TB-Profiler result

Run: ERR4798139
Summary

Run ID: ERR4798139

Sample name:

Date: 2025-09-15T14:44:37.108128

Number of reads: 2127162

Percentage reads mapped: 86.75

Median coverage: 65.0

Strain: lineage1.1.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1 Indo-Oceanic RD239 100.0
lineage1.1 Indo-Oceanic RD239 100.0
lineage1.1.2 Indo-Oceanic RD239 100.0
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 1519 p.Arg507Cys missense_variant 1.0 isoniazid Uncertain significance
gyrB 6112 p.Met291Ile missense_variant 0.98 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.97 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.89 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8897 c.1596T>C synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9143 c.1842T>C synonymous_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.98 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 1.0 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 1.0 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
delamanid Not assoc w R - Interim
pretomanid Uncertain significance
mshA 575884 c.537G>C synonymous_variant 0.14 ethionamide Uncertain significance
isoniazid Uncertain significance
mshA 575887 c.540G>T synonymous_variant 0.14 ethionamide Uncertain significance
isoniazid Uncertain significance
mshA 575893 c.546C>G synonymous_variant 0.14 ethionamide Uncertain significance
isoniazid Uncertain significance
mshA 575896 c.549G>T synonymous_variant 0.14 ethionamide Uncertain significance
isoniazid Uncertain significance
mshA 575905 c.558G>C synonymous_variant 0.14 ethionamide Uncertain significance
isoniazid Uncertain significance
mshA 575914 c.567C>G synonymous_variant 0.13 ethionamide Uncertain significance
isoniazid Uncertain significance
mshA 575926 c.579A>G synonymous_variant 0.13 ethionamide Uncertain significance
isoniazid Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide Uncertain significance
hadA 732389 p.Ser154Thr missense_variant 0.16 isoniazid Uncertain significance
hadA 732396 p.Gly156Ala missense_variant 0.17 isoniazid Uncertain significance
hadA 732398 p.Ala157Thr missense_variant 0.17 isoniazid Uncertain significance
nusG 734116 c.-138T>C upstream_gene_variant 0.89 rifampicin Not assoc w R
nusG 734132 c.-122G>C upstream_gene_variant 0.14 rifampicin Uncertain significance
nusG 734143 c.-111C>T upstream_gene_variant 0.18 rifampicin Uncertain significance
nusG 734147 c.-107T>C upstream_gene_variant 0.18 rifampicin Uncertain significance
nusG 734150 c.-104G>C upstream_gene_variant 0.18 rifampicin Uncertain significance
nusG 734173 c.-81C>G upstream_gene_variant 0.17 rifampicin Uncertain significance
nusG 734175 c.-79_-77delGGTinsCTG upstream_gene_variant 0.17 rifampicin Uncertain significance
nusG 734183 c.-71C>T upstream_gene_variant 0.17 rifampicin Uncertain significance
nusG 734505 c.252G>A synonymous_variant 0.15 rifampicin Uncertain significance
nusG 734532 c.279A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760591 p.Val262Ala missense_variant 0.14 rifampicin Uncertain significance
rpoB 760634 c.828T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761057 c.1251G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761129 c.1323G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761133 c.1327_1329delTTGinsCTC synonymous_variant 0.17 rifampicin Uncertain significance
rpoB 761150 c.1344A>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761165 c.1359G>A synonymous_variant 0.16 rifampicin Uncertain significance
rpoB 761168 c.1362C>G synonymous_variant 0.17 rifampicin Uncertain significance
rpoB 761171 c.1365C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761180 c.1374A>G synonymous_variant 0.15 rifampicin Uncertain significance
rpoB 761189 c.1383T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761249 c.1443A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761252 c.1446C>T synonymous_variant 0.16 rifampicin Uncertain significance
rpoB 761261 c.1455G>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761264 c.1458C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761282 c.1476C>G synonymous_variant 0.16 rifampicin Uncertain significance
rpoB 761286 c.1480C>T synonymous_variant 0.17 rifampicin Uncertain significance
rpoB 761300 c.1494G>A synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761327 c.1521A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761354 c.1548C>T synonymous_variant 0.25 rifampicin Uncertain significance
rpoB 761360 c.1554T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 761363 c.1557C>T synonymous_variant 0.22 rifampicin Uncertain significance
rpoB 761378 c.1572C>T synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 761393 c.1587G>A synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761408 c.1602G>C synonymous_variant 0.16 rifampicin Uncertain significance
