TB-Profiler result

Run: ERR4798139
Summary

Run ID: ERR4798139

Sample name:

Date: 2024-04-15T23:59:49.828180

Number of reads: 2127162

Percentage reads mapped: 86.75

Median coverage: 65.0

Strain: lineage1.1.2

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.2 Indo-Oceanic RD239 0.98
lineage1.1 Indo-Oceanic RD239 1.0
lineage1 Indo-Oceanic RD239 0.97
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB c.1327_1329delTTGinsCC Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
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
rpoB 761133 c.1327_1329delTTGinsCC frameshift_variant&missense_variant 0.17 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
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
pretomanid
delamanid Not assoc w R - Interim
mshA 575884 c.537G>C synonymous_variant 0.14 ethionamide
isoniazid
mshA 575887 c.540G>T synonymous_variant 0.14 ethionamide
isoniazid
mshA 575893 c.546C>G synonymous_variant 0.14 ethionamide
isoniazid
mshA 575896 c.549G>T synonymous_variant 0.14 ethionamide
isoniazid
mshA 575905 c.558G>C synonymous_variant 0.14 ethionamide
isoniazid
mshA 575914 c.567C>G synonymous_variant 0.13 ethionamide
isoniazid
mshA 575926 c.579A>G synonymous_variant 0.13 ethionamide
isoniazid
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
hadA 732389 p.Ser154Thr missense_variant 0.16 isoniazid
hadA 732396 p.Gly156Ala missense_variant 0.17 isoniazid
hadA 732398 p.Ala157Thr missense_variant 0.17 isoniazid
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
nusG 734143 c.-111C>T upstream_gene_variant 0.18 rifampicin
nusG 734147 c.-107T>C upstream_gene_variant 0.18 rifampicin
nusG 734150 c.-104G>C upstream_gene_variant 0.18 rifampicin
nusG 734173 c.-81C>G upstream_gene_variant 0.17 rifampicin
nusG 734175 c.-79_-77delGGTinsCTG upstream_gene_variant 0.17 rifampicin
nusG 734183 c.-71C>T upstream_gene_variant 0.17 rifampicin
nusG 734505 c.252G>A synonymous_variant 0.15 rifampicin
nusG 734532 c.279A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760591 p.Val262Ala missense_variant 0.14 rifampicin
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 761150 c.1344A>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761165 c.1359G>A synonymous_variant 0.16 rifampicin
rpoB 761168 c.1362C>G synonymous_variant 0.17 rifampicin
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
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
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
rpoB 761286 c.1480C>T synonymous_variant 0.17 rifampicin
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
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
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
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
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
rpoB 762795 p.Asp997Asn missense_variant 0.14 rifampicin Uncertain significance
rpoC 762800 c.-570C>A upstream_gene_variant 0.15 rifampicin
rpoB 762812 c.3006C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762814 p.Met1003Arg missense_variant 0.16 rifampicin
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
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
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
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
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
rpoC 763991 c.622_624delATCinsCG frameshift_variant&missense_variant 0.17 rifampicin
rpoC 763996 c.627T>C synonymous_variant 0.17 rifampicin
rpoC 764002 c.633C>G synonymous_variant 0.18 rifampicin
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
rpoC 764024 c.655_657delTTGinsCC frameshift_variant&missense_variant 0.16 rifampicin
rpoC 764040 p.Ser224Thr missense_variant 0.15 rifampicin
rpoC 764044 c.675T>G synonymous_variant 0.15 rifampicin
rpoC 764059 c.690G>C synonymous_variant 0.16 rifampicin
rpoC 764083 c.714A>G synonymous_variant 0.14 rifampicin
rpoC 764536 c.1167G>C synonymous_variant 0.14 rifampicin
rpoC 764554 c.1185C>T synonymous_variant 0.18 rifampicin
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
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
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
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
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
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
rpoC 765751 c.2382C>G synonymous_variant 0.14 rifampicin
