TB-Profiler result

Run: SRR6785227
Summary

Run ID: SRR6785227

Sample name:

Date: 2024-10-04T22:24:20.023019

Number of reads: 3529150

Percentage reads mapped: 83.75

Median coverage: 95.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.98
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.98
lineage2.2 East-Asian (Beijing) RD105;RD207 0.99
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol embB p.His312Arg Mutation from literature
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
rrs n.462C>T Uncertain significance Mutation from literature
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
rpsL 781687 p.Lys43Arg missense_variant 0.85 streptomycin Assoc w R
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.25 streptomycin Uncertain significance Mutation from literature
embB 4247448 p.His312Arg missense_variant 0.15 ethambutol Mutation from literature
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 750 c.750C>G synonymous_variant 0.12 isoniazid
dnaA 1230 c.1230A>G synonymous_variant 0.18 isoniazid
dnaA 1236 c.1236C>T synonymous_variant 0.16 isoniazid
dnaA 1242 c.1242G>C synonymous_variant 0.19 isoniazid
dnaA 1245 c.1245G>C synonymous_variant 0.18 isoniazid Not assoc w R - Interim
dnaA 1299 c.1299G>C synonymous_variant 0.14 isoniazid Not assoc w R - Interim
dnaA 1314 c.1314A>G synonymous_variant 0.13 isoniazid
dnaA 1317 c.1317A>G synonymous_variant 0.13 isoniazid
dnaA 1320 c.1320G>C synonymous_variant 0.13 isoniazid
dnaA 1332 c.1332A>C synonymous_variant 0.13 isoniazid Not assoc w R - Interim
dnaA 1353 c.1353T>C synonymous_variant 0.12 isoniazid
gyrB 6238 c.999G>A synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6242 p.Arg335Ser missense_variant 0.13 levofloxacin
moxifloxacin
gyrB 6250 c.1011A>G synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6256 c.1017G>A synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrB 6280 c.1041T>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrB 6286 c.1047T>C synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrB 6289 c.1050C>T synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrB 6292 c.1053G>C synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrB 6307 c.1068T>G synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 6649 c.-653T>C upstream_gene_variant 0.15 levofloxacin
moxifloxacin
gyrA 6655 c.-647T>C upstream_gene_variant 0.15 levofloxacin
moxifloxacin
gyrA 6670 c.-632G>C upstream_gene_variant 0.15 levofloxacin
moxifloxacin
gyrA 6673 c.-629A>C upstream_gene_variant 0.15 levofloxacin
moxifloxacin
gyrA 6676 c.-626T>G upstream_gene_variant 0.15 levofloxacin
moxifloxacin
gyrA 6700 c.-602T>C upstream_gene_variant 0.18 levofloxacin
moxifloxacin
gyrA 6703 c.-599G>C upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 6709 c.-593A>G upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 6712 c.-590G>C upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 6728 c.-574_-572delCTAinsTTG upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrB 7186 c.1947C>G synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491106 c.324T>C synonymous_variant 0.13 pretomanid
delamanid
clofazimine
fgd1 491130 c.348C>G synonymous_variant 0.15 pretomanid
delamanid
clofazimine
fgd1 491144 p.Ala121Asp missense_variant 0.15 pretomanid
delamanid
clofazimine
fgd1 491151 c.369G>A synonymous_variant 0.15 pretomanid
delamanid
clofazimine
fgd1 491173 c.391C>A synonymous_variant 0.13 pretomanid
delamanid
clofazimine
fgd1 491181 c.399T>C synonymous_variant 0.13 pretomanid
delamanid
clofazimine
fgd1 491191 p.Gly137Arg missense_variant 0.13 pretomanid
delamanid
clofazimine
fgd1 491232 c.450T>C synonymous_variant 0.14 pretomanid
delamanid
clofazimine
fgd1 491241 p.Asp153Glu missense_variant 0.15 pretomanid
delamanid
clofazimine
fgd1 491244 c.462T>C synonymous_variant 0.14 pretomanid
delamanid
clofazimine
fgd1 491259 c.477T>C synonymous_variant 0.16 pretomanid
delamanid
clofazimine
fgd1 491742 c.960T>C synonymous_variant 0.97 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.89 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.99 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 656841 c.630G>A synonymous_variant 0.96 ethionamide Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.97 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.95 ethionamide Uncertain significance
hadA 732378 c.450_452dupAGA disruptive_inframe_insertion 0.17 isoniazid
rpoB 760196 c.390C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760223 c.417T>C synonymous_variant 0.14 rifampicin
rpoB 760235 c.429T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760283 c.477G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760298 c.492G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760307 c.501T>C synonymous_variant 0.13 rifampicin
rpoB 760328 c.522G>C synonymous_variant 0.13 rifampicin
rpoB 760340 c.534G>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760361 c.555T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760370 c.564C>G synonymous_variant 0.14 rifampicin
rpoB 760376 p.Asp190Glu missense_variant 0.14 rifampicin Uncertain significance
rpoB 760381 p.Thr192Met missense_variant 0.13 rifampicin
rpoB 760406 c.600G>C synonymous_variant 0.14 rifampicin
rpoB 760412 c.606C>G synonymous_variant 0.12 rifampicin
rpoB 760481 c.675G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 760611 c.805T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760646 c.840C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761102 c.1296A>G synonymous_variant 0.17 rifampicin
rpoB 761165 c.1359G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761207 c.1401C>T synonymous_variant 0.13 rifampicin
rpoB 761261 c.1455G>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761306 c.1500C>G synonymous_variant 0.14 rifampicin
rpoB 762101 c.2295C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762114 p.Ile770Val missense_variant 0.15 rifampicin Uncertain significance
rpoB 762131 c.2325C>G synonymous_variant 0.16 rifampicin
rpoB 762140 c.2334G>C synonymous_variant 0.14 rifampicin
rpoB 762143 c.2337T>C synonymous_variant 0.13 rifampicin
rpoB 762149 c.2343G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762167 c.2361T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762176 c.2370T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762185 c.2379G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762206 c.2400C>G synonymous_variant 0.17 rifampicin
rpoB 762233 c.2427G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762246 c.2440C>T synonymous_variant 0.14 rifampicin
rpoC 762419 c.-951C>G upstream_gene_variant 0.12 rifampicin
rpoC 762434 c.-936T>C upstream_gene_variant 0.15 rifampicin
rpoB 762449 c.2643C>A synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 762467 c.-903C>T upstream_gene_variant 0.18 rifampicin
rpoB 762488 c.2682G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762490 p.Val895Asp missense_variant 0.12 rifampicin
rpoC 762509 c.-861T>G upstream_gene_variant 0.13 rifampicin
rpoB 762510 p.Ala902Pro missense_variant 0.13 rifampicin Uncertain significance
rpoC 762989 c.-381G>C upstream_gene_variant 0.16 rifampicin
rpoB 762995 c.3189G>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763013 c.-357C>G upstream_gene_variant 0.17 rifampicin
rpoB 763028 c.3222T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.99 rifampicin Not assoc w R
rpoB 763034 c.3228C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 763040 c.3234C>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 763085 c.3279C>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 763136 c.3330C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763158 c.-212C>T upstream_gene_variant 0.13 rifampicin
rpoC 763441 c.72C>T synonymous_variant 0.14 rifampicin
rpoC 763444 c.75T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763456 c.87A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763486 c.117T>G synonymous_variant 0.24 rifampicin
rpoC 763528 c.159G>A synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 763603 c.234C>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763636 c.267T>C synonymous_variant 0.22 rifampicin
rpoC 763660 c.291T>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 763675 c.306C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763696 c.327T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763702 c.333C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763723 c.354G>C synonymous_variant 0.17 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.18 rifampicin
rpoC 763741 c.372C>T synonymous_variant 0.17 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.18 rifampicin
rpoC 763765 c.396T>C synonymous_variant 0.2 rifampicin
rpoC 763774 c.405G>C synonymous_variant 0.2 rifampicin
rpoC 763807 c.438T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763816 c.447C>G synonymous_variant 0.16 rifampicin
rpoC 763987 c.618C>T synonymous_variant 0.12 rifampicin
rpoC 764026 p.Leu219Phe missense_variant 0.13 rifampicin
rpoC 764098 c.729A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764101 c.732C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764102 p.Val245Ile missense_variant 0.13 rifampicin
rpoC 764112 p.Tyr248Phe missense_variant 0.13 rifampicin
rpoC 764140 c.771C>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764188 c.819A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764195 p.Ser276Ile missense_variant 0.13 rifampicin
rpoC 764203 c.834G>C synonymous_variant 0.13 rifampicin
rpoC 764206 c.837T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764215 c.846A>G synonymous_variant 0.16 rifampicin
rpoC 764236 c.867G>A synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764248 c.879C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764405 c.1036A>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764489 c.1120C>T synonymous_variant 0.13 rifampicin
rpoC 764575 c.1206T>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 765383 p.Met672Leu missense_variant 0.15 rifampicin Uncertain significance
rpoC 765404 p.Leu679Val missense_variant 0.17 rifampicin
rpoC 765409 c.2040T>C synonymous_variant 0.19 rifampicin
rpoC 765421 c.2052C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 765478 c.2109T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765499 c.2130C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765529 c.2160C>T synonymous_variant 0.15 rifampicin
rpoC 765580 c.2211G>C synonymous_variant 0.13 rifampicin
rpoC 765613 p.His748Gln missense_variant 0.18 rifampicin
rpoC 765625 c.2256C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 765631 p.Asp754Glu missense_variant 0.14 rifampicin
rpoC 765700 c.2331T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765734 c.2365T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765739 c.2370G>T synonymous_variant 0.15 rifampicin
rpoC 766645 p.Glu1092Asp missense_variant 0.9 rifampicin Not assoc w R
rpoC 766765 c.3396A>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766774 c.3405T>C synonymous_variant 0.16 rifampicin
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 0.99 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 1.0 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.96 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781703 c.144G>T synonymous_variant 0.12 streptomycin
rpsL 781728 c.169T>C synonymous_variant 0.14 streptomycin
rpsL 781736 c.177T>C synonymous_variant 0.13 streptomycin
rpsL 781742 c.183C>T synonymous_variant 0.13 streptomycin
rpsL 781748 c.189C>G synonymous_variant 0.13 streptomycin
rpsL 781754 c.195G>C synonymous_variant 0.16 streptomycin
rpsL 781760 c.201T>C synonymous_variant 0.15 streptomycin
rpsL 781772 c.213C>A synonymous_variant 0.15 streptomycin
rpsL 781808 c.249C>T synonymous_variant 0.14 streptomycin
rpsL 781811 c.252C>T synonymous_variant 0.15 streptomycin
rpsL 781832 c.273T>C synonymous_variant 0.15 streptomycin
rpsL 781838 c.279G>C synonymous_variant 0.16 streptomycin
rpsL 781841 c.282C>G synonymous_variant 0.15 streptomycin
rpsL 781865 c.306G>C synonymous_variant 0.14 streptomycin
rpsL 781868 c.309T>C synonymous_variant 0.14 streptomycin
rpsL 781871 c.312G>C synonymous_variant 0.14 streptomycin
rpsL 781877 c.318T>C synonymous_variant 0.14 streptomycin
rpsL 781892 c.333A>G synonymous_variant 0.15 streptomycin
rpsL 781898 c.339A>T synonymous_variant 0.14 streptomycin
rpsL 781929 p.Gly124Ser missense_variant 0.14 streptomycin Uncertain significance
rplC 800693 c.-116A>G upstream_gene_variant 0.13 linezolid
rplC 800703 c.-106T>C upstream_gene_variant 0.14 linezolid
rplC 800715 c.-94A>C upstream_gene_variant 0.15 linezolid
rplC 800720 c.-89T>C upstream_gene_variant 0.15 linezolid
rplC 800723 c.-86C>G upstream_gene_variant 0.16 linezolid
rplC 800747 c.-62C>G upstream_gene_variant 0.15 linezolid
rplC 800771 c.-38C>T upstream_gene_variant 0.17 linezolid
rplC 800794 c.-15A>G upstream_gene_variant 0.15 linezolid
rplC 800796 c.-13A>G upstream_gene_variant 0.14 linezolid
rplC 800798 c.-10_-9delGG upstream_gene_variant 0.14 linezolid
rplC 800814 c.6A>G synonymous_variant 0.13 linezolid
rplC 800817 c.9A>T synonymous_variant 0.13 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.97 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1304832 c.1902C>T synonymous_variant 0.14 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fbiC 1304856 c.1926C>G synonymous_variant 0.14 pretomanid
delamanid
clofazimine
fbiC 1304869 c.1939C>T synonymous_variant 0.14 pretomanid
delamanid
clofazimine
fbiC 1304875 p.Ile649Val missense_variant 0.15 pretomanid
delamanid
clofazimine
fbiC 1304883 p.Glu651Asp missense_variant 0.15 pretomanid
delamanid
clofazimine
fbiC 1304891 p.Ile654Thr missense_variant 0.15 pretomanid
delamanid
clofazimine
fbiC 1304893 p.Gly655Ser missense_variant 0.15 pretomanid
delamanid
clofazimine
fbiC 1304907 c.1977C>G synonymous_variant 0.17 pretomanid
delamanid
clofazimine
fbiC 1304910 c.1980G>C synonymous_variant 0.19 pretomanid
delamanid
clofazimine
fbiC 1304916 c.1986T>C synonymous_variant 0.2 pretomanid
delamanid
clofazimine
fbiC 1304928 c.1998T>C synonymous_variant 0.18 pretomanid
delamanid
clofazimine
fbiC 1304937 c.2007G>C synonymous_variant 0.18 pretomanid
delamanid
clofazimine
fbiC 1304958 c.2028T>G synonymous_variant 0.19 pretomanid
delamanid
clofazimine
fbiC 1304983 c.2053C>T synonymous_variant 0.17 pretomanid
delamanid
clofazimine
fbiC 1304994 c.2064A>G synonymous_variant 0.16 pretomanid
delamanid
clofazimine
fbiC 1304995 p.Leu689Met missense_variant 0.16 pretomanid
delamanid
clofazimine
sigE 1364706 c.294G>A synonymous_variant 0.95 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
atpE 1460840 c.-205A>G upstream_gene_variant 0.13 bedaquiline
atpE 1460852 c.-193C>G upstream_gene_variant 0.13 bedaquiline
atpE 1460855 c.-190T>C upstream_gene_variant 0.13 bedaquiline
atpE 1460882 c.-163T>C upstream_gene_variant 0.13 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472300 n.455C>T non_coding_transcript_exon_variant 0.27 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.2 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.28 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrl 1473756 n.99G>A non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473899 n.242A>C non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid
rrl 1473986 n.329T>C non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1473987 n.330G>A non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475199 n.1542G>A non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid
rrl 1475249 n.1592T>C non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475275 n.1618C>T non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.33 capreomycin
linezolid Uncertain significance
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1475761 n.2104_2106delCGCinsGT non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1475765 n.2111delG non_coding_transcript_exon_variant 0.41 capreomycin
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.46 capreomycin
linezolid
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476089 n.2432T>C non_coding_transcript_exon_variant 0.41 capreomycin
linezolid
rrl 1476095 n.2438C>G non_coding_transcript_exon_variant 0.37 capreomycin
linezolid
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.2 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.23 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476689 n.3032A>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1476690 n.3033C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1476693 n.3036G>A non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1476695 n.3038T>A non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
inhA 1673380 c.-822C>G upstream_gene_variant 0.19 isoniazid
ethionamide
rpsA 1833721 c.180A>G synonymous_variant 0.14 pyrazinamide
rpsA 1833724 c.183C>G synonymous_variant 0.14 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.14 pyrazinamide
rpsA 1833742 c.201A>G synonymous_variant 0.15 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.15 pyrazinamide
rpsA 1833748 c.207C>G synonymous_variant 0.15 pyrazinamide
rpsA 1833787 c.246C>G synonymous_variant 0.14 pyrazinamide
rpsA 1833790 c.249T>C synonymous_variant 0.14 pyrazinamide
rpsA 1833802 c.261A>G synonymous_variant 0.15 pyrazinamide
rpsA 1833811 c.270G>T synonymous_variant 0.15 pyrazinamide
rpsA 1833838 c.297G>C synonymous_variant 0.14 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.14 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.15 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.15 pyrazinamide
rpsA 1833940 c.399C>G synonymous_variant 0.13 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 0.99 pyrazinamide Not assoc w R - Interim
rpsA 1834489 c.948T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834690 c.1149T>C synonymous_variant 0.17 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
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 2169221 c.1392T>C synonymous_variant 0.96 pyrazinamide Not assoc w R - Interim
PPE35 2170048 p.Leu189Val missense_variant 0.18 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.18 pyrazinamide
PPE35 2170623 c.-11G>A upstream_gene_variant 0.98 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
eis 2714955 c.378C>T synonymous_variant 0.97 kanamycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2477c 2782936 c.1107G>T synonymous_variant 0.16 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2782948 c.1095A>G synonymous_variant 0.16 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2782957 c.1086A>G synonymous_variant 0.15 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 2782966 c.1077C>A synonymous_variant 0.16 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2782969 c.1074A>C synonymous_variant 0.15 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2782972 c.1071G>C synonymous_variant 0.15 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2782981 c.1062G>C synonymous_variant 0.16 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2782984 c.1059T>C synonymous_variant 0.16 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2782990 c.1053C>G synonymous_variant 0.16 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783002 c.1041T>C synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783008 c.1035C>G synonymous_variant 0.15 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783013 c.1030T>C synonymous_variant 0.16 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 2783015 p.Ser343Thr missense_variant 0.17 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783035 c.1008G>C synonymous_variant 0.15 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783040 p.Ala335Thr missense_variant 0.15 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
amikacin Uncertain significance
Rv2477c 2783044 c.999G>C synonymous_variant 0.15 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783048 p.Asp332Gly missense_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783059 c.984T>C synonymous_variant 0.15 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783092 c.951A>G synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
amikacin
Rv2477c 2783751 p.Ile98Val missense_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783761 c.282G>C synonymous_variant 0.13 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
thyX 3067465 p.Ile161Val missense_variant 0.16 para-aminosalicylic_acid
thyX 3067475 c.471A>G synonymous_variant 0.15 para-aminosalicylic_acid
thyX 3067490 c.456C>G synonymous_variant 0.18 para-aminosalicylic_acid
thyX 3067493 c.453A>G synonymous_variant 0.18 para-aminosalicylic_acid
thyX 3067515 p.Ser144Thr missense_variant 0.17 para-aminosalicylic_acid
thyX 3067530 p.Ala139Ser missense_variant 0.16 para-aminosalicylic_acid
thyX 3067545 p.Glu134Ala missense_variant 0.17 para-aminosalicylic_acid
thyX 3067549 p.Thr133Ala missense_variant 0.16 para-aminosalicylic_acid
thyX 3067559 c.387C>G synonymous_variant 0.14 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.97 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626987 c.-374C>G upstream_gene_variant 0.14 rifampicin
bedaquiline
mtrB 3627008 c.-395G>C upstream_gene_variant 0.15 rifampicin
bedaquiline
mtrB 3627011 c.-398T>G upstream_gene_variant 0.14 rifampicin
bedaquiline
mtrA 3627119 c.231T>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3627122 c.-509T>C upstream_gene_variant 0.13 rifampicin
bedaquiline
mtrB 3627167 c.-554T>C upstream_gene_variant 0.13 rifampicin
bedaquiline
mtrA 3627221 c.129C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
bedaquiline
rpoA 3877679 p.Ala277Ser missense_variant 0.13 rifampicin
rpoA 3877743 c.765T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877764 c.744C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877770 c.738A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3877776 c.732T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3877782 c.726T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3877791 c.717C>G synonymous_variant 0.13 rifampicin
rpoA 3877890 c.618C>T synonymous_variant 0.12 rifampicin
rpoA 3877896 c.612G>C synonymous_variant 0.13 rifampicin
rpoA 3877905 c.603A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877909 p.Asn200Ser missense_variant 0.15 rifampicin
rpoA 3877920 c.588G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3877923 c.585C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3877926 c.582G>C synonymous_variant 0.14 rifampicin
rpoA 3877962 c.546G>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878217 c.291A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3878346 c.162T>C synonymous_variant 0.14 rifampicin
rpoA 3878376 c.132G>C synonymous_variant 0.14 rifampicin
rpoA 3878385 c.123C>G synonymous_variant 0.13 rifampicin
rpoA 3878388 c.120C>G synonymous_variant 0.13 rifampicin
rpoA 3878391 c.117T>C synonymous_variant 0.13 rifampicin
rpoA 3878415 c.93C>T synonymous_variant 0.16 rifampicin
rpoA 3878424 c.84G>C synonymous_variant 0.13 rifampicin
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247434 c.921C>G synonymous_variant 0.14 ethambutol
embB 4247437 c.924A>G synonymous_variant 0.14 ethambutol Not assoc w R - Interim
embB 4247440 c.927C>G synonymous_variant 0.14 ethambutol
embB 4247446 c.933C>T synonymous_variant 0.14 ethambutol
embB 4247464 c.951C>G synonymous_variant 0.18 ethambutol
embB 4247470 c.957T>C synonymous_variant 0.17 ethambutol
embB 4247491 c.978G>C synonymous_variant 0.16 ethambutol
embB 4247497 c.984T>C synonymous_variant 0.16 ethambutol
aftB 4267647 p.Asp397Gly missense_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 4338711 c.-190C>A upstream_gene_variant 0.93 kanamycin
capreomycin
amikacin
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.99 streptomycin Not assoc w R