TB-Profiler result

Run: SRR28351455
Summary

Run ID: SRR28351455

Sample name:

Date: 2024-10-04T10:21:27.931961

Number of reads: 3934092

Percentage reads mapped: 98.25

Median coverage: 119.0

Strain: lineage3.1.2.1;lineage4

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.95
lineage3.1.2 East-African-Indian RD750 0.95
lineage4 Euro-American None 0.06
lineage3.1.2.1 East-African-Indian RD750 0.93
lineage3.1 East-African-Indian RD750 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 gyrB p.Thr500Asn Uncertain significance Mutation from literature
gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrB p.Thr500Asn Uncertain significance Mutation from literature
gyrA p.Ala90Val Assoc w R
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
gyrB 6738 p.Thr500Asn missense_variant 0.28 levofloxacin Uncertain significance Mutation from literature
moxifloxacin Uncertain significance Mutation from literature
gyrA 7570 p.Ala90Val missense_variant 0.68 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
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
gyrA 6700 c.-602T>C upstream_gene_variant 0.25 levofloxacin
moxifloxacin
gyrA 6703 c.-599G>C upstream_gene_variant 0.27 levofloxacin
moxifloxacin
gyrA 6709 c.-593A>G upstream_gene_variant 0.26 levofloxacin
moxifloxacin
gyrA 6712 c.-590G>C upstream_gene_variant 0.25 levofloxacin
moxifloxacin
gyrB 6715 c.1476C>G synonymous_variant 0.27 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 6730 c.-572A>G upstream_gene_variant 0.29 levofloxacin
moxifloxacin
gyrA 6742 c.-560A>G upstream_gene_variant 0.29 levofloxacin
moxifloxacin
gyrB 6745 c.1506T>C synonymous_variant 0.3 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 6760 c.-542G>C upstream_gene_variant 0.32 levofloxacin
moxifloxacin
gyrA 6778 c.-524C>T upstream_gene_variant 0.34 levofloxacin
moxifloxacin
gyrB 6793 c.1554T>C synonymous_variant 0.32 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6798 p.Gly520Ala missense_variant 0.3 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
gyrB 6811 c.1572C>T synonymous_variant 0.27 levofloxacin
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 7442 c.141G>C synonymous_variant 0.19 levofloxacin
moxifloxacin
gyrA 7451 c.150C>G synonymous_variant 0.22 levofloxacin
moxifloxacin
gyrA 7457 c.156T>C synonymous_variant 0.23 levofloxacin
moxifloxacin
gyrA 7472 c.171T>C synonymous_variant 0.23 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrA 7475 c.174A>G synonymous_variant 0.24 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7480 p.Phe60Tyr missense_variant 0.23 levofloxacin
moxifloxacin
gyrA 7484 c.183T>C synonymous_variant 0.26 levofloxacin
moxifloxacin
gyrA 7490 c.189C>G synonymous_variant 0.26 levofloxacin
moxifloxacin
gyrA 7499 c.198G>C synonymous_variant 0.29 levofloxacin
moxifloxacin
gyrA 7514 c.213C>G synonymous_variant 0.31 levofloxacin
moxifloxacin
gyrA 7517 c.216G>A synonymous_variant 0.31 levofloxacin
moxifloxacin
gyrA 7520 c.219G>C synonymous_variant 0.31 levofloxacin
moxifloxacin
gyrA 7523 c.222C>G synonymous_variant 0.31 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7541 c.240C>G synonymous_variant 0.32 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7547 c.246C>T synonymous_variant 0.33 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7565 c.264C>T synonymous_variant 0.31 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7585 p.Ser95Thr missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7595 c.294C>G synonymous_variant 0.25 levofloxacin
moxifloxacin
gyrA 7607 c.306C>G synonymous_variant 0.22 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7613 c.312G>A synonymous_variant 0.19 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7619 c.318C>T synonymous_variant 0.18 levofloxacin
moxifloxacin
