TB-Profiler result

Run: ERR3797060
Summary

Run ID: ERR3797060

Sample name:

Date: 2024-10-04T16:23:44.023386

Number of reads: 540952

Percentage reads mapped: 24.33

Median coverage: 16.0

Strain: La1.8.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
La1.8 M.bovis None 1.0
La1.8.1 M.bovis None 0.98
La1 M.bovis None 0.97
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 pncA p.His57Asp Assoc w R
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
pncA 2289073 p.His57Asp missense_variant 1.0 pyrazinamide Assoc w R
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 467 p.His156Arg missense_variant 1.0 isoniazid Not assoc w R
dnaA 654 c.654A>G synonymous_variant 0.32 isoniazid
gyrA 6673 c.-629A>C upstream_gene_variant 0.58 levofloxacin
moxifloxacin
gyrA 6676 c.-626T>G upstream_gene_variant 0.58 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 8048 c.747C>A synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 8285 c.984C>T synonymous_variant 1.0 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 9217 p.Asp639Ala missense_variant 0.81 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9275 c.1974G>A synonymous_variant 0.3 levofloxacin
moxifloxacin
gyrA 9296 c.1995T>C synonymous_variant 0.3 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Glu missense_variant 1.0 levofloxacin
moxifloxacin
Rv0010c 13197 p.Thr121Ser missense_variant 1.0 isoniazid Not assoc w R
Rv0010c 13228 c.330delG frameshift_variant 1.0 isoniazid Uncertain significance
Rv0010c 13460 c.99T>C synonymous_variant 1.0 isoniazid Not assoc w R
mshA 575771 p.Val142Thr missense_variant 0.27 isoniazid
ethionamide
mshA 575782 c.435G>C synonymous_variant 0.27 isoniazid
ethionamide
mshA 575785 c.438T>C synonymous_variant 0.35 isoniazid
ethionamide
mshA 575795 p.Ile150Val missense_variant 0.3 isoniazid
ethionamide
mshA 575803 c.456C>T synonymous_variant 0.3 isoniazid Not assoc w R - Interim
ethionamide
mshA 575821 c.474G>C synonymous_variant 0.27 isoniazid
ethionamide
mshA 575824 c.477T>C synonymous_variant 0.3 isoniazid
ethionamide
mshA 575833 c.486C>G synonymous_variant 0.3 isoniazid
ethionamide
mshA 575857 c.510G>C synonymous_variant 0.29 isoniazid
ethionamide
ccsA 620709 c.819G>C synonymous_variant 0.33 kanamycin
capreomycin
amikacin
ccsA 620733 c.843G>C synonymous_variant 0.36 kanamycin
capreomycin
amikacin
ccsA 620739 c.849A>G synonymous_variant 0.35 kanamycin
capreomycin
amikacin
ccsA 620742 c.852G>C synonymous_variant 0.3 kanamycin
capreomycin
amikacin
ccsA 620778 c.888T>C synonymous_variant 0.35 kanamycin
capreomycin
amikacin
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
nusG 734329 p.Ala26Thr missense_variant 1.0 rifampicin Uncertain significance
rpoB 761015 c.1209G>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 761027 c.1221A>G synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 761327 c.1521A>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoB 761615 c.1809A>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoB 761636 c.1830G>T synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 761645 c.1839C>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoB 761648 c.1842T>C synonymous_variant 0.38 rifampicin
rpoB 761681 c.1875G>A synonymous_variant 0.26 rifampicin
rpoB 762053 c.2247T>C synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoB 762065 c.2259T>C synonymous_variant 0.48 rifampicin Not assoc w R - Interim
rpoB 762083 c.2277T>C synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoB 762086 c.2280G>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoB 762101 c.2295C>G synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoB 762114 p.Ile770Val missense_variant 0.39 rifampicin Uncertain significance
rpoB 762140 c.2334G>C synonymous_variant 0.32 rifampicin
rpoB 762143 c.2337T>C synonymous_variant 0.37 rifampicin
rpoB 762149 c.2343G>C synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoB 762167 c.2361T>C synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoB 762176 c.2370T>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoB 762284 c.2478G>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoB 762293 c.2487T>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 762317 c.2511A>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 762329 c.2523G>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 762989 c.-381G>C upstream_gene_variant 0.24 rifampicin
rpoB 763028 c.3222T>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.83 rifampicin Not assoc w R
rpoC 763675 c.306C>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 763702 c.333C>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 763714 c.345G>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 764278 c.909A>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764296 c.927G>C synonymous_variant 0.25 rifampicin
