TB-Profiler result

Run: SRR6785263
Summary

Run ID: SRR6785263

Sample name:

Date: 2024-04-15T10:39:10.641165

Number of reads: 2491233

Percentage reads mapped: 82.31

Median coverage: 58.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.99
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.99
lineage2.2 East-Asian (Beijing) RD105;RD207 0.98
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 741 c.741T>C synonymous_variant 0.14 isoniazid Not assoc w R - Interim
dnaA 849 c.849A>G synonymous_variant 0.15 isoniazid
dnaA 885 c.885T>C synonymous_variant 0.14 isoniazid
dnaA 1245 c.1245G>C synonymous_variant 0.15 isoniazid Not assoc w R - Interim
dnaA 1254 c.1254T>C synonymous_variant 0.18 isoniazid
dnaA 1278 c.1278T>C synonymous_variant 0.15 isoniazid
gyrB 6238 c.999G>A synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6242 p.Arg335Asn missense_variant 0.14 levofloxacin
moxifloxacin
gyrB 6250 c.1011A>G synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6256 c.1017G>A synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrB 6268 c.1029C>G synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrB 6280 c.1041T>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrB 6286 c.1047T>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrB 6289 c.1050C>T synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrB 6292 c.1053G>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrB 6307 c.1068T>G synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 6362 c.-940T>C upstream_gene_variant 0.16 levofloxacin
moxifloxacin
gyrA 6649 c.-653T>C upstream_gene_variant 0.15 levofloxacin
moxifloxacin
gyrA 6655 c.-647T>C upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 6670 c.-632G>C upstream_gene_variant 0.17 levofloxacin
moxifloxacin
gyrA 6673 c.-629A>C upstream_gene_variant 0.16 levofloxacin
moxifloxacin
gyrA 6676 c.-626T>G upstream_gene_variant 0.16 levofloxacin
moxifloxacin
gyrA 6700 c.-602T>C upstream_gene_variant 0.19 levofloxacin
moxifloxacin
gyrA 6703 c.-599G>C upstream_gene_variant 0.19 levofloxacin
moxifloxacin
gyrA 6709 c.-593A>G upstream_gene_variant 0.2 levofloxacin
moxifloxacin
gyrA 6712 c.-590G>C upstream_gene_variant 0.21 levofloxacin
moxifloxacin
gyrB 6728 c.1489_1491delCTAinsTG frameshift_variant&stop_gained 0.17 levofloxacin Uncertain significance
moxifloxacin
gyrB 6745 c.1506T>G synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6775 c.1536G>C synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7078 c.-224A>C upstream_gene_variant 0.15 levofloxacin
moxifloxacin
gyrA 7084 c.-218A>G upstream_gene_variant 0.16 levofloxacin
moxifloxacin
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 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.94 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620310 c.420C>T synonymous_variant 0.18 capreomycin
amikacin
kanamycin
ccsA 620317 c.427_429delGTCinsCG frameshift_variant&missense_variant 0.18 capreomycin
amikacin
kanamycin
ccsA 620340 c.450C>G synonymous_variant 0.21 capreomycin
amikacin
kanamycin
ccsA 620346 c.456C>G synonymous_variant 0.22 capreomycin
amikacin
kanamycin
ccsA 620362 p.Ala158Thr missense_variant 0.21 capreomycin
amikacin
kanamycin
ccsA 620367 c.477T>C synonymous_variant 0.22 capreomycin
amikacin
kanamycin
ccsA 620373 c.483C>G synonymous_variant 0.22 capreomycin
amikacin
kanamycin
ccsA 620376 c.486G>C synonymous_variant 0.22 capreomycin
amikacin
kanamycin
ccsA 620385 c.495G>C synonymous_variant 0.21 capreomycin
amikacin
kanamycin
ccsA 620388 c.498A>G synonymous_variant 0.19 capreomycin
amikacin
kanamycin
ccsA 620389 c.499C>T synonymous_variant 0.19 capreomycin
amikacin
kanamycin
ccsA 620412 c.522T>C synonymous_variant 0.19 capreomycin
amikacin
kanamycin
ccsA 620415 c.525T>C synonymous_variant 0.16 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
ccsA 620421 c.531G>C synonymous_variant 0.13 capreomycin
amikacin
kanamycin
ccsA 620424 c.534G>C synonymous_variant 0.16 capreomycin
amikacin
kanamycin
ccsA 620460 c.570T>G synonymous_variant 0.13 capreomycin
amikacin
kanamycin
ccsA 620625 p.Ile245Met missense_variant 0.98 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.97 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.98 ethionamide Uncertain significance
Rv0565c 657671 c.-201A>G upstream_gene_variant 0.14 ethionamide
hadA 732329 p.Leu134Val missense_variant 0.17 isoniazid Uncertain significance
hadA 732337 c.408G>A synonymous_variant 0.15 isoniazid
hadA 732378 c.450_452dupAGA disruptive_inframe_insertion 0.17 isoniazid
hadA 732396 p.Gly156Ala missense_variant 0.19 isoniazid
hadA 732398 p.Ala157Thr missense_variant 0.19 isoniazid