rpoB 761414 c.1608A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 762758 c.-612G>C upstream_gene_variant 0.14 rifampicin Uncertain significance
rpoB 762782 c.2976T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762788 c.2982G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762789 p.Leu995Met missense_variant 0.14 rifampicin Uncertain significance
rpoC 762794 c.-576C>G upstream_gene_variant 0.14 rifampicin Uncertain significance
rpoB 762795 p.Asp997Asn missense_variant 0.14 rifampicin Uncertain significance
rpoC 762800 c.-570C>A upstream_gene_variant 0.15 rifampicin Uncertain significance
rpoB 762812 c.3006C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762814 p.Met1003Arg missense_variant 0.16 rifampicin Uncertain significance
rpoB 762818 c.3012C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 762824 c.-546C>T upstream_gene_variant 0.16 rifampicin Uncertain significance
rpoB 762827 c.3021G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762833 c.3027C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 762836 c.-534C>G upstream_gene_variant 0.17 rifampicin Uncertain significance
rpoB 762857 c.3051C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 762860 c.3054G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 762890 c.-480C>T upstream_gene_variant 0.16 rifampicin Uncertain significance
rpoB 762962 c.3156C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763028 c.3222T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 763034 c.3228C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 763040 c.3234C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763082 c.-288C>G upstream_gene_variant 0.2 rifampicin Uncertain significance
rpoB 763085 c.3279C>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763136 c.3330C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763528 c.159G>A synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763884 p.Ala172Val missense_variant 0.91 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.91 rifampicin Not assoc w R
rpoC 763969 c.600C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763978 c.609C>T synonymous_variant 0.2 rifampicin Uncertain significance
rpoC 763991 p.Ile208Leu missense_variant 0.17 rifampicin Uncertain significance
rpoC 763996 c.627T>C synonymous_variant 0.17 rifampicin Uncertain significance
rpoC 764002 c.633C>G synonymous_variant 0.18 rifampicin Uncertain significance
rpoC 764005 c.636G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764011 c.642T>C synonymous_variant 0.17 rifampicin Uncertain significance
rpoC 764024 c.655_657delTTGinsCTC synonymous_variant 0.16 rifampicin Uncertain significance
rpoC 764040 p.Ser224Thr missense_variant 0.15 rifampicin Uncertain significance
rpoC 764044 c.675T>G synonymous_variant 0.15 rifampicin Uncertain significance
rpoC 764059 c.690G>C synonymous_variant 0.16 rifampicin Uncertain significance
rpoC 764083 c.714A>G synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 764536 c.1167G>C synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 764554 c.1185C>T synonymous_variant 0.18 rifampicin Uncertain significance
rpoC 764575 c.1206T>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764578 c.1209C>G synonymous_variant 0.15 rifampicin Uncertain significance
rpoC 764626 c.1257C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764737 c.1368G>C synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 764764 c.1395T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764782 c.1413C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764797 c.1428G>C synonymous_variant 0.15 rifampicin Uncertain significance
rpoC 764809 c.1440C>T synonymous_variant 0.14 rifampicin Not assoc w R
rpoC 764824 c.1455T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765040 c.1671T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765047 c.1678T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 765052 c.1683C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765053 p.Ser562Thr missense_variant 0.14 rifampicin Uncertain significance
rpoC 765171 p.Pro601Leu missense_variant 1.0 rifampicin Not assoc w R
rpoC 765370 c.2001G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765728 p.Gln787Lys missense_variant 0.16 rifampicin Uncertain significance
rpoC 765734 c.2365T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 765739 c.2370G>T synonymous_variant 0.16 rifampicin Uncertain significance
rpoC 765751 c.2382C>G synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 765753 p.Asp795Ala missense_variant 0.13 rifampicin Uncertain significance
rpoC 765772 c.2403C>G synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 765787 c.2418C>T synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 765793 c.2424C>G synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 765796 c.2427C>T synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 765811 c.2442T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765844 c.2475C>T synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 765850 c.2481G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766366 c.2997C>T synonymous_variant 0.13 rifampicin Uncertain significance
