsL 781709 c.150G>C synonymous_variant 0.26 streptomycin Not assoc w R - Interim
rpsL 781715 c.156T>C synonymous_variant 0.28 streptomycin
rpsL 781718 c.159C>G synonymous_variant 0.29 streptomycin
rpsL 781728 c.169T>C synonymous_variant 0.27 streptomycin
rpsL 781733 c.174G>C synonymous_variant 0.23 streptomycin
rpsL 781736 c.177T>C synonymous_variant 0.22 streptomycin
rpsL 781751 c.192G>C synonymous_variant 0.18 streptomycin
rpsL 781754 c.195G>A synonymous_variant 0.18 streptomycin Not assoc w R - Interim
rpsL 781760 c.201T>C synonymous_variant 0.25 streptomycin
rpsL 781766 c.207C>T synonymous_variant 0.25 streptomycin Not assoc w R - Interim
rpsL 781811 c.252C>T synonymous_variant 0.28 streptomycin
rpsL 781814 c.255C>T synonymous_variant 0.28 streptomycin
rpsL 781817 c.258G>T synonymous_variant 0.26 streptomycin
rpsL 781829 c.270G>C synonymous_variant 0.25 streptomycin
rpsL 781832 c.273T>C synonymous_variant 0.25 streptomycin
rpsL 781841 c.282C>T synonymous_variant 0.34 streptomycin
rpsL 781865 c.306G>C synonymous_variant 0.22 streptomycin
rpsL 781868 c.309T>C synonymous_variant 0.21 streptomycin
rpsL 781871 c.312G>C synonymous_variant 0.2 streptomycin
rpsL 781880 c.321C>G synonymous_variant 0.19 streptomycin
rpsL 781907 c.348T>C synonymous_variant 0.16 streptomycin
rpsL 781916 c.357T>C synonymous_variant 0.16 streptomycin
rpsL 781929 p.Gly124Ser missense_variant 0.21 streptomycin Uncertain significance
rplC 800516 c.-293G>C upstream_gene_variant 0.28 linezolid
rplC 800531 c.-278T>C upstream_gene_variant 0.17 linezolid
rplC 800537 c.-272C>G upstream_gene_variant 0.2 linezolid
rplC 800540 c.-269T>C upstream_gene_variant 0.19 linezolid
rplC 800546 c.-263T>C upstream_gene_variant 0.19 linezolid
rplC 800594 c.-215C>G upstream_gene_variant 0.18 linezolid
rplC 800597 c.-212A>G upstream_gene_variant 0.19 linezolid
rplC 800600 c.-209G>C upstream_gene_variant 0.19 linezolid
rplC 800603 c.-206G>C upstream_gene_variant 0.21 linezolid
rplC 800612 c.-197A>G upstream_gene_variant 0.19 linezolid
rplC 800618 c.-191T>C upstream_gene_variant 0.2 linezolid
rplC 800633 c.-176T>C upstream_gene_variant 0.24 linezolid
rplC 800654 c.-155T>C upstream_gene_variant 0.28 linezolid
rplC 800672 c.-137G>T upstream_gene_variant 0.28 linezolid
rplC 800690 c.-119C>T upstream_gene_variant 0.21 linezolid
rplC 800693 c.-116A>T upstream_gene_variant 0.21 linezolid
rplC 800715 c.-94A>C upstream_gene_variant 0.22 linezolid
rplC 800720 c.-89T>C upstream_gene_variant 0.23 linezolid
rplC 800723 c.-86C>G upstream_gene_variant 0.22 linezolid
rplC 800738 c.-71T>C upstream_gene_variant 0.2 linezolid
rplC 800949 c.141T>C synonymous_variant 0.19 linezolid
rplC 800955 c.147C>G synonymous_variant 0.2 linezolid
fbiC 1304580 c.1650T>C synonymous_variant 0.35 clofazimine
pretomanid
delamanid
fbiC 1304613 c.1683T>G synonymous_variant 0.32 clofazimine
pretomanid
delamanid
sigE 1364811 c.399A>G synonymous_variant 0.14 pyrazinamide
sigE 1364835 c.423C>G synonymous_variant 0.17 pyrazinamide
sigE 1364839 c.427T>C synonymous_variant 0.17 pyrazinamide
sigE 1364847 c.435G>C synonymous_variant 0.18 pyrazinamide
sigE 1364859 c.447C>G synonymous_variant 0.25 pyrazinamide
sigE 1364865 c.453G>C synonymous_variant 0.27 pyrazinamide
sigE 1364867 p.Ala152Gly missense_variant 0.27 pyrazinamide
sigE 1364877 c.465G>C synonymous_variant 0.32 pyrazinamide Not assoc w R - Interim
sigE 1364887 c.475_477delTTAinsCG frameshift_variant&missense_variant 0.23 pyrazinamide Uncertain significance
sigE 1364919 c.507T>C synonymous_variant 0.38 pyrazinamide
sigE 1364922 p.Glu170Asp missense_variant 0.38 pyrazinamide
sigE 1364925 c.513C>G synonymous_variant 0.38 pyrazinamide
sigE 1364931 c.519C>G synonymous_variant 0.43 pyrazinamide
atpE 1461132 p.Val30Ile missense_variant 0.16 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472380 n.535G>C non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472445 n.601_604delTCTC non_coding_transcript_exon_variant 0.32 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472451 n.606_607insCGGG non_coding_transcript_exon_variant 0.35 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472460 n.615T>C non_coding_transcript_exon_variant 0.38 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472461 n.616G>C non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472463 n.618G>C non_coding_transcript_exon_variant 0.41 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.41 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.43 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474287 n.630_635delTCCTTTinsCTCGACTTG non_coding_transcript_exon_variant 0.47 capreomycin