rpoB 760181 c.375T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760184 c.378A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760196 c.390C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760223 c.417T>C synonymous_variant 0.15 rifampicin
rpoB 760298 c.492G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760307 c.501T>C synonymous_variant 0.14 rifampicin
rpoB 760328 c.522G>C synonymous_variant 0.18 rifampicin
rpoB 760331 c.525G>C synonymous_variant 0.18 rifampicin
rpoB 760340 c.534G>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 760361 c.555T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 760370 c.564C>G synonymous_variant 0.22 rifampicin
rpoB 760376 p.Asp190Glu missense_variant 0.21 rifampicin Uncertain significance
rpoB 760380 p.Thr192Leu missense_variant 0.19 rifampicin
rpoB 760406 c.600G>C synonymous_variant 0.23 rifampicin
rpoB 760412 c.606C>G synonymous_variant 0.2 rifampicin
rpoB 760424 c.618C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760430 c.624T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 760475 c.669A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760481 c.675G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760484 c.678A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760522 p.Ser239Asn missense_variant 0.16 rifampicin Uncertain significance
rpoB 760532 c.726T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760533 p.Val243Thr missense_variant 0.14 rifampicin
rpoB 760541 c.735G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760547 c.741G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760563 p.Arg253Ile missense_variant 0.13 rifampicin
rpoB 760591 p.Val262Ala missense_variant 0.21 rifampicin
rpoB 760611 c.805T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760646 c.840C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760661 c.855A>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760670 c.864G>C synonymous_variant 0.14 rifampicin
rpoB 761129 c.1323G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761150 c.1344A>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761153 c.1347G>C synonymous_variant 0.17 rifampicin
rpoB 761165 c.1359G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 761180 c.1374A>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761207 c.1401C>T synonymous_variant 0.13 rifampicin
rpoB 761219 c.1413G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761249 c.1443A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761255 c.1449T>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761261 c.1455G>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761306 c.1500C>G synonymous_variant 0.15 rifampicin
rpoB 761312 c.1506G>C synonymous_variant 0.15 rifampicin
rpoB 761327 c.1521A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761330 c.1524G>C synonymous_variant 0.15 rifampicin
rpoB 761354 c.1548C>T synonymous_variant 0.17 rifampicin
rpoB 761360 c.1554T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761362 p.Ser519Thr missense_variant 0.16 rifampicin
rpoB 761636 c.1830G>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761645 c.1839C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761648 c.1842T>C synonymous_variant 0.14 rifampicin
rpoB 761657 c.1851C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762008 c.2202C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762065 c.2259T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762083 c.2277T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762086 c.2280G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762329 c.2523G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762338 c.2532T>C synonymous_variant 0.14 rifampicin
rpoB 762347 c.2541T>C synonymous_variant 0.13 rifampicin
rpoC 762434 c.-936T>C upstream_gene_variant 0.13 rifampicin
rpoB 762449 c.2643C>A synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 762989 c.-381G>C upstream_gene_variant 0.2 rifampicin
rpoB 762995 c.3189G>T synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763013 c.-357C>G upstream_gene_variant 0.18 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 0.94 rifampicin Not assoc w R
rpoB 763115 c.3309T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763136 c.3330C>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 763148 c.-222G>C upstream_gene_variant 0.18 rifampicin
rpoC 763158 c.-212C>T upstream_gene_variant 0.19 rifampicin
rpoB 763166 c.3360A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 763190 c.-180C>T upstream_gene_variant 0.16 rifampicin
rpoC 763206 c.-164_-162delAGTinsTCG upstream_gene_variant 0.14 rifampicin
rpoB 763214 c.3408T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763226 c.-144A>G upstream_gene_variant 0.15 rifampicin
rpoB 763227 c.3421C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763238 c.3432T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763253 c.-117G>C upstream_gene_variant 0.15 rifampicin
rpoC 763256 c.-114G>A upstream_gene_variant 0.15 rifampicin
rpoC 763456 c.87A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763486 c.117T>G synonymous_variant 0.15 rifampicin
rpoC 763528 c.159G>A synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763603 c.234C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763636 c.267T>C synonymous_variant 0.16 rifampicin
rpoC 763660 c.291T>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763675 c.306C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763696 c.327T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763702 c.333C>G synonymous_variant 0.2 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 0.18 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.18 rifampicin
rpoC 763741 c.372C>T synonymous_variant 0.18 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.16 rifampicin
rpoC 763765 c.396T>C synonymous_variant 0.21 rifampicin
rpoC 763774 c.405G>C synonymous_variant 0.24 rifampicin
rpoC 763807 c.438T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763816 c.447C>G synonymous_variant 0.17 rifampicin
rpoC 763835 p.Ala156Met missense_variant 0.15 rifampicin
rpoC 763853 p.Val162Ile missense_variant 0.15 rifampicin
rpoC 763858 c.489A>G synonymous_variant 0.17 rifampicin
rpoC 763872 p.Gly168Ala missense_variant 0.16 rifampicin
rpoC 763876 p.Glu169Asp missense_variant 0.16 rifampicin
rpoC 763879 c.510A>G synonymous_variant 0.14 rifampicin
rpoC 763888 c.519G>C synonymous_variant 0.15 rifampicin
rpoC 763891 c.522G>C synonymous_variant 0.15 rifampicin
rpoC 763894 c.525A>G synonymous_variant 0.16 rifampicin
rpoC 763900 c.531G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 763936 c.567C>G synonymous_variant 0.18 rifampicin
rpoC 763939 c.570G>A synonymous_variant 0.18 rifampicin
rpoC 763942 c.573C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763948 c.579G>A synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763949 c.580C>A synonymous_variant 0.17 rifampicin
rpoC 763954 c.585C>G synonymous_variant 0.16 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 764024 c.655_657delTTGinsCC frameshift_variant&missense_variant 0.18 rifampicin
rpoC 764032 p.Asp221Glu missense_variant 0.19 rifampicin
rpoC 764040 p.Ser224Thr missense_variant 0.19 rifampicin
rpoC 764044 c.675T>C synonymous_variant 0.21 rifampicin
rpoC 764059 c.690G>T synonymous_variant 0.2 rifampicin
rpoC 764083 c.714A>G synonymous_variant 0.16 rifampicin
rpoC 764098 c.729A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764101 c.732C>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764102 p.Val245Ile missense_variant 0.2 rifampicin
rpoC 764112 p.Tyr248Phe missense_variant 0.2 rifampicin
rpoC 764116 c.747C>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764131 c.762T>C synonymous_variant 0.2 rifampicin
rpoC 764140 c.771C>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764434 c.1065A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764446 c.1077T>C synonymous_variant 0.18 rifampicin
rpoC 764449 c.1080G>C synonymous_variant 0.18 rifampicin
rpoC 764452 c.1083T>C synonymous_variant 0.19 rifampicin
rpoC 764458 c.1089G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764461 c.1092A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764497 c.1128A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764510 c.1141C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764521 c.1152T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764527 c.1158C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764536 c.1167G>C synonymous_variant 0.16 rifampicin
rpoC 764872 c.1503A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764932 c.1563C>A synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764935 c.1566T>C synonymous_variant 0.13 rifampicin
rpoC 765553 c.2184C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765556 c.2187G>C synonymous_variant 0.17 rifampicin
rpoC 765559 c.2190G>C synonymous_variant 0.17 rifampicin
rpoC 765580 c.2211G>C synonymous_variant 0.16 rifampicin
rpoC 765613 p.His748Gln missense_variant 0.18 rifampicin
rpoC 765835 c.2466C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765994 c.2625A>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766043 p.Gln892Glu missense_variant 0.15 rifampicin
rpoC 766054 c.2685C>G synonymous_variant 0.16 rifampicin
rpoC 766531 c.3162G>C synonymous_variant 0.12 rifampicin
rpoC 766645 p.Glu1092Asp missense_variant 0.83 rifampicin Not assoc w R
rpoC 766894 c.3525T>C synonymous_variant 0.17 rifampicin
rpoC 766900 c.3531T>C synonymous_variant 0.18 rifampicin
rpoC 766933 c.3564A>G synonymous_variant 0.17 rifampicin
rpoC 766945 c.3576A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.98 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.98 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.96 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
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 0.14 streptomycin
rpsL 781760 c.201T>C synonymous_variant 0.14 streptomycin
rpsL 781772 c.213C>A synonymous_variant 0.14 streptomycin
rplC 801321 c.513C>T synonymous_variant 0.14 linezolid Not assoc w R - Interim
rplC 801324 c.516T>C synonymous_variant 0.17 linezolid
rplC 801339 c.531T>C synonymous_variant 0.13 linezolid
rplC 801341 p.Leu178Gln missense_variant 0.13 linezolid
rplC 801348 c.540T>G synonymous_variant 0.15 linezolid
rplC 801357 c.549T>C synonymous_variant 0.14 linezolid
rplC 801367 p.Ala187Thr missense_variant 0.15 linezolid
rplC 801402 c.594T>C synonymous_variant 0.15 linezolid
rplC 801405 c.597T>C synonymous_variant 0.15 linezolid
rplC 801423 c.615G>C synonymous_variant 0.14 linezolid
rplC 801426 c.618C>G synonymous_variant 0.14 linezolid
rplC 801427 p.Met207Val missense_variant 0.15 linezolid
rplC 801438 c.630T>C synonymous_variant 0.18 linezolid
rplC 801442 p.Ile212Val missense_variant 0.16 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
sigE 1364706 c.294G>A synonymous_variant 0.98 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.94 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1473986 n.329T>C non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1473987 n.330G>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.17 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1474009 n.352A>G non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474012 n.355C>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474970 n.1313G>A non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475013 n.1356G>A non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475199 n.1542G>A non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1475249 n.1592T>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475275 n.1618C>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.25 capreomycin
linezolid Uncertain significance
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.16 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.15 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833811 c.270G>T synonymous_variant 0.14 pyrazinamide
rpsA 1833838 c.297G>C synonymous_variant 0.15 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.16 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.14 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.14 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.2 pyrazinamide
rpsA 1833940 c.399C>G synonymous_variant 0.23 pyrazinamide
rpsA 1833971 c.430C>T synonymous_variant 0.19 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.22 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.19 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.17 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.17 pyrazinamide
rpsA 1834096 c.555G>C synonymous_variant 0.16 pyrazinamide
rpsA 1834099 c.558C>G synonymous_variant 0.15 pyrazinamide
rpsA 1834102 c.561T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834105 c.564C>G synonymous_variant 0.16 pyrazinamide
rpsA 1834108 c.567C>G synonymous_variant 0.16 pyrazinamide
rpsA 1834123 c.582C>G synonymous_variant 0.16 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 0.99 pyrazinamide Not assoc w R - Interim
rpsA 1834210 c.669C>T synonymous_variant 0.15 pyrazinamide
rpsA 1834222 c.681T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834231 c.690T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
rpsA 1834366 c.825A>G synonymous_variant 0.18 pyrazinamide Not assoc w R - Interim
rpsA 1834435 c.894G>C synonymous_variant 0.19 pyrazinamide
rpsA 1834465 c.924T>C synonymous_variant 0.21 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.24 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.31 pyrazinamide
rpsA 1834513 c.972C>G synonymous_variant 0.26 pyrazinamide
rpsA 1834528 c.987T>C synonymous_variant 0.24 pyrazinamide
rpsA 1834540 c.999G>C synonymous_variant 0.21 pyrazinamide
rpsA 1834546 c.1005T>C synonymous_variant 0.22 pyrazinamide
rpsA 1834555 c.1014T>G synonymous_variant 0.24 pyrazinamide
rpsA 1834609 c.1068T>C synonymous_variant 0.26 pyrazinamide
rpsA 1834618 c.1077G>C synonymous_variant 0.26 pyrazinamide
rpsA 1834633 c.1092A>G synonymous_variant 0.24 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.26 pyrazinamide
rpsA 1834654 p.Glu371Asp missense_variant 0.25 pyrazinamide
rpsA 1834690 c.1149T>C synonymous_variant 0.21 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.97 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2517950 c.-165C>G upstream_gene_variant 0.19 isoniazid
Rv2477c 2783116 c.927T>C synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783665 c.378A>G synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783674 c.369T>C synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783683 c.360A>G synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783700 p.Thr115Ser missense_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783718 c.325T>C synonymous_variant 0.19 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783719 c.324A>G synonymous_variant 0.2 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2752c 3066360 c.-169T>C upstream_gene_variant 0.17 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
thyX 3067439 c.507A>G synonymous_variant 0.33 para-aminosalicylic_acid
thyX 3067445 c.501C>G synonymous_variant 0.33 para-aminosalicylic_acid
thyX 3067457 c.489C>G synonymous_variant 0.37 para-aminosalicylic_acid
thyX 3067465 p.Ile161Val missense_variant 0.38 para-aminosalicylic_acid
thyX 3067475 c.471A>G synonymous_variant 0.41 para-aminosalicylic_acid
thyX 3067490 c.456C>G synonymous_variant 0.39 para-aminosalicylic_acid
thyX 3067493 c.453A>G synonymous_variant 0.38 para-aminosalicylic_acid
thyX 3067515 p.Ser144Thr missense_variant 0.33 para-aminosalicylic_acid
thyX 3067530 p.Ala139Ser missense_variant 0.26 para-aminosalicylic_acid
thyX 3067545 p.Glu134Ala missense_variant 0.26 para-aminosalicylic_acid
thyX 3067549 p.Thr133Ala missense_variant 0.22 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3625687 c.-777G>C upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3625755 p.Ala287Thr missense_variant 0.13 bedaquiline
rifampicin Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.97 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrA 3627188 c.162A>G synonymous_variant 0.13 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627209 c.-596G>A upstream_gene_variant 0.13 bedaquiline
rifampicin
mtrA 3627221 c.129C>T synonymous_variant 0.13 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3627227 c.123T>C synonymous_variant 0.13 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627233 c.-620T>C upstream_gene_variant 0.13 bedaquiline
rifampicin
mtrB 3627236 c.-623T>C upstream_gene_variant 0.13 bedaquiline
rifampicin
mtrA 3627242 c.108C>T synonymous_variant 0.14 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627254 c.-641C>T upstream_gene_variant 0.18 bedaquiline
rifampicin
mtrB 3627263 c.-650C>T upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3627266 c.-653A>G upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3627272 c.-659G>T upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3627275 c.-662G>T upstream_gene_variant 0.16 bedaquiline
rifampicin
mtrB 3627296 c.-683T>C upstream_gene_variant 0.16 bedaquiline
rifampicin
mtrA 3627299 c.49_51delTTGinsCA frameshift_variant&missense_variant 0.14 bedaquiline
rifampicin
mtrB 3627314 c.-701C>T upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3627317 c.-704T>C upstream_gene_variant 0.14 bedaquiline
rifampicin
rpoA 3877704 c.804G>C synonymous_variant 0.15 rifampicin
rpoA 3877743 c.765T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3877764 c.744C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3877770 c.738A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877776 c.732T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
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 4040291 c.414G>C synonymous_variant 0.16 pyrazinamide
clpC1 4040318 c.387C>G synonymous_variant 0.17 pyrazinamide
clpC1 4040330 c.375C>G synonymous_variant 0.14 pyrazinamide
clpC1 4040342 c.363C>G synonymous_variant 0.15 pyrazinamide
glpK 4138670 c.1086G>C synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138681 p.Met359Val missense_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138695 p.Pro354Asp missense_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138718 c.1038T>C synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138721 c.1035G>A synonymous_variant 0.14 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
glpK 4138724 c.1032A>G synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138730 c.1026C>G synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138757 c.999A>G synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4241107 c.1245G>C synonymous_variant 0.13 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.98 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.94 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.98 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R