rpoC 766369 c.3000C>G synonymous_variant 0.13 rifampicin Uncertain significance
rpoC 766384 c.3015A>G synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 766390 c.3021C>T synonymous_variant 0.15 rifampicin Uncertain significance
rpoC 766408 c.3039C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 766426 c.3057C>T synonymous_variant 0.15 rifampicin Uncertain significance
rpoC 766774 c.3405T>C synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 766963 c.3594T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 766978 c.3609C>A synonymous_variant 0.18 rifampicin Uncertain significance
rpoC 766981 c.3612T>C synonymous_variant 0.18 rifampicin Uncertain significance
rpoC 766996 c.3627C>T synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.24 rifampicin Uncertain significance
rpoC 767059 c.3690T>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.22 rifampicin Uncertain significance
rpoC 767098 c.3729T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 767107 c.3738C>T synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 767119 c.3750A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 767134 c.3765C>A synonymous_variant 0.19 rifampicin Uncertain significance
rpoC 767152 c.3783T>G synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 767158 c.3789T>A synonymous_variant 0.14 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 0.99 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 1.0 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
rpsL 781868 c.309T>C synonymous_variant 0.13 streptomycin Uncertain significance
rpsL 781892 c.333A>G synonymous_variant 0.16 streptomycin Uncertain significance
rpsL 781898 c.339A>T synonymous_variant 0.16 streptomycin Uncertain significance
rpsL 781916 c.357T>C synonymous_variant 0.18 streptomycin Uncertain significance
rpsL 781929 p.Gly124Ser missense_variant 0.2 streptomycin Uncertain significance
rpsL 781933 c.374G>A splice_region_variant&stop_retained_variant 0.19 streptomycin Uncertain significance
rplC 800357 c.-452C>A upstream_gene_variant 1.0 linezolid Not assoc w R
rplC 801222 c.414T>C synonymous_variant 0.13 linezolid Uncertain significance
rplC 801246 c.438C>T synonymous_variant 0.15 linezolid Uncertain significance
rplC 801252 c.444G>C synonymous_variant 0.16 linezolid Uncertain significance
rplC 801255 c.447C>T synonymous_variant 0.17 linezolid Uncertain significance
rplC 801267 c.459A>T synonymous_variant 0.17 linezolid Uncertain significance
rplC 801270 c.462T>C synonymous_variant 0.16 linezolid Uncertain significance
rplC 801276 c.468G>T synonymous_variant 0.15 linezolid Uncertain significance
rplC 801279 c.471G>A synonymous_variant 0.15 linezolid Uncertain significance
rplC 801285 c.477G>C synonymous_variant 0.14 linezolid Uncertain significance
rplC 801288 c.480G>C synonymous_variant 0.14 linezolid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
fbiC 1303377 p.Asp149Glu missense_variant 0.99 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiC 1304502 c.1572G>A synonymous_variant 0.15 clofazimine Not assoc w R - Interim
delamanid Not assoc w R - Interim
pretomanid Uncertain significance
fbiC 1304520 c.1590A>G synonymous_variant 0.16 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiC 1304526 c.1596T>G synonymous_variant 0.16 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiC 1304538 c.1608C>A synonymous_variant 0.16 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiC 1304544 c.1614T>C synonymous_variant 0.16 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiC 1304545 p.Val539Thr missense_variant 0.17 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiC 1304550 c.1620C>T synonymous_variant 0.17 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiC 1304559 p.Glu543Asp missense_variant 0.18 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiC 1304562 c.1632G>C synonymous_variant 0.18 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiC 1304565 c.1635C>G synonymous_variant 0.18 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiC 1304568 c.1638T>C synonymous_variant 0.18 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiC 1304574 c.1644C>G synonymous_variant 0.18 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiC 1304580 c.1650T>C synonymous_variant 0.15 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
Rv1258c 1406503 p.Val280Leu missense_variant 1.0 isoniazid Uncertain significance
pyrazinamide Uncertain significance
streptomycin Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 1.0 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol Uncertain significance