linezolid
rrl 1474294 n.638_649delCTCTCCGGAGGA non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.49 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.47 capreomycin
linezolid
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.63 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474374 n.717T>G non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid
rrl 1474387 n.730C>T non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474629 n.972G>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1474672 n.1015C>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474708 n.1052_1053insACAAG non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1474711 n.1055_1058delGTGT non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1474717 n.1060A>G non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid
rrl 1474720 n.1063C>T non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475202 n.1545G>A non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475479 n.1822C>T non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475480 n.1823A>G non_coding_transcript_exon_variant 0.46 capreomycin
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475544 n.1887A>T non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.34 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475989 n.2332T>A non_coding_transcript_exon_variant 0.34 capreomycin
linezolid
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1476032 n.2375C>G non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1476033 n.2376T>G non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1476035 n.2378G>C non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1476044 n.2387T>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1476046 n.2389G>T non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1476047 n.2390G>T non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476088 n.2431A>T non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1476095 n.2438C>T non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1476103 n.2446C>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1476105 n.2448G>A non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1476106 n.2449A>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1476110 n.2453G>C non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833589 c.48A>C synonymous_variant 0.17 pyrazinamide
rpsA 1833634 c.93G>A synonymous_variant 0.14 pyrazinamide
rpsA 1833745 c.204G>T synonymous_variant 0.18 pyrazinamide
rpsA 1833772 c.231C>T synonymous_variant 0.29 pyrazinamide
rpsA 1833778 c.237C>T synonymous_variant 0.26 pyrazinamide
rpsA 1833781 c.240T>G synonymous_variant 0.26 pyrazinamide
rpsA 1833904 c.363G>A synonymous_variant 0.3 pyrazinamide
rpsA 1834069 c.528G>C synonymous_variant 0.28 pyrazinamide
rpsA 1834282 c.741C>T synonymous_variant 0.17 pyrazinamide
rpsA 1834294 c.753G>C synonymous_variant 0.2 pyrazinamide
rpsA 1834298 p.Gln253Thr missense_variant 0.19 pyrazinamide
rpsA 1834303 c.762T>G synonymous_variant 0.21 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.23 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.25 pyrazinamide Not assoc w R - Interim
rpsA 1834361 c.820T>C synonymous_variant 0.28 pyrazinamide
rpsA 1834366 c.825A>G synonymous_variant 0.27 pyrazinamide Not assoc w R - Interim
rpsA 1834378 c.837T>C synonymous_variant 0.25 pyrazinamide Not assoc w R - Interim
rpsA 1834387 c.846C>T synonymous_variant 0.25 pyrazinamide
rpsA 1834396 c.855G>C synonymous_variant 0.19 pyrazinamide
rpsA 1834483 c.942G>A synonymous_variant 0.24 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.33 pyrazinamide
rpsA 1834495 c.954G>A synonymous_variant 0.32 pyrazinamide
rpsA 1834609 c.1068T>C synonymous_variant 0.31 pyrazinamide
rpsA 1834619 c.1078T>C synonymous_variant 0.26 pyrazinamide
rpsA 1834633 c.1092A>G synonymous_variant 0.29 pyrazinamide
rpsA 1834678 c.1137C>T synonymous_variant 0.18 pyrazinamide
rpsA 1834690 c.1149T>C synonymous_variant 0.17 pyrazinamide
rpsA 1834753 c.1212T>C synonymous_variant 0.25 pyrazinamide
rpsA 1834756 c.1215G>A synonymous_variant 0.23 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2477c 2782465 c.1578G>A synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2782480 c.1563G>A synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2782486 c.1557G>A synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783992 c.51T>C synonymous_variant 0.16 ethambutol Not assoc w R - Interim
moxifloxacin
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin
Rv2477c 2784016 c.25_27delAAGinsCC frameshift_variant&missense_variant 0.14 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
thyX 3067646 c.300C>G synonymous_variant 0.3 para-aminosalicylic_acid
thyX 3067652 c.294T>C synonymous_variant 0.3 para-aminosalicylic_acid
thyX 3067685 c.261A>G synonymous_variant 0.22 para-aminosalicylic_acid
thyX 3067688 c.258G>C synonymous_variant 0.21 para-aminosalicylic_acid
thyX 3067694 c.252G>C synonymous_variant 0.22 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.97 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626773 c.-160C>T upstream_gene_variant 0.27 bedaquiline
rifampicin
mtrA 3626774 c.574_576delAGGinsCT frameshift_variant&missense_variant 0.26 bedaquiline
rifampicin
mtrB 3626780 c.-167T>C upstream_gene_variant 0.25 bedaquiline
rifampicin
mtrB 3626783 c.-170C>G upstream_gene_variant 0.25 bedaquiline
rifampicin
mtrB 3626786 c.-173A>C upstream_gene_variant 0.24 bedaquiline
rifampicin
mtrA 3626792 c.558G>T synonymous_variant 0.24 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626798 c.-185T>A upstream_gene_variant 0.24 bedaquiline
rifampicin
mtrA 3626804 c.546A>G synonymous_variant 0.22 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3626825 c.525T>A synonymous_variant 0.27 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626876 c.-263A>G upstream_gene_variant 0.24 bedaquiline
rifampicin
mtrB 3627116 c.-503G>C upstream_gene_variant 0.24 bedaquiline
rifampicin
mtrA 3627119 c.231T>G synonymous_variant 0.21 bedaquiline
rifampicin Not assoc w R - Interim
alr 3840719 c.702A>G synonymous_variant 1.0 cycloserine
rpoA 3877638 c.870T>C synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoA 3877656 c.852T>G synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoA 3877856 c.652T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3877875 c.633T>G synonymous_variant 0.31 rifampicin
rpoA 3877881 c.627G>C synonymous_variant 0.29 rifampicin
rpoA 3877884 c.624G>C synonymous_variant 0.27 rifampicin
rpoA 3877893 c.615C>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoA 3877900 p.Ser203Thr missense_variant 0.22 rifampicin
rpoA 3877905 c.603A>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoA 3877908 c.600T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoA 3877920 c.588G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3877926 c.582G>C synonymous_variant 0.24 rifampicin
rpoA 3877962 c.546G>C synonymous_variant 0.18 rifampicin
rpoA 3878157 c.351C>G synonymous_variant 0.24 rifampicin
rpoA 3878160 c.348C>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoA 3878163 c.345C>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoA 3878175 c.333G>C synonymous_variant 0.3 rifampicin
rpoA 3878187 c.321C>G synonymous_variant 0.23 rifampicin
rpoA 3878193 c.315T>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoA 3878202 c.306G>C synonymous_variant 0.31 rifampicin
rpoA 3878217 c.291A>G synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoA 3878247 c.261G>C synonymous_variant 0.32 rifampicin
rpoA 3878256 c.252G>C synonymous_variant 0.27 rifampicin
rpoA 3878271 c.237T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoA 3878283 p.Glu75Asp missense_variant 0.19 rifampicin Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
clpC1 4038551 c.2154C>G synonymous_variant 0.17 pyrazinamide
clpC1 4038842 c.1863G>C synonymous_variant 0.19 pyrazinamide
clpC1 4038860 c.1845G>C synonymous_variant 0.25 pyrazinamide Not assoc w R - Interim
clpC1 4039310 c.1395A>G synonymous_variant 0.2 pyrazinamide
clpC1 4039313 c.1392C>G synonymous_variant 0.2 pyrazinamide
clpC1 4039319 c.1386T>C synonymous_variant 0.2 pyrazinamide Not assoc w R - Interim
clpC1 4040459 c.246C>G synonymous_variant 0.23 pyrazinamide
clpC1 4040465 c.240T>C synonymous_variant 0.22 pyrazinamide
clpC1 4040468 c.237G>C synonymous_variant 0.22 pyrazinamide
clpC1 4040471 c.234T>C synonymous_variant 0.21 pyrazinamide Not assoc w R - Interim
clpC1 4040477 c.228G>T synonymous_variant 0.19 pyrazinamide
clpC1 4040480 c.225T>C synonymous_variant 0.2 pyrazinamide Not assoc w R - Interim
clpC1 4040644 c.61A>C synonymous_variant 0.35 pyrazinamide
clpC1 4040648 c.57G>A synonymous_variant 0.35 pyrazinamide
clpC1 4040654 c.51G>A synonymous_variant 0.31 pyrazinamide
clpC1 4040693 c.12A>T synonymous_variant 0.33 pyrazinamide
clpC1 4040711 c.-7G>A upstream_gene_variant 0.17 pyrazinamide
embC 4241095 c.1233C>T synonymous_variant 0.29 ethambutol
embB 4247512 c.999T>C synonymous_variant 0.15 ethambutol
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin