TB-Profiler result

Run: ERR11465232
Summary

Run ID: ERR11465232

Sample name:

Date: 2024-04-16T04:12:18.410560

Number of reads: 1930846

Percentage reads mapped: 97.98

Median coverage: 54.0

Strain: lineage4.1.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 1.0
lineage4.1.2 Euro-American None 1.0
lineage4.1.2.1 Euro-American (Haarlem) RD182 1.0
lineage4 Euro-American None 1.0
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
dnaA 576 c.576G>C synonymous_variant 0.12 isoniazid
dnaA 594 c.594C>T synonymous_variant 0.16 isoniazid
gyrB 6262 c.1023G>A synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 6610 c.-692C>G upstream_gene_variant 0.13 levofloxacin
moxifloxacin
gyrA 6634 c.-668T>C upstream_gene_variant 0.17 levofloxacin
moxifloxacin
gyrA 6640 c.-662A>C upstream_gene_variant 0.18 levofloxacin
moxifloxacin
gyrA 6643 c.-659A>G upstream_gene_variant 0.19 levofloxacin
moxifloxacin
gyrA 6724 c.-578G>C upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrB 6841 c.1602T>C synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 6844 c.-458T>C upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7427 c.126G>C synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 7442 c.141G>C synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 7448 c.147G>A synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 7472 c.171T>C synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrA 7520 c.219G>C synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 7523 c.222C>A synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 7526 c.225G>C synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7529 c.228G>C synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 7532 c.231T>C synonymous_variant 0.19 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7541 c.240C>G synonymous_variant 0.23 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7571 c.270G>T synonymous_variant 0.29 levofloxacin
moxifloxacin
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7592 c.291G>C synonymous_variant 0.34 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7619 c.318C>G synonymous_variant 0.32 levofloxacin
moxifloxacin
gyrA 7626 c.325C>T synonymous_variant 0.32 levofloxacin
moxifloxacin
gyrA 7631 c.330G>C synonymous_variant 0.31 levofloxacin
moxifloxacin
gyrA 7637 c.336C>G synonymous_variant 0.29 levofloxacin
moxifloxacin
gyrA 7655 c.354G>A synonymous_variant 0.27 levofloxacin
moxifloxacin
gyrA 7658 c.357A>G synonymous_variant 0.27 levofloxacin
moxifloxacin
gyrA 7664 c.363T>C synonymous_variant 0.24 levofloxacin
moxifloxacin
gyrA 7670 c.369A>G synonymous_variant 0.26 levofloxacin
moxifloxacin
gyrA 7679 c.378G>C synonymous_variant 0.23 levofloxacin
moxifloxacin
gyrA 7683 c.382_384delAGGinsCC frameshift_variant&missense_variant 0.23 levofloxacin
moxifloxacin
gyrA 7691 c.390C>A synonymous_variant 0.2 levofloxacin
moxifloxacin
gyrA 7694 c.393A>G synonymous_variant 0.2 levofloxacin
moxifloxacin
gyrA 7697 c.396C>G synonymous_variant 0.19 levofloxacin
moxifloxacin
gyrA 7706 c.405C>T synonymous_variant 0.2 levofloxacin
moxifloxacin
gyrA 7709 c.408G>A synonymous_variant 0.2 levofloxacin
moxifloxacin Not assoc w R - Interim
gyrA 7710 c.409_411delTTGinsCC frameshift_variant&missense_variant 0.2 levofloxacin
moxifloxacin
gyrA 7728 c.427_429delAGGinsCC frameshift_variant&missense_variant 0.24 levofloxacin
moxifloxacin
gyrA 7763 c.462T>G synonymous_variant 0.26 levofloxacin
moxifloxacin
gyrA 8897 c.1596T>C synonymous_variant 0.12 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8903 c.1602T>C synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8915 c.1614A>G synonymous_variant 0.12 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8918 c.1617C>G synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 8930 c.1629C>A synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8996 c.1695T>C synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491472 c.690A>G synonymous_variant 0.25 clofazimine
pretomanid
delamanid
fgd1 491591 p.Lys270Met missense_variant 0.87 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.94 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620316 c.426G>C synonymous_variant 0.15 capreomycin
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
ccsA 620319 c.429C>T synonymous_variant 0.17 capreomycin
amikacin
kanamycin
ccsA 620331 c.441C>T synonymous_variant 0.13 capreomycin
amikacin
kanamycin
ccsA 620335 c.445_447delCTCinsTG frameshift_variant&missense_variant 0.14 capreomycin
amikacin
kanamycin
ccsA 620340 c.450C>G synonymous_variant 0.13 capreomycin
amikacin
kanamycin
ccsA 620349 c.459A>G synonymous_variant 0.14 capreomycin
amikacin
kanamycin
ccsA 620358 c.468C>G synonymous_variant 0.14 capreomycin
amikacin
kanamycin
ccsA 620362 p.Ala158Thr missense_variant 0.18 capreomycin
amikacin
kanamycin
ccsA 620367 c.477T>C synonymous_variant 0.19 capreomycin
amikacin
kanamycin
ccsA 620388 c.498A>C synonymous_variant 0.22 capreomycin
amikacin
kanamycin
ccsA 620412 c.522T>C synonymous_variant 0.16 capreomycin
amikacin
kanamycin
ccsA 620415 c.525T>C synonymous_variant 0.16 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
ccsA 620418 c.528G>A synonymous_variant 0.16 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
hadA 731789 c.-141A>G upstream_gene_variant 0.18 isoniazid
nusG 734499 c.246G>C synonymous_variant 0.22 rifampicin
nusG 734508 c.255C>G synonymous_variant 0.27 rifampicin
nusG 734511 c.258C>A synonymous_variant 0.26 rifampicin
nusG 734532 c.279A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
nusG 734895 c.642A>G synonymous_variant 0.16 rifampicin
nusG 734910 c.657C>G synonymous_variant 0.16 rifampicin
rpoB 760115 c.309C>T synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 760361 c.555T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760475 c.669A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760481 c.675G>T synonymous_variant 0.14 rifampicin
rpoB 760484 c.678A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760511 c.705G>C synonymous_variant 0.13 rifampicin
rpoB 760611 c.805_807delTTGinsCC frameshift_variant&missense_variant 0.13 rifampicin
rpoB 760646 c.840C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 760649 c.843G>C synonymous_variant 0.12 rifampicin
rpoB 760670 c.864G>C synonymous_variant 0.18 rifampicin
rpoB 760674 c.868T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760679 c.873A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760683 c.877T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761234 c.1428G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761249 c.1443A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761252 c.1446C>T synonymous_variant 0.16 rifampicin
rpoB 761255 c.1449T>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761273 c.1467T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761615 c.1809A>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 762101 c.2295C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 762104 c.2298C>T synonymous_variant 0.21 rifampicin
rpoB 762114 p.Ile770Val missense_variant 0.23 rifampicin Uncertain significance
rpoB 762122 c.2316C>T synonymous_variant 0.23 rifampicin
rpoB 762257 c.2451C>G synonymous_variant 0.15 rifampicin
rpoB 762275 c.2469C>G synonymous_variant 0.13 rifampicin
rpoC 762434 c.-936T>C upstream_gene_variant 0.13 rifampicin
rpoB 762449 c.2643C>A synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762452 c.2646G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762470 c.2664G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 762488 c.2682G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 762851 c.-519C>T upstream_gene_variant 0.26 rifampicin
rpoB 762857 c.3051C>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 762863 c.-507T>G upstream_gene_variant 0.19 rifampicin
rpoB 762929 c.3123G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 763040 c.3234C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763052 c.-318G>C upstream_gene_variant 0.14 rifampicin
rpoB 763070 c.3264T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763085 c.3279C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 763166 c.3360A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 763175 c.3369G>A synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763179 c.-191C>T upstream_gene_variant 0.16 rifampicin
rpoB 763214 c.3408T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763217 c.-153G>C upstream_gene_variant 0.15 rifampicin
rpoC 763468 c.99G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763486 c.117T>G synonymous_variant 0.16 rifampicin
rpoC 763570 c.201G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763600 c.231C>G synonymous_variant 0.17 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.21 rifampicin
rpoC 763741 c.372C>T synonymous_variant 0.2 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.18 rifampicin
rpoC 763765 c.396T>C synonymous_variant 0.13 rifampicin
rpoC 763807 c.438T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763813 c.444C>G synonymous_variant 0.18 rifampicin
rpoC 764024 c.655_657delTTGinsCC frameshift_variant&missense_variant 0.15 rifampicin
rpoC 764032 p.Asp221Glu missense_variant 0.19 rifampicin
rpoC 764071 c.702G>C synonymous_variant 0.23 rifampicin
rpoC 764134 c.765C>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764140 c.771C>T synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764143 c.774G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764147 p.Ser260Ala missense_variant 0.2 rifampicin Uncertain significance
rpoC 764153 p.Gln262Lys missense_variant 0.18 rifampicin
rpoC 764161 c.792G>C synonymous_variant 0.28 rifampicin
rpoC 764176 c.807C>T synonymous_variant 0.16 rifampicin
rpoC 764182 p.Asp271Glu missense_variant 0.13 rifampicin Uncertain significance
rpoC 764285 p.Gly306Ser missense_variant 0.15 rifampicin
rpoC 764317 c.948C>G synonymous_variant 0.24 rifampicin
rpoC 764320 c.951C>T synonymous_variant 0.24 rifampicin
rpoC 764339 c.970C>T synonymous_variant 0.25 rifampicin
rpoC 764347 c.978G>C synonymous_variant 0.34 rifampicin
rpoC 764353 c.984G>T synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoC 764365 c.996C>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764383 c.1014C>G synonymous_variant 0.15 rifampicin
rpoC 764387 c.1018_1020delTTGinsCC frameshift_variant&missense_variant 0.15 rifampicin
rpoC 764405 c.1036_1038delAGGinsCT frameshift_variant&missense_variant 0.19 rifampicin
rpoC 764410 c.1041G>C synonymous_variant 0.19 rifampicin
rpoC 764431 c.1062G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764434 c.1065A>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764449 c.1080G>C synonymous_variant 0.21 rifampicin
rpoC 764452 c.1083T>C synonymous_variant 0.21 rifampicin
rpoC 764455 c.1086G>A synonymous_variant 0.21 rifampicin
rpoC 764458 c.1089G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764461 c.1092A>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764485 c.1116G>C synonymous_variant 0.17 rifampicin
rpoC 764491 c.1122G>T synonymous_variant 0.17 rifampicin
rpoC 764497 c.1128A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764500 c.1131C>G synonymous_variant 0.15 rifampicin
rpoC 764503 c.1134G>T synonymous_variant 0.15 rifampicin
rpoC 764510 c.1141C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764521 c.1152T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764533 c.1164C>T synonymous_variant 0.14 rifampicin
rpoC 764536 c.1167G>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764539 c.1170C>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764548 c.1179G>A synonymous_variant 0.18 rifampicin
rpoC 764686 c.1317C>T synonymous_variant 0.17 rifampicin
rpoC 764713 c.1344G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764716 c.1347G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764746 c.1377G>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764791 c.1422C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764797 c.1428G>C synonymous_variant 0.13 rifampicin
rpoC 764803 c.1434C>G synonymous_variant 0.14 rifampicin
rpoC 764827 c.1458G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764875 c.1506C>G synonymous_variant 0.14 rifampicin
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
rpoC 765478 c.2109T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 765499 c.2130C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765517 c.2148C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 766384 c.3015A>G synonymous_variant 0.14 rifampicin
rpoC 766393 c.3024C>G synonymous_variant 0.15 rifampicin
rpoC 766411 c.3042C>G synonymous_variant 0.15 rifampicin
rpoC 766423 c.3054T>C synonymous_variant 0.22 rifampicin
rpoC 766429 c.3060C>G synonymous_variant 0.23 rifampicin
rpoC 766459 c.3090G>C synonymous_variant 0.13 rifampicin
rpoC 766537 c.3168G>A synonymous_variant 0.14 rifampicin
rpoC 766540 p.Asp1057Glu missense_variant 0.14 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781929 p.Gly124Ser missense_variant 0.2 streptomycin Uncertain significance
fbiC 1304694 c.1764A>G synonymous_variant 0.19 clofazimine
pretomanid
delamanid
fbiC 1304703 c.1773C>G synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fbiC 1304715 c.1785G>T synonymous_variant 0.2 clofazimine
pretomanid
delamanid
fbiC 1304724 c.1794A>G synonymous_variant 0.26 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fbiC 1304727 c.1797A>G synonymous_variant 0.26 clofazimine
pretomanid
delamanid
fbiC 1304742 c.1812T>C synonymous_variant 0.19 clofazimine
pretomanid
delamanid
fbiC 1304748 c.1818T>C synonymous_variant 0.17 clofazimine
pretomanid
delamanid
fbiC 1304757 c.1827A>T synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fbiC 1304760 c.1830G>C synonymous_variant 0.16 clofazimine
pretomanid
delamanid
sigE 1364703 c.291G>C synonymous_variant 0.13 pyrazinamide
sigE 1364709 c.297T>C synonymous_variant 0.15 pyrazinamide
sigE 1364712 c.300T>C synonymous_variant 0.16 pyrazinamide
sigE 1364718 c.306C>G synonymous_variant 0.17 pyrazinamide
sigE 1364724 c.312C>T synonymous_variant 0.16 pyrazinamide
sigE 1364727 c.315C>T synonymous_variant 0.16 pyrazinamide
sigE 1364742 c.330A>G synonymous_variant 0.18 pyrazinamide
sigE 1364763 c.351T>C synonymous_variant 0.17 pyrazinamide
sigE 1364781 c.369G>C synonymous_variant 0.17 pyrazinamide
sigE 1364782 c.370_372delGTCinsCG frameshift_variant&missense_variant 0.17 pyrazinamide Uncertain significance
sigE 1364790 c.378T>C synonymous_variant 0.21 pyrazinamide
sigE 1364802 c.390C>A synonymous_variant 0.2 pyrazinamide
sigE 1364805 c.393C>A synonymous_variant 0.19 pyrazinamide
sigE 1364811 c.399A>G synonymous_variant 0.2 pyrazinamide
sigE 1364814 c.402C>T synonymous_variant 0.19 pyrazinamide
sigE 1364820 c.408A>G synonymous_variant 0.2 pyrazinamide
Rv1258c 1406622 p.Leu240Arg missense_variant 1.0 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
atpE 1460816 c.-229T>C upstream_gene_variant 0.19 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471986 n.141C>T non_coding_transcript_exon_variant 0.25 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472489 n.644A>G non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.32 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.42 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1473770 n.113T>G non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473788 n.131A>G non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473807 n.150T>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1473812 n.155G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1473813 n.156C>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1473814 n.157A>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473815 n.158T>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1473822 n.165A>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473829 n.172G>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1473830 n.173T>G non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1473831 n.174G>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1473832 n.175C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.15 capreomycin
linezolid Uncertain significance
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474174 n.517A>G non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1474185 n.528G>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1474186 n.529A>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474202 n.545T>C non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1475088 n.1431A>G non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475376 n.1719A>C non_coding_transcript_exon_variant 0.21 capreomycin
linezolid Uncertain significance
rrl 1475380 n.1723C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475458 n.1801C>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475460 n.1803A>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475480 n.1823A>G non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475532 n.1875A>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475544 n.1887A>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475707 n.2050T>G non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476256 n.2599A>C non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1476664 n.3007T>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1476665 n.3008T>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