embR 1417793 c.-446C>T upstream_gene_variant 1.0 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.23 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.23 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473123 n.1278delAinsTT non_coding_transcript_exon_variant 0.17 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1473861 n.205dupC non_coding_transcript_exon_variant 0.88 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476095 n.2438C>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476104 n.2448delG non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476580 n.2923G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833589 c.48A>T synonymous_variant 0.14 pyrazinamide Uncertain significance
rpsA 1833595 c.54T>G synonymous_variant 0.15 pyrazinamide Uncertain significance
rpsA 1833949 c.408T>C synonymous_variant 0.13 pyrazinamide Uncertain significance
rpsA 1834306 c.765T>C synonymous_variant 0.14 pyrazinamide Uncertain significance
rpsA 1834411 c.870T>C synonymous_variant 0.14 pyrazinamide Uncertain significance
rpsA 1834417 c.876G>C synonymous_variant 0.14 pyrazinamide Uncertain significance
rpsA 1834423 c.882G>T synonymous_variant 0.14 pyrazinamide Uncertain significance
rpsA 1834432 c.891G>T synonymous_variant 0.13 pyrazinamide Uncertain significance
rpsA 1834528 c.987T>C synonymous_variant 0.13 pyrazinamide Uncertain significance
rpsA 1834546 c.1005T>C synonymous_variant 0.12 pyrazinamide Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.98 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.98 linezolid Not assoc w R
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
bacA 2062922 p.Ile603Val missense_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
streptomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2169636 p.Ser326Thr missense_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine 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
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid Uncertain significance
kasA 2518639 c.525G>C synonymous_variant 0.3 isoniazid Uncertain significance
kasA 2518642 c.528A>G synonymous_variant 0.29 isoniazid Uncertain significance
kasA 2518645 c.531G>C synonymous_variant 0.29 isoniazid Uncertain significance
kasA 2518651 c.537C>G synonymous_variant 0.31 isoniazid Uncertain significance
kasA 2518657 c.543G>C synonymous_variant 0.3 isoniazid Uncertain significance
kasA 2518663 c.549T>C synonymous_variant 0.26 isoniazid Uncertain significance
kasA 2518672 c.558G>C synonymous_variant 0.24 isoniazid Uncertain significance
kasA 2518678 c.564C>T synonymous_variant 0.24 isoniazid Uncertain significance
kasA 2518711 c.597A>G synonymous_variant 0.23 isoniazid Uncertain significance
kasA 2518717 c.603C>G synonymous_variant 0.23 isoniazid Uncertain significance
kasA 2518747 c.633C>G synonymous_variant 0.24 isoniazid Uncertain significance
kasA 2518778 p.Glu222Gln missense_variant 0.14 isoniazid Uncertain significance
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0 isoniazid Uncertain significance
ahpC 2726090 c.-103C>T upstream_gene_variant 1.0 isoniazid Uncertain significance
Rv2477c 2783422 c.621T>C synonymous_variant 0.13 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783427 p.Pro206Ala missense_variant 0.13 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783428 c.615C>T synonymous_variant 0.13 amikacin Not assoc w R - Interim
ethambutol Uncertain significance
kanamycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
streptomycin Uncertain significance
Rv2477c 2783914 c.129T>C synonymous_variant 0.21 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783920 c.123G>C synonymous_variant 0.19 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
ribD 2987449 p.Glu204Ala missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
Rv2681 2996912 c.174C>T synonymous_variant 1.0 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0 ethambutol Not assoc w R
isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
Rv2752c 3066390 c.-199C>G upstream_gene_variant 0.15 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv2752c 3066399 c.-210_-208delATTinsGTC upstream_gene_variant 0.14 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv2752c 3066420 c.-229C>G upstream_gene_variant 0.14 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv2752c 3066426 c.-235T>C upstream_gene_variant 0.16 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv2752c 3066432 c.-241T>C upstream_gene_variant 0.15 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv2752c 3066456 c.-265A>G upstream_gene_variant 0.15 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv2752c 3066707 c.-516A>G upstream_gene_variant 0.16 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv2752c 3066714 c.-523G>A upstream_gene_variant 0.17 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv2752c 3066720 c.-529G>C upstream_gene_variant 0.17 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv2752c 3066741 c.