gyrA 7814 c.513C>G synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7835 c.534A>C synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 9167 c.1866C>T synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 9182 c.1881T>C synonymous_variant 0.19 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9197 c.1896G>C synonymous_variant 0.22 levofloxacin
moxifloxacin
gyrA 9200 c.1899A>G synonymous_variant 0.24 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9227 c.1926C>G synonymous_variant 0.34 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9230 c.1929T>C synonymous_variant 0.33 levofloxacin
moxifloxacin
gyrA 9233 c.1932C>G synonymous_variant 0.33 levofloxacin
moxifloxacin
gyrA 9242 c.1941A>C synonymous_variant 0.38 levofloxacin
moxifloxacin
gyrA 9248 c.1947G>C synonymous_variant 0.37 levofloxacin
moxifloxacin
gyrA 9252 p.Val651Ile missense_variant 0.38 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9267 p.Asn656Gly missense_variant 0.41 levofloxacin
moxifloxacin
gyrA 9296 c.1995T>C synonymous_variant 0.46 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Glu missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 9308 c.2007C>T synonymous_variant 0.45 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9323 c.2022C>G synonymous_variant 0.42 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9335 c.2034G>C synonymous_variant 0.4 levofloxacin
moxifloxacin
gyrA 9345 c.2044A>C synonymous_variant 0.38 levofloxacin
moxifloxacin
gyrA 9377 c.2076A>G synonymous_variant 0.27 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9383 c.2082T>C synonymous_variant 0.24 levofloxacin
moxifloxacin
gyrA 9386 c.2085T>G synonymous_variant 0.23 levofloxacin
moxifloxacin
gyrA 9395 c.2094G>C synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9398 c.2097T>G synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 9401 c.2100G>T synonymous_variant 0.15 levofloxacin
moxifloxacin
Rv0010c 13236 p.Ser108Asn missense_variant 0.91 isoniazid Uncertain significance
fgd1 491349 c.567T>C synonymous_variant 0.21 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fgd1 491364 c.582T>C synonymous_variant 0.32 pretomanid
delamanid
clofazimine
fgd1 491367 c.585G>C synonymous_variant 0.32 pretomanid
delamanid
clofazimine
fgd1 491379 c.597C>T synonymous_variant 0.37 pretomanid
delamanid
clofazimine
fgd1 491382 c.600G>A synonymous_variant 0.39 pretomanid
delamanid
clofazimine
fgd1 491412 c.630G>C synonymous_variant 0.38 pretomanid
delamanid
clofazimine
fgd1 491416 p.Arg212Leu missense_variant 0.36 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
fgd1 491428 p.Ala216Lys missense_variant 0.35 pretomanid
delamanid
clofazimine
fgd1 491436 c.654T>C synonymous_variant 0.34 pretomanid
delamanid
clofazimine
fgd1 491439 p.Asp219Glu missense_variant 0.34 pretomanid
delamanid
clofazimine
fgd1 491442 c.660A>G synonymous_variant 0.35 pretomanid
delamanid
clofazimine
fgd1 491443 p.Ser221Asp missense_variant 0.35 pretomanid
delamanid
clofazimine
fgd1 491447 p.Val222Ala missense_variant 0.34 pretomanid
delamanid
clofazimine
fgd1 491472 c.690A>G synonymous_variant 0.37 pretomanid
delamanid
clofazimine
fgd1 491493 c.711C>G synonymous_variant 0.39 pretomanid
delamanid
clofazimine
fgd1 491499 c.717G>C synonymous_variant 0.33 pretomanid
delamanid
clofazimine
fgd1 491508 c.726A>G synonymous_variant 0.27 pretomanid
delamanid
clofazimine
fgd1 491509 c.727T>C synonymous_variant 0.25 pretomanid
delamanid
clofazimine
fgd1 491526 c.744T>C synonymous_variant 0.18 pretomanid
delamanid
clofazimine
fgd1 491542 c.760T>C synonymous_variant 0.17 pretomanid
delamanid
clofazimine
fgd1 491546 p.Thr255Ser missense_variant 0.17 pretomanid
delamanid
clofazimine
fgd1 491550 c.768T>C synonymous_variant 0.16 pretomanid
delamanid
clofazimine
fgd1 491563 c.781_782delAGinsTC synonymous_variant 0.18 pretomanid
delamanid
clofazimine
fgd1 491571 c.789C>T synonymous_variant 0.23 pretomanid
delamanid
clofazimine
fgd1 491595 c.813C>G synonymous_variant 0.26 pretomanid
delamanid
clofazimine
fgd1 491601 c.819T>C synonymous_variant 0.24 pretomanid
delamanid
clofazimine
fgd1 491610 c.828A>G synonymous_variant 0.23 pretomanid
delamanid
clofazimine
fgd1 491616 c.834A>G synonymous_variant 0.22 pretomanid
delamanid
clofazimine
fgd1 491742 c.960T>C synonymous_variant 0.95 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 656332 p.Asp380Gly missense_variant 0.19 ethionamide Uncertain significance
Rv0565c 656358 c.1113T>C synonymous_variant 0.19 ethionamide Not assoc w R - Interim
Rv0565c 656364 c.1107T>C synonymous_variant 0.21 ethionamide
Rv0565c 656366 c.1100_1104delCTCGG frameshift_variant 0.2 ethionamide Uncertain significance
Rv0565c 656375 c.1095_1096insAAGCC frameshift_variant 0.2 ethionamide Uncertain significance
Rv0565c 656383 p.Val363Asn missense_variant 0.18 ethionamide
Rv0565c 656391 c.1080C>G synonymous_variant 0.17 ethionamide
Rv0565c 656401 p.Ala357Arg missense_variant 0.17 ethionamide
Rv0565c 656403 c.1068C>G synonymous_variant 0.17 ethionamide
Rv0565c 656412 c.1059T>C synonymous_variant 0.17 ethionamide
Rv0565c 656415 c.1056G>A synonymous_variant 0.17 ethionamide
Rv0565c 656423 c.1048T>C synonymous_variant 0.19 ethionamide
Rv0565c 656442 c.1029C>G synonymous_variant 0.16 ethionamide
Rv0565c 656448 c.1023T>C synonymous_variant 0.15 ethionamide
Rv0565c 657081 c.390G>A synonymous_variant 0.94 ethionamide Not assoc w R - Interim
Rv0565c 657120 c.351C>G synonymous_variant 0.93 ethionamide Not assoc w R - Interim
nusG 734472 c.219T>C synonymous_variant 0.28 rifampicin
nusG 734475 c.222T>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
nusG 734532 c.279A>G synonymous_variant 0.34 rifampicin Not assoc w R - Interim
nusG 734541 c.288A>G synonymous_variant 0.32 rifampicin Not assoc w R - Interim
nusG 734559 c.306T>C synonymous_variant 0.29 rifampicin
nusG 734566 c.313C>T synonymous_variant 0.27 rifampicin
nusG 734571 c.318C>G synonymous_variant 0.26 rifampicin
nusG 734580 c.327T>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
nusG 734595 c.342C>T synonymous_variant 0.22 rifampicin Not assoc w R - Interim
nusG 734596 c.343T>C synonymous_variant 0.22 rifampicin
nusG 734614 p.Ala121Ser missense_variant 0.17 rifampicin
rpoB 759746 c.-61C>T upstream_gene_variant 0.95 rifampicin Not assoc w R
rpoB 761654 c.1848G>A synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761657 c.1851C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761675 c.1869G>T synonymous_variant 0.18 rifampicin
rpoB 761690 c.1884G>C synonymous_variant 0.19 rifampicin
rpoB 761705 c.1899C>T synonymous_variant 0.19 rifampicin
rpoB 762434 c.2628T>G synonymous_variant 0.96 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.91 rifampicin Not assoc w R
rpoC 764085 p.Asn239Thr missense_variant 0.21 rifampicin Uncertain significance
rpoC 764098 c.729A>G synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 764101 c.732C>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764104 c.735C>G synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 764134 c.765C>G synonymous_variant 0.57 rifampicin Not assoc w R - Interim
rpoC 764140 c.771C>T synonymous_variant 0.59 rifampicin Not assoc w R - Interim
rpoC 764143 c.774G>C synonymous_variant 0.61 rifampicin Not assoc w R - Interim
rpoC 764188 c.819A>G synonymous_variant 0.69 rifampicin Not assoc w R - Interim
rpoC 764203 c.834G>C synonymous_variant 0.66 rifampicin
rpoC 764206 c.837T>C synonymous_variant 0.65 rifampicin Not assoc w R - Interim
rpoC 764207 p.Val280Thr missense_variant 0.65 rifampicin Uncertain significance
rpoC 764213 p.Arg282Lys missense_variant 0.66 rifampicin Uncertain significance
rpoC 764248 c.879C>G synonymous_variant 0.64 rifampicin Not assoc w R - Interim
rpoC 764254 c.885G>T synonymous_variant 0.6 rifampicin Not assoc w R - Interim
rpoC 764255 c.886C>T synonymous_variant 0.6 rifampicin Not assoc w R - Interim
rpoC 764278 c.909A>G synonymous_variant 0.56 rifampicin Not assoc w R - Interim
rpoC 764497 c.1128A>G synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 764503 c.1134G>C synonymous_variant 0.35 rifampicin
rpoC 764521 c.1152T>C synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoC 764527 c.1158C>A synonymous_variant 0.45 rifampicin
rpoC 764539 c.1170C>G synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoC 764548 c.1179G>C synonymous_variant 0.54 rifampicin
rpoC 764560 c.1191T>C synonymous_variant 0.53 rifampicin Not assoc w R - Interim
rpoC 764566 c.1197C>G synonymous_variant 0.54 rifampicin Not assoc w R - Interim
rpoC 764626 c.1257C>T synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.45 rifampicin Not assoc w R - Interim
rpoC 764668 c.1299C>T synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoC 765478 c.2109T>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 765508 c.2139C>G synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoC 765526 c.2157C>G synonymous_variant 0.54 rifampicin Not assoc w R - Interim
rpoC 765547 c.2178C>G synonymous_variant 0.53 rifampicin Not assoc w R - Interim
rpoC 765548 c.2179_2181delAGCinsTCG synonymous_variant 0.53 rifampicin
rpoC 765553 c.2184C>G synonymous_variant 0.52 rifampicin
rpoC 765556 c.2187G>C synonymous_variant 0.51 rifampicin
rpoC 765559 c.2190G>C synonymous_variant 0.52 rifampicin
rpoC 765562 c.2193G>C synonymous_variant 0.52 rifampicin
rpoC 765611 p.His748Ser missense_variant 0.57 rifampicin Uncertain significance
rpoC 765625 c.2256C>G synonymous_variant 0.55 rifampicin Not assoc w R - Interim
rpoC 765628 c.2259G>C synonymous_variant 0.55 rifampicin Not assoc w R - Interim
rpoC 765655 c.2286T>C synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoC 765658 c.2289C>T synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoC 765662 c.2293_2295delTTGinsCTC synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 765700 c.2331T>C synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoC 765850 c.2481G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765871 c.2502T>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 765875 p.Val836Ile missense_variant 0.19 rifampicin Uncertain significance
rpoC 765892 c.2523T>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 765904 c.2535C>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 765937 c.2568T>C synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoC 765961 c.2592G>A synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoC 765967 c.2598C>T synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoC 765979 c.2610C>G synonymous_variant 0.46 rifampicin Not assoc w R - Interim
rpoC 765982 c.2613C>T synonymous_variant 0.46 rifampicin Not assoc w R - Interim
rpoC 765994 c.2625A>T synonymous_variant 0.48 rifampicin Not assoc w R - Interim
rpoC 766009 c.2640G>C synonymous_variant 0.45 rifampicin Not assoc w R - Interim
rpoC 766012 c.2643C>G synonymous_variant 0.46 rifampicin Not assoc w R - Interim
rpoC 766043 p.Gln892Gly missense_variant 0.38 rifampicin
rpoC 766061 p.Val898Ile missense_variant 0.34 rifampicin
rpoC 766381 c.3012C>T synonymous_variant 0.17 rifampicin
rpoC 766384 c.3015A>G synonymous_variant 0.17 rifampicin
rpoC 766387 c.3018C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 766390 c.3021C>T synonymous_variant 0.17 rifampicin
rpoC 766426 c.3057C>T synonymous_variant 0.19 rifampicin
rpoC 766447 c.3078T>C synonymous_variant 0.21 rifampicin
rpoC 766456 c.3087C>G synonymous_variant 0.21 rifampicin
rpoC 766459 c.3090G>C synonymous_variant 0.21 rifampicin
rpoC 766483 c.3114G>C synonymous_variant 0.17 rifampicin
rpoC 766484 p.Val1039Ile missense_variant 0.17 rifampicin Uncertain significance
rpoC 766492 c.3123T>C synonymous_variant 0.18 rifampicin
rpoC 766945 c.3576A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 766963 c.3594T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 766978 c.3609C>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 766996 c.3627C>T synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoC 767002 c.3633G>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 767032 c.3663G>T synonymous_variant 0.46 rifampicin Not assoc w R - Interim
rpoC 767035 c.3666G>C synonymous_variant 0.48 rifampicin Not assoc w R - Interim
rpoC 767059 c.3690T>G synonymous_variant 0.48 rifampicin Not assoc w R - Interim
rpoC 767098 c.3729T>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 767104 c.3735C>G synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoC 767105 p.Asn1246Gln missense_variant 0.37 rifampicin Uncertain significance
rpoC 767119 c.3750A>G synonymous_variant 0.34 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.97 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.98 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
atpE 1460965 c.-80A>G upstream_gene_variant 0.92 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 0.99 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.81 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.66 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473290 n.1445delCinsTT non_coding_transcript_exon_variant 0.66 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.63 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475276 n.1619T>A non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475277 n.1620G>C non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475278 n.1621G>C non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834423 c.882G>C synonymous_variant 0.39 pyrazinamide
rpsA 1834451 c.910T>C synonymous_variant 0.57 pyrazinamide
rpsA 1834456 c.915T>G synonymous_variant 0.59 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.64 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.67 pyrazinamide
rpsA 1834522 c.981C>T synonymous_variant 0.71 pyrazinamide
rpsA 1834527 p.Arg329Gln missense_variant 0.71 pyrazinamide
rpsA 1834546 c.1005T>C synonymous_variant 0.71 pyrazinamide
rpsA 1834555 c.1014T>C synonymous_variant 0.7 pyrazinamide
rpsA 1834573 c.1032G>C synonymous_variant 0.68 pyrazinamide
rpsA 1834603 p.Glu354Asp missense_variant 0.49 pyrazinamide
rpsA 1834606 c.1065C>G synonymous_variant 0.45 pyrazinamide
rpsA 1834609 c.1068T>C synonymous_variant 0.43 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
katG 2154724 p.Arg463Leu missense_variant 0.96 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.94 pyrazinamide Not assoc w R
PPE35 2168604 p.Pro670Leu missense_variant 0.93 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 0.93 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.97 pyrazinamide
kasA 2518480 c.366T>C synonymous_variant 0.15 isoniazid
kasA 2518488 p.Ser125Thr missense_variant 0.22 isoniazid
kasA 2518504 c.390T>C synonymous_variant 0.31 isoniazid
kasA 2518506 p.Ala131Glu missense_variant 0.32 isoniazid
kasA 2518519 c.405G>T synonymous_variant 0.39 isoniazid
kasA 2518528 c.414C>G synonymous_variant 0.41 isoniazid
kasA 2518561 c.447T>C synonymous_variant 0.46 isoniazid
kasA 2518567 c.453G>T synonymous_variant 0.44 isoniazid
kasA 2518574 p.Ile154Val missense_variant 0.44 isoniazid
kasA 2518579 c.465T>C synonymous_variant 0.43 isoniazid
kasA 2518585 c.471G>A synonymous_variant 0.43 isoniazid
kasA 2518588 c.474T>G synonymous_variant 0.43 isoniazid
kasA 2518591 c.477G>C synonymous_variant 0.43 isoniazid
kasA 2518606 c.492G>C synonymous_variant 0.44 isoniazid
kasA 2518609 p.Met165Ile missense_variant 0.46 isoniazid