rpoC 765753 p.Asp795Ala missense_variant 0.13 rifampicin Uncertain significance
rpoC 765772 c.2403C>G synonymous_variant 0.14 rifampicin
rpoC 765787 c.2418C>T synonymous_variant 0.14 rifampicin
rpoC 765793 c.2424C>G synonymous_variant 0.14 rifampicin
rpoC 765796 c.2427C>T synonymous_variant 0.14 rifampicin
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
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
rpoC 766369 c.3000C>G synonymous_variant 0.13 rifampicin
rpoC 766384 c.3015A>G synonymous_variant 0.14 rifampicin
rpoC 766390 c.3021C>T synonymous_variant 0.15 rifampicin
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
rpoC 766774 c.3405T>C synonymous_variant 0.14 rifampicin
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
rpoC 766981 c.3612T>C synonymous_variant 0.18 rifampicin
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
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
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
rpoC 767152 c.3783T>G synonymous_variant 0.14 rifampicin
rpoC 767158 c.3789T>A synonymous_variant 0.14 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 0.99 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile 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 781868 c.309T>C synonymous_variant 0.13 streptomycin
rpsL 781892 c.333A>G synonymous_variant 0.16 streptomycin
rpsL 781898 c.339A>T synonymous_variant 0.16 streptomycin
rpsL 781916 c.357T>C synonymous_variant 0.18 streptomycin
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
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
rplC 801246 c.438C>T synonymous_variant 0.15 linezolid
rplC 801252 c.444G>C synonymous_variant 0.16 linezolid
rplC 801255 c.447C>T synonymous_variant 0.17 linezolid
rplC 801267 c.459A>T synonymous_variant 0.17 linezolid
rplC 801270 c.462T>C synonymous_variant 0.16 linezolid
rplC 801276 c.468G>T synonymous_variant 0.15 linezolid
rplC 801279 c.471G>A synonymous_variant 0.15 linezolid
rplC 801285 c.477G>C synonymous_variant 0.14 linezolid
rplC 801288 c.480G>C synonymous_variant 0.14 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1303377 p.Asp149Glu missense_variant 0.99 clofazimine
pretomanid
delamanid
fbiC 1304502 c.1572G>A synonymous_variant 0.15 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fbiC 1304520 c.1590A>G synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fbiC 1304526 c.1596T>G synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fbiC 1304538 c.1608C>A synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fbiC 1304544 c.1614T>C synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fbiC 1304545 p.Val539Thr missense_variant 0.17 clofazimine
pretomanid
delamanid
fbiC 1304550 c.1620C>T synonymous_variant 0.17 clofazimine
pretomanid
delamanid
fbiC 1304559 p.Glu543Asp missense_variant 0.18 clofazimine
pretomanid
delamanid
fbiC 1304562 c.1632G>C synonymous_variant 0.18 clofazimine
pretomanid
delamanid
fbiC 1304565 c.1635C>G synonymous_variant 0.18 clofazimine
pretomanid
delamanid
fbiC 1304568 c.1638T>C synonymous_variant 0.18 clofazimine
pretomanid
delamanid
fbiC 1304574 c.1644C>G synonymous_variant 0.18 clofazimine
pretomanid
delamanid
fbiC 1304580 c.1650T>C synonymous_variant 0.15 clofazimine
pretomanid
delamanid
Rv1258c 1406503 p.Val280Leu missense_variant 1.0 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide 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
embR 1417793 c.-446C>T upstream_gene_variant 1.0 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.23 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.23 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473123 n.1278delAinsTT non_coding_transcript_exon_variant 0.17 streptomycin
kanamycin
capreomycin
amikacin
rrl 1473861 n.205dupC non_coding_transcript_exon_variant 0.88 capreomycin
linezolid
rrl 1476095 n.2438C>T non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1476104 n.2448delG non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
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
linezolid
rpsA 1833589 c.48A>T synonymous_variant 0.14 pyrazinamide
rpsA 1833595 c.54T>G synonymous_variant 0.15 pyrazinamide
rpsA 1833949 c.408T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834411 c.870T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834417 c.876G>C synonymous_variant 0.14 pyrazinamide
rpsA 1834423 c.882G>T synonymous_variant 0.14 pyrazinamide