-550T>C upstream_gene_variant 0.16 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv2752c 3066744 c.-553C>G upstream_gene_variant 0.16 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv2752c 3066747 c.-558_-556delCAAinsATC upstream_gene_variant 0.16 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv2752c 3066756 c.-565G>C upstream_gene_variant 0.17 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv2752c 3066769 c.-579_-578delAAinsCG upstream_gene_variant 0.15 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv2752c 3066771 c.-580C>G upstream_gene_variant 0.15 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv2752c 3066774 c.-583T>C upstream_gene_variant 0.15 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv2752c 3066780 c.-589C>G upstream_gene_variant 0.15 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv2752c 3066804 c.-613G>A upstream_gene_variant 0.14 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine Uncertain significance
Rv3083 3448714 p.Asp71His missense_variant 1.0 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3625345 c.-435T>C upstream_gene_variant 0.14 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrA 3626804 c.546A>G synonymous_variant 0.15 bedaquiline Uncertain significance
rifampicin Not assoc w R - Interim
mtrB 3626819 c.-206G>A upstream_gene_variant 0.14 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3626930 c.-317A>G upstream_gene_variant 0.12 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrA 3626939 c.411A>G synonymous_variant 0.13 bedaquiline Uncertain significance
rifampicin Not assoc w R - Interim
mtrB 3626942 c.-329A>C upstream_gene_variant 0.15 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3627122 c.-509T>C upstream_gene_variant 0.17 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrA 3627175 c.175C>T synonymous_variant 0.17 bedaquiline Uncertain significance
rifampicin Not assoc w R - Interim
mtrB 3627181 c.-568T>C upstream_gene_variant 0.14 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3627182 c.-569T>C upstream_gene_variant 0.14 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrA 3627185 p.Leu55Phe missense_variant 0.14 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrA 3627188 c.162A>G synonymous_variant 0.14 bedaquiline Uncertain significance
rifampicin Not assoc w R - Interim
mtrB 3627197 c.-584T>C upstream_gene_variant 0.14 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3627203 c.-590C>G upstream_gene_variant 0.15 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3627233 c.-620T>G upstream_gene_variant 0.15 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3627236 c.-623T>C upstream_gene_variant 0.15 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrA 3627239 c.111C>T synonymous_variant 0.16 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
mtrA 3627242 c.108C>T synonymous_variant 0.16 bedaquiline Uncertain significance
rifampicin Not assoc w R - Interim
mtrB 3627254 c.-641C>T upstream_gene_variant 0.17 bedaquiline Uncertain significance
rifampicin Uncertain significance
rpoA 3877818 c.690A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3877839 c.669G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878022 c.486T>C synonymous_variant 0.14 rifampicin Uncertain significance
rpoA 3878025 c.483C>T synonymous_variant 0.15 rifampicin Uncertain significance
rpoA 3878028 c.480G>C synonymous_variant 0.15 rifampicin Uncertain significance
rpoA 3878031 c.477T>C synonymous_variant 0.15 rifampicin Uncertain significance
rpoA 3878043 c.465G>C synonymous_variant 0.15 rifampicin Uncertain significance
rpoA 3878046 c.462T>C synonymous_variant 0.15 rifampicin Uncertain significance
rpoA 3878049 c.459G>T synonymous_variant 0.15 rifampicin Uncertain significance
rpoA 3878055 c.453A>G synonymous_variant 0.22 rifampicin Uncertain significance
rpoA 3878061 c.447G>C synonymous_variant 0.22 rifampicin Uncertain significance
rpoA 3878070 c.438T>C synonymous_variant 0.21 rifampicin Uncertain significance
rpoA 3878073 c.435C>T synonymous_variant 0.21 rifampicin Uncertain significance
rpoA 3878076 c.432C>T synonymous_variant 0.22 rifampicin Uncertain significance
rpoA 3878079 c.429C>T synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoA 3878082 c.426T>C synonymous_variant 0.21 rifampicin Uncertain significance
rpoA 3878103 c.405A>G synonymous_variant 0.24 rifampicin Uncertain significance
rpoA 3878106 c.402G>C synonymous_variant 0.25 rifampicin Uncertain significance
rpoA 3878118 c.390T>C synonymous_variant 0.24 rifampicin Uncertain significance
rpoA 3878126 c.382C>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoA 3878130 c.378C>G synonymous_variant 0.21 rifampicin Uncertain significance
rpoA 3878193 c.315T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3878217 c.291A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878247 c.261G>C synonymous_variant 0.15 rifampicin Uncertain significance