inhA 1673901 c.-301A>G upstream_gene_variant 0.14 ethionamide
isoniazid
fabG1 1673905 p.Ser156Ala missense_variant 0.15 ethionamide
isoniazid
inhA 1673955 c.-247G>C upstream_gene_variant 0.14 ethionamide
isoniazid
rpsA 1833589 c.48A>C synonymous_variant 0.13 pyrazinamide
rpsA 1833778 c.237C>T synonymous_variant 0.17 pyrazinamide
rpsA 1833781 c.240T>G synonymous_variant 0.17 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.14 pyrazinamide
rpsA 1834069 c.528G>C synonymous_variant 0.13 pyrazinamide
rpsA 1834090 c.549G>C synonymous_variant 0.13 pyrazinamide
rpsA 1834411 c.870T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834417 c.876G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834423 c.882G>C synonymous_variant 0.16 pyrazinamide
rpsA 1834720 c.1179C>G synonymous_variant 0.17 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ndh 2102281 c.762C>G synonymous_variant 0.15 ethionamide
delamanid
isoniazid
PPE35 2169356 c.1257C>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
PPE35 2169902 c.709_711delCTGinsTC frameshift_variant&synonymous_variant 0.17 pyrazinamide Uncertain significance
PPE35 2169910 p.Asn235Tyr missense_variant 0.2 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 1.0 isoniazid
Rv2477c 2783901 c.142T>C synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783914 c.129T>C synonymous_variant 0.19 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783929 c.114C>T synonymous_variant 0.23 ethambutol Not assoc w R - Interim
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin Not assoc w R - Interim
amikacin
Rv2477c 2783938 c.105T>C synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2680 2996136 p.Ser11Asn missense_variant 0.2 capreomycin
thyX 3067802 c.144C>G synonymous_variant 0.16 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3625144 c.-234G>A upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3625149 p.Val489Ile missense_variant 0.15 bedaquiline
rifampicin
lpqB 3625189 c.-279A>C upstream_gene_variant 0.17 bedaquiline
rifampicin
mtrB 3625222 c.1392T>C synonymous_variant 0.18 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3625594 c.-684T>C upstream_gene_variant 0.13 bedaquiline
rifampicin
lpqB 3625678 c.-768C>G upstream_gene_variant 0.16 bedaquiline
rifampicin
lpqB 3625683 c.-773C>T upstream_gene_variant 0.16 bedaquiline
rifampicin
rpoA 3877587 c.921A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoA 3877638 c.870T>C synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoA 3877656 c.852T>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoA 3877668 c.840A>G synonymous_variant 0.31 rifampicin
rpoA 3877671 c.837C>G synonymous_variant 0.29 rifampicin
rpoA 3877677 c.831G>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoA 3877680 c.828G>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoA 3877685 c.823C>T synonymous_variant 0.25 rifampicin
rpoA 3877686 c.822A>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoA 3877695 c.813C>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoA 3877704 c.804G>T synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoA 3877728 c.780C>G synonymous_variant 0.21 rifampicin
rpoA 3877734 c.774G>C synonymous_variant 0.25 rifampicin
rpoA 3877740 c.768G>C synonymous_variant 0.24 rifampicin
rpoA 3877743 c.765T>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoA 3877749 c.759C>T synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoA 3877763 c.745C>T synonymous_variant 0.25 rifampicin
rpoA 3877764 c.744C>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoA 3877770 c.738A>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoA 3877773 c.735G>T synonymous_variant 0.25 rifampicin
rpoA 3877776 c.732T>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoA 3877797 c.711G>C synonymous_variant 0.32 rifampicin
rpoA 3877821 c.687C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877848 c.660C>T synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoA 3877857 c.651G>A synonymous_variant 0.34 rifampicin
rpoA 3877875 c.633T>G synonymous_variant 0.24 rifampicin
rpoA 3877878 c.630G>A synonymous_variant 0.24 rifampicin
rpoA 3877884 c.624G>T synonymous_variant 0.25 rifampicin
rpoA 3877887 c.621G>T synonymous_variant 0.25 rifampicin
rpoA 3877893 c.615C>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoA 3877899 p.Ser203Thr missense_variant 0.23 rifampicin