rpsA 1834432 c.891G>T synonymous_variant 0.13 pyrazinamide
rpsA 1834528 c.987T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834546 c.1005T>C synonymous_variant 0.12 pyrazinamide
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 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin 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
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
kasA 2518639 c.525G>C synonymous_variant 0.3 isoniazid
kasA 2518642 c.528A>G synonymous_variant 0.29 isoniazid
kasA 2518645 c.531G>C synonymous_variant 0.29 isoniazid
kasA 2518651 c.537C>G synonymous_variant 0.31 isoniazid
kasA 2518657 c.543G>C synonymous_variant 0.3 isoniazid
kasA 2518663 c.549T>C synonymous_variant 0.26 isoniazid
kasA 2518672 c.558G>C synonymous_variant 0.24 isoniazid
kasA 2518678 c.564C>T synonymous_variant 0.24 isoniazid
kasA 2518711 c.597A>G synonymous_variant 0.23 isoniazid
kasA 2518717 c.603C>G synonymous_variant 0.23 isoniazid
kasA 2518747 c.633C>G synonymous_variant 0.24 isoniazid
kasA 2518778 p.Glu222Gln missense_variant 0.14 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0 isoniazid
ahpC 2726090 c.-103C>T upstream_gene_variant 1.0 isoniazid
Rv2477c 2783422 c.621T>C synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783427 p.Pro206Ala missense_variant 0.13 ethambutol Uncertain significance
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin Uncertain significance
amikacin
Rv2477c 2783428 c.615C>T synonymous_variant 0.13 ethambutol
moxifloxacin Not assoc w R - Interim
streptomycin
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2477c 2783914 c.129T>C synonymous_variant 0.21 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783920 c.123G>C synonymous_variant 0.19 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
ribD 2987449 p.Glu204Ala missense_variant 1.0 para-aminosalicylic_acid
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
moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv2752c 3066390 c.-199C>G upstream_gene_variant 0.15 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066399 c.-210_-208delATTinsGC upstream_gene_variant 0.14 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066420 c.-229C>G upstream_gene_variant 0.14 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066426 c.-235T>C upstream_gene_variant 0.16 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066432 c.-241T>C upstream_gene_variant 0.15 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066456 c.-265A>G upstream_gene_variant 0.15 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066707 c.-516A>G upstream_gene_variant 0.16 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066714 c.-523G>A upstream_gene_variant 0.17 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066720 c.-529G>C upstream_gene_variant 0.17 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066741 c.-550T>C upstream_gene_variant 0.16 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066744 c.-553C>G upstream_gene_variant 0.16 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066747 c.-558_-556delCAAinsATC upstream_gene_variant 0.16 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066756 c.-565G>C upstream_gene_variant 0.17 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066769 c.-579_-578delAAinsCG upstream_gene_variant 0.15 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066771 c.-580C>G upstream_gene_variant 0.15 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066774 c.-583T>C upstream_gene_variant 0.15 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066780 c.-589C>G upstream_gene_variant 0.15 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066804 c.-613G>A upstream_gene_variant 0.14 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
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
rifampicin
mtrA 3626804 c.546A>G synonymous_variant 0.15 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626819 c.-206G>A upstream_gene_variant 0.14 bedaquiline
rifampicin
mtrB 3626930 c.-317A>G upstream_gene_variant 0.12 bedaquiline
rifampicin
mtrA 3626939 c.411A>G synonymous_variant 0.13 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626942 c.-329A>C upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3627122 c.-509T>C upstream_gene_variant 0.17 bedaquiline
rifampicin
mtrA 3627175 c.175C>T synonymous_variant 0.17 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627181 c.-568T>C upstream_gene_variant 0.14 bedaquiline
rifampicin
mtrB 3627182 c.-569T>C upstream_gene_variant 0.14 bedaquiline
rifampicin
mtrA 3627185 p.Leu55Phe missense_variant 0.14 bedaquiline
rifampicin
mtrA 3627188 c.162A>G synonymous_variant 0.14 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627197 c.-584T>C upstream_gene_variant 0.14 bedaquiline
rifampicin
mtrB 3627203 c.-590C>G upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3627233 c.-620T>G upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3627236 c.-623T>C upstream_gene_variant 0.15 bedaquiline
rifampicin
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
rifampicin Not assoc w R - Interim
mtrB 3627254 c.-641C>T upstream_gene_variant 0.17 bedaquiline
rifampicin
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
rpoA 3878025 c.483C>T synonymous_variant 0.15 rifampicin
rpoA 3878028 c.480G>C synonymous_variant 0.15 rifampicin
rpoA 3878031 c.477T>C synonymous_variant 0.15 rifampicin
rpoA 3878043 c.465G>C synonymous_variant 0.15 rifampicin
rpoA 3878046 c.462T>C synonymous_variant 0.15 rifampicin
rpoA 3878049 c.459G>T synonymous_variant 0.15 rifampicin
rpoA 3878055 c.453A>G synonymous_variant 0.22 rifampicin
rpoA 3878061 c.447G>C synonymous_variant 0.22 rifampicin
rpoA 3878070 c.438T>C synonymous_variant 0.21 rifampicin
rpoA 3878073 c.435C>T synonymous_variant 0.21 rifampicin
rpoA 3878076 c.432C>T synonymous_variant 0.22 rifampicin
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
rpoA 3878103 c.405A>G synonymous_variant 0.24 rifampicin
rpoA 3878106 c.402G>C synonymous_variant 0.25 rifampicin
rpoA 3878118 c.390T>C synonymous_variant 0.24 rifampicin
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
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
rpoA 3878262 c.244_246delAGCinsGT frameshift_variant&synonymous_variant 0.18 rifampicin
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
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
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
rpoA 3878853 c.-346G>A upstream_gene_variant 0.16 rifampicin
rpoA 3878878 c.-371T>C upstream_gene_variant 0.14 rifampicin Uncertain significance
rpoA 3878887 c.-380C>T upstream_gene_variant 0.17 rifampicin
rpoA 3878914 c.-407T>C upstream_gene_variant 0.14 rifampicin Uncertain significance
rpoA 3879148 c.-641G>A upstream_gene_variant 0.16 rifampicin
rpoA 3879154 c.-647T>C upstream_gene_variant 0.15 rifampicin
rpoA 3879160 c.-653A>G upstream_gene_variant 0.16 rifampicin
clpC1 4038647 c.2058T>G synonymous_variant 0.14 pyrazinamide
clpC1 4038658 p.Lys683Gln missense_variant 0.15 pyrazinamide
clpC1 4038661 p.Ser682Thr missense_variant 0.15 pyrazinamide
clpC1 4038662 c.2043T>C synonymous_variant 0.14 pyrazinamide
clpC1 4038671 c.2034T>C synonymous_variant 0.21 pyrazinamide
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
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
clpC1 4038704 c.2001T>C synonymous_variant 0.21 pyrazinamide
clpC1 4038713 c.1992T>C synonymous_variant 0.21 pyrazinamide
clpC1 4038740 c.1965G>C synonymous_variant 0.2 pyrazinamide
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
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
clpC1 4038845 c.1860G>C synonymous_variant 0.14 pyrazinamide
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
clpC1 4038905 c.1800A>C synonymous_variant 0.15 pyrazinamide
clpC1 4038908 c.1797C>G synonymous_variant 0.15 pyrazinamide
clpC1 4038914 c.1791G>C synonymous_variant 0.15 pyrazinamide
clpC1 4038923 c.1780_1782delCTAinsTG frameshift_variant&synonymous_variant 0.14 pyrazinamide
clpC1 4039124 c.1581C>T synonymous_variant 0.14 pyrazinamide
clpC1 4039328 c.1377A>C synonymous_variant 0.13 pyrazinamide
clpC1 4039338 p.Thr456Gln missense_variant 0.15 pyrazinamide
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
glpK 4138377 p.Val460Ala missense_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid 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
whiB6 4338224 c.297delC frameshift_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338301 p.Gly74Glu missense_variant 0.99 capreomycin
amikacin Uncertain significance
kanamycin Uncertain significance
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 4338603 c.-82C>T 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
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