rpoC 764320 c.951C>T synonymous_variant 0.22 rifampicin
rpoC 764365 c.996C>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764371 c.1002G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764380 c.1011G>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 764458 c.1089G>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 764461 c.1092A>G synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 764485 c.1116G>C synonymous_variant 0.27 rifampicin
rpoC 764497 c.1128A>G synonymous_variant 0.54 rifampicin Not assoc w R - Interim
rpoC 764500 c.1131C>G synonymous_variant 0.29 rifampicin
rpoC 764521 c.1152T>C synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoC 764536 c.1167G>C synonymous_variant 0.39 rifampicin
rpoC 764539 c.1170C>G synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoC 764560 c.1191T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 764602 c.1233C>T synonymous_variant 0.26 rifampicin
rpoC 764632 c.1263T>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoC 764716 c.1347G>C synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoC 764746 c.1377G>C synonymous_variant 0.38 rifampicin
rpoC 764752 c.1383G>C synonymous_variant 0.52 rifampicin Not assoc w R - Interim
rpoC 764755 c.1386C>T synonymous_variant 0.33 rifampicin
rpoC 764758 c.1389C>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.52 rifampicin Not assoc w R - Interim
rpoC 764809 c.1440C>T synonymous_variant 0.43 rifampicin Not assoc w R
rpoC 764812 c.1443C>G synonymous_variant 0.32 rifampicin
rpoC 764815 c.1446A>G synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 764824 c.1455T>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 764858 c.1489T>C synonymous_variant 0.45 rifampicin Not assoc w R - Interim
rpoC 764878 c.1509C>G synonymous_variant 0.4 rifampicin
rpoC 764893 c.1524T>C synonymous_variant 0.27 rifampicin
rpoC 765826 c.2457T>C synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoC 765904 c.2535C>G synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 765967 c.2598C>T synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 765979 c.2610C>G synonymous_variant 0.54 rifampicin Not assoc w R - Interim
rpoC 766021 c.2652G>C synonymous_variant 0.48 rifampicin
rpoC 766726 c.3357T>C synonymous_variant 0.33 rifampicin
rpoC 766738 c.3369G>T synonymous_variant 0.32 rifampicin
rpoC 766750 c.3381C>G synonymous_variant 0.3 rifampicin
rpoC 766765 c.3396A>C synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 766774 c.3405T>C synonymous_variant 0.39 rifampicin
rpoC 766804 c.3435A>G synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoC 766933 c.3564A>G synonymous_variant 0.33 rifampicin
rpoC 766945 c.3576A>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 766963 c.3594T>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 766996 c.3627C>T synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoC 767002 c.3633G>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 767023 c.3654C>T synonymous_variant 0.27 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781715 c.156T>C synonymous_variant 0.34 streptomycin
rpsL 781728 c.169T>C synonymous_variant 0.31 streptomycin
rpsL 781736 c.177T>C synonymous_variant 0.28 streptomycin
rpsL 781751 c.192G>C synonymous_variant 0.3 streptomycin
rpsL 781760 c.201T>C synonymous_variant 0.32 streptomycin
rpsL 781814 c.255C>T synonymous_variant 0.32 streptomycin
rpsL 781817 c.258G>T synonymous_variant 0.36 streptomycin
rplC 801454 p.Glu216Gln missense_variant 0.93 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254582 c.-48A>G upstream_gene_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
fbiC 1303884 c.954T>C synonymous_variant 0.3 pretomanid
delamanid
clofazimine
fbiC 1303891 p.Ala321Thr missense_variant 0.27 pretomanid
delamanid
clofazimine
fbiC 1303912 p.Gly328Lys missense_variant 0.25 pretomanid
delamanid
clofazimine
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.58 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.69 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.52 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.45 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472912 n.1067C>T non_coding_transcript_exon_variant 0.76 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472917 n.1072G>A non_coding_transcript_exon_variant 0.77 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.83 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.82 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.82 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.8 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>C non_coding_transcript_exon_variant 0.77 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.78 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.8 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.76 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.75 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.81 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.75 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.75 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.75 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.76 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.76 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.66 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.42 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.27 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473054 n.1209C>G non_coding_transcript_exon_variant 0.28 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.36 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.3 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.28 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.53 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.44 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.44 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.3 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.46 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.54 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.54 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.6 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.61 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.63 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.6 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.7 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.64 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.64 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.65 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.63 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.59 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.74 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.52 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.41 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1673715 c.-487C>G upstream_gene_variant 1.0 isoniazid Uncertain significance
ethionamide Uncertain significance
inhA 1674822 c.621C>G synonymous_variant 0.26 isoniazid
ethionamide
inhA 1674828 p.Glu209Asp missense_variant 0.23 isoniazid
ethionamide
inhA 1674838 p.Ala213Gln missense_variant 0.22 isoniazid
ethionamide
inhA 1674846 p.Ile215Met missense_variant 0.19 isoniazid
ethionamide
inhA 1674858 c.657G>A synonymous_variant 0.19 isoniazid
ethionamide
inhA 1674879 c.678T>G synonymous_variant 0.19 isoniazid
ethionamide
inhA 1674883 p.Ile228Leu missense_variant 0.2 isoniazid
ethionamide
inhA 1674903 c.702T>C synonymous_variant 0.23 isoniazid
ethionamide
inhA 1674904 p.Ala235Pro missense_variant 0.23 isoniazid
ethionamide
inhA 1674912 c.711G>C synonymous_variant 0.2 isoniazid
ethionamide
inhA 1674924 c.723G>C synonymous_variant 0.19 isoniazid
ethionamide
rpsA 1833727 c.186G>C synonymous_variant 0.41 pyrazinamide
rpsA 1833734 p.Ala65Ser missense_variant 0.47 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.47 pyrazinamide
rpsA 1833811 c.270G>C synonymous_variant 0.41 pyrazinamide
rpsA 1833829 c.288A>G synonymous_variant 0.35 pyrazinamide
rpsA 1833832 c.291G>A synonymous_variant 0.35 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.59 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.56 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.53 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.47 pyrazinamide Not assoc w R - Interim
rpsA 1834366 c.825A>G synonymous_variant 0.37 pyrazinamide Not assoc w R - Interim
rpsA 1834451 c.910T>C synonymous_variant 0.29 pyrazinamide
rpsA 1834456 c.915T>G synonymous_variant 0.24 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
bacA 2062922 p.Ile603Val missense_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
ndh 2103173 c.-132delG upstream_gene_variant 1.0 isoniazid
delamanid
ethionamide
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155503 c.609C>T synonymous_variant 1.0 isoniazid Not assoc w R
katG 2156025 c.87C>A synonymous_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2168011 p.Ser868Arg missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2168319 p.Thr765Ile missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2168814 c.1798dupA frameshift_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
eis 2715125 p.Thr70Ala missense_variant 1.0 kanamycin Uncertain significance
amikacin Uncertain significance
Rv2477c 2782927 c.1116A>G synonymous_variant 1.0 kanamycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R - Interim