rpoA 3877905 c.603A>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoA 3877908 c.600T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoA 3877920 c.588G>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoA 3877926 c.582G>C synonymous_variant 0.23 rifampicin
rpoA 3877962 c.546G>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
clpC1 4038596 c.2109A>G synonymous_variant 0.16 pyrazinamide
clpC1 4038602 c.2103G>C synonymous_variant 0.16 pyrazinamide
clpC1 4038713 c.1992T>C synonymous_variant 0.22 pyrazinamide
clpC1 4038740 c.1965G>C synonymous_variant 0.29 pyrazinamide
clpC1 4038755 c.1950G>T synonymous_variant 0.23 pyrazinamide
clpC1 4038761 c.1944C>T synonymous_variant 0.23 pyrazinamide
clpC1 4038767 c.1938G>C synonymous_variant 0.24 pyrazinamide
clpC1 4038773 c.1932T>C synonymous_variant 0.24 pyrazinamide
clpC1 4038779 c.1926C>T synonymous_variant 0.22 pyrazinamide Not assoc w R - Interim
clpC1 4038782 c.1923G>C synonymous_variant 0.23 pyrazinamide
clpC1 4038790 c.1915C>T synonymous_variant 0.22 pyrazinamide Not assoc w R - Interim
clpC1 4038812 c.1893T>C synonymous_variant 0.23 pyrazinamide
clpC1 4038878 c.1827A>G synonymous_variant 0.26 pyrazinamide Not assoc w R - Interim
clpC1 4038905 c.1800A>C synonymous_variant 0.18 pyrazinamide
clpC1 4038908 c.1797C>G synonymous_variant 0.18 pyrazinamide
clpC1 4038911 c.1794G>T synonymous_variant 0.18 pyrazinamide
clpC1 4038914 c.1791G>C synonymous_variant 0.18 pyrazinamide
clpC1 4038917 c.1788C>T synonymous_variant 0.18 pyrazinamide
clpC1 4038923 c.1782A>G synonymous_variant 0.19 pyrazinamide
clpC1 4038932 c.1773G>C synonymous_variant 0.19 pyrazinamide
clpC1 4039082 c.1623C>T synonymous_variant 0.15 pyrazinamide
clpC1 4039085 c.1620A>G synonymous_variant 0.15 pyrazinamide
clpC1 4039091 c.1614G>C synonymous_variant 0.16 pyrazinamide
clpC1 4039097 c.1608G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039118 c.1587C>G synonymous_variant 0.17 pyrazinamide
clpC1 4039121 c.1584T>C synonymous_variant 0.18 pyrazinamide
clpC1 4039139 c.1566G>A synonymous_variant 0.13 pyrazinamide
clpC1 4039142 c.1563A>G synonymous_variant 0.13 pyrazinamide
clpC1 4039145 c.1560G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039169 c.1536A>G synonymous_variant 0.14 pyrazinamide
clpC1 4039178 c.1527G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039199 c.1506C>G synonymous_variant 0.13 pyrazinamide
clpC1 4039208 c.1497C>G synonymous_variant 0.19 pyrazinamide
clpC1 4039220 c.1485G>C synonymous_variant 0.21 pyrazinamide
clpC1 4039274 c.1431G>C synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
clpC1 4039280 c.1425G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039283 c.1422C>T synonymous_variant 0.17 pyrazinamide
clpC1 4039286 c.1419T>C synonymous_variant 0.17 pyrazinamide
clpC1 4039292 c.1413C>T synonymous_variant 0.18 pyrazinamide
clpC1 4039298 c.1407T>C synonymous_variant 0.13 pyrazinamide
clpC1 4039757 c.948A>G synonymous_variant 0.12 pyrazinamide
clpC1 4039898 c.807C>G synonymous_variant 0.16 pyrazinamide
clpC1 4039904 c.801A>G synonymous_variant 0.17 pyrazinamide
clpC1 4039907 c.798G>A synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
clpC1 4039931 c.774T>C synonymous_variant 0.12 pyrazinamide
clpC1 4040441 c.264C>G synonymous_variant 0.17 pyrazinamide
clpC1 4040444 c.261C>G synonymous_variant 0.17 pyrazinamide
clpC1 4040450 c.255A>G synonymous_variant 0.2 pyrazinamide Not assoc w R - Interim
clpC1 4040459 c.246C>G synonymous_variant 0.17 pyrazinamide
clpC1 4040465 c.240T>C synonymous_variant 0.18 pyrazinamide
clpC1 4040477 c.228G>C synonymous_variant 0.2 pyrazinamide
clpC1 4040480 c.225T>G synonymous_variant 0.21 pyrazinamide
clpC1 4040522 c.183T>C synonymous_variant 0.21 pyrazinamide Not assoc w R - Interim
clpC1 4040531 c.174T>C synonymous_variant 0.17 pyrazinamide
clpC1 4040537 c.168G>C synonymous_variant 0.18 pyrazinamide
clpC1 4040644 c.61A>C synonymous_variant 0.13 pyrazinamide
clpC1 4040648 c.57G>A synonymous_variant 0.14 pyrazinamide
clpC1 4040654 c.51G>A synonymous_variant 0.14 pyrazinamide
panD 4044186 p.Leu32Phe missense_variant 0.12 pyrazinamide
panD 4044195 c.87T>C synonymous_variant 0.12 pyrazinamide
embC 4239298 c.-565C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Not assoc w R
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