kasA 2518612 c.498C>T synonymous_variant 0.47 isoniazid
kasA 2518618 c.504G>A synonymous_variant 0.46 isoniazid
kasA 2518627 c.513T>C synonymous_variant 0.43 isoniazid
kasA 2518636 c.522C>T synonymous_variant 0.43 isoniazid
kasA 2518642 c.528A>G synonymous_variant 0.39 isoniazid
kasA 2518657 c.543G>C synonymous_variant 0.29 isoniazid
kasA 2518663 c.549T>G synonymous_variant 0.26 isoniazid
kasA 2518672 c.558G>C synonymous_variant 0.2 isoniazid
kasA 2518678 c.564C>T synonymous_variant 0.17 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.97 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.91 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
Rv2477c 2783601 c.442C>T synonymous_variant 0.16 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783605 c.438T>C synonymous_variant 0.17 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783623 c.420G>A synonymous_variant 0.22 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783626 p.Ala139Ser missense_variant 0.21 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783634 p.Leu137Ile missense_variant 0.23 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783646 p.Asp133Asn missense_variant 0.24 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783650 c.393C>T synonymous_variant 0.24 kanamycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2477c 2783656 c.387G>C synonymous_variant 0.26 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783665 c.378A>G synonymous_variant 0.26 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783674 c.369T>C synonymous_variant 0.24 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783683 c.360A>G synonymous_variant 0.23 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783700 p.Thr115Ser missense_variant 0.25 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2752c 3065916 c.276T>C synonymous_variant 0.2 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3065922 c.270T>C synonymous_variant 0.2 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3065925 c.267G>C synonymous_variant 0.22 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3065928 c.264G>C synonymous_variant 0.25 levofloxacin
moxifloxacin
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
Rv2752c 3065947 p.Gly82Ala missense_variant 0.4 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3065957 c.235T>C synonymous_variant 0.46 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3065972 p.Ile74Val missense_variant 0.51 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3065979 c.213T>C synonymous_variant 0.52 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3065990 p.Glu68Gln missense_variant 0.54 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3065993 p.Val67Ile missense_variant 0.54 levofloxacin
moxifloxacin
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
Rv2752c 3065994 c.198T>C synonymous_variant 0.55 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3066000 p.Met64Ile missense_variant 0.57 levofloxacin
moxifloxacin
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
Rv2752c 3066003 c.189C>T synonymous_variant 0.59 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid
rifampicin
ethambutol
Rv2752c 3066042 c.150T>G synonymous_variant 0.56 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3066045 c.147T>C synonymous_variant 0.57 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3066054 c.138T>G synonymous_variant 0.55 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3066066 c.126T>C synonymous_variant 0.51 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3066071 c.121T>C synonymous_variant 0.51 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3066084 c.108C>T synonymous_variant 0.46 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3066096 c.96G>C synonymous_variant 0.39 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3066117 p.Asn25Ser missense_variant 0.26 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3066123 c.69C>T synonymous_variant 0.24 levofloxacin
moxifloxacin
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
Rv2752c 3066135 c.57C>G synonymous_variant 0.21 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3066141 c.51G>C synonymous_variant 0.21 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3066144 c.46_48delTTGinsCTA synonymous_variant 0.2 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3066155 p.Ser13Pro missense_variant 0.15 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3877647 c.861C>T synonymous_variant 0.2 rifampicin
rpoA 3877656 c.852T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3877668 c.840A>G synonymous_variant 0.26 rifampicin
rpoA 3877686 c.822A>G synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoA 3877689 c.819C>G synonymous_variant 0.31 rifampicin
rpoA 3877692 c.816G>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoA 3877695 c.813C>G synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoA 3877704 c.804G>T synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoA 3877743 c.765T>C synonymous_variant 0.48 rifampicin Not assoc w R - Interim
rpoA 3877764 c.744C>G synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoA 3877770 c.738A>G synonymous_variant 0.51 rifampicin Not assoc w R - Interim
rpoA 3877776 c.732T>C synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoA 3877782 c.726T>C synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoA 3877785 c.723C>G synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoA 3877794 c.714G>C synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoA 3877818 c.690A>G synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoA 3877848 c.660C>T synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoA 3877857 c.651G>A synonymous_variant 0.23 rifampicin
clpC1 4039208 c.1497C>G synonymous_variant 0.3 pyrazinamide
clpC1 4039271 c.1434G>A synonymous_variant 0.55 pyrazinamide
clpC1 4039283 c.1422C>T synonymous_variant 0.59 pyrazinamide
clpC1 4039286 c.1419T>G synonymous_variant 0.6 pyrazinamide
clpC1 4039292 c.1413C>T synonymous_variant 0.61 pyrazinamide
clpC1 4039295 c.1410A>C synonymous_variant 0.6 pyrazinamide
clpC1 4039313 c.1392C>T synonymous_variant 0.64 pyrazinamide
clpC1 4039319 c.1386T>C synonymous_variant 0.65 pyrazinamide Not assoc w R - Interim
clpC1 4039322 c.1383T>G synonymous_variant 0.65 pyrazinamide
clpC1 4039328 c.1377A>G synonymous_variant 0.64 pyrazinamide
clpC1 4039331 c.1374C>G synonymous_variant 0.64 pyrazinamide
clpC1 4039338 p.Thr456Gln missense_variant 0.63 pyrazinamide
clpC1 4039352 c.1353C>G synonymous_variant 0.62 pyrazinamide
clpC1 4039382 c.1323C>G synonymous_variant 0.49 pyrazinamide
clpC1 4039391 c.1314T>G synonymous_variant 0.48 pyrazinamide
clpC1 4039394 c.1311G>C synonymous_variant 0.45 pyrazinamide
clpC1 4039397 c.1308A>G synonymous_variant 0.45 pyrazinamide
clpC1 4039406 c.1299G>C synonymous_variant 0.42 pyrazinamide
clpC1 4039409 c.1296T>C synonymous_variant 0.41 pyrazinamide
clpC1 4039412 c.1293T>A synonymous_variant 0.4 pyrazinamide
clpC1 4039415 p.Glu430Asp missense_variant 0.41 pyrazinamide Uncertain significance
clpC1 4039430 c.1275T>C synonymous_variant 0.35 pyrazinamide
clpC1 4039442 c.1263A>G synonymous_variant 0.32 pyrazinamide
clpC1 4039448 c.1257A>G synonymous_variant 0.26 pyrazinamide Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.89 pyrazinamide
panD 4045270 c.-990delA upstream_gene_variant 0.94 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.91 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.92 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.98 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.94 streptomycin Not assoc w R