rpoA 3878262 p.Ser82Gly missense_variant 0.18 rifampicin Uncertain significance
rpoA 3878271 c.237T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoA 3878283 p.Glu75Asp missense_variant 0.24 rifampicin Uncertain significance
rpoA 3878295 c.213A>G synonymous_variant 0.22 rifampicin Uncertain significance
rpoA 3878298 c.210A>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoA 3878304 c.204G>C synonymous_variant 0.21 rifampicin Uncertain significance
rpoA 3878313 c.195G>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoA 3878322 c.186A>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoA 3878331 c.177A>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoA 3878334 c.174T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoA 3878337 c.171T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoA 3878355 c.153C>G synonymous_variant 0.2 rifampicin Uncertain significance
rpoA 3878853 c.-346G>A upstream_gene_variant 0.16 rifampicin Uncertain significance
rpoA 3878878 c.-371T>C upstream_gene_variant 0.14 rifampicin Uncertain significance
rpoA 3878887 c.-380C>T upstream_gene_variant 0.17 rifampicin Uncertain significance
rpoA 3878914 c.-407T>C upstream_gene_variant 0.14 rifampicin Uncertain significance
rpoA 3879148 c.-641G>A upstream_gene_variant 0.16 rifampicin Uncertain significance
rpoA 3879154 c.-647T>C upstream_gene_variant 0.15 rifampicin Uncertain significance
rpoA 3879160 c.-653A>G upstream_gene_variant 0.16 rifampicin Uncertain significance
clpC1 4038647 c.2058T>G synonymous_variant 0.14 pyrazinamide Uncertain significance
clpC1 4038658 p.Lys683Gln missense_variant 0.15 pyrazinamide Uncertain significance
clpC1 4038661 p.Ser682Thr missense_variant 0.15 pyrazinamide Uncertain significance
clpC1 4038662 c.2043T>C synonymous_variant 0.14 pyrazinamide Uncertain significance
clpC1 4038671 c.2034T>C synonymous_variant 0.21 pyrazinamide Uncertain significance
clpC1 4038683 c.2022T>C synonymous_variant 0.22 pyrazinamide Not assoc w R - Interim
clpC1 4038692 c.2013C>G synonymous_variant 0.21 pyrazinamide Not assoc w R - Interim
clpC1 4038695 c.2010C>G synonymous_variant 0.21 pyrazinamide Uncertain significance
clpC1 4038698 c.2007C>T synonymous_variant 0.21 pyrazinamide Not assoc w R - Interim
clpC1 4038701 c.2004G>C synonymous_variant 0.21 pyrazinamide Uncertain significance
clpC1 4038704 c.2001T>C synonymous_variant 0.21 pyrazinamide Uncertain significance
clpC1 4038713 c.1992T>C synonymous_variant 0.21 pyrazinamide Uncertain significance
clpC1 4038740 c.1965G>C synonymous_variant 0.2 pyrazinamide Uncertain significance
clpC1 4038749 c.1956C>T synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
clpC1 4038782 c.1923G>C synonymous_variant 0.19 pyrazinamide Uncertain significance
clpC1 4038790 c.1915C>T synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
clpC1 4038812 c.1893T>C synonymous_variant 0.13 pyrazinamide Uncertain significance
clpC1 4038845 c.1860G>C synonymous_variant 0.14 pyrazinamide Uncertain significance
clpC1 4038860 c.1845G>C synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
clpC1 4038878 c.1827A>G synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4038884 c.1821C>T synonymous_variant 0.14 pyrazinamide Uncertain significance
clpC1 4038905 c.1800A>C synonymous_variant 0.15 pyrazinamide Uncertain significance
clpC1 4038908 c.1797C>G synonymous_variant 0.15 pyrazinamide Uncertain significance
clpC1 4038914 c.1791G>C synonymous_variant 0.15 pyrazinamide Uncertain significance
clpC1 4038923 c.1780_1782delCTAinsTTG synonymous_variant 0.14 pyrazinamide Uncertain significance
clpC1 4039124 c.1581C>T synonymous_variant 0.14 pyrazinamide Uncertain significance
clpC1 4039328 c.1377A>C synonymous_variant 0.13 pyrazinamide Uncertain significance
clpC1 4039338 p.Thr456Gln missense_variant 0.15 pyrazinamide Uncertain significance
clpC1 4040267 c.438A>G synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4040517 p.Val63Ala missense_variant 0.89 pyrazinamide Not assoc w R - Interim
clpC1 4040546 c.159G>T synonymous_variant 0.14 pyrazinamide Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 1.0 ethambutol Not assoc w R
isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
streptomycin Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.95 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 1.0 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 1.0 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
aftB 4268156 c.681C>T synonymous_variant 0.94 ethambutol Not assoc w R - Interim
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326654 p.Glu274Lys missense_variant 1.0 ethionamide Uncertain significance
whiB6 4338224 c.297delC frameshift_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
whiB6 4338301 p.Gly74Glu missense_variant 0.99 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 1.0 streptomycin Not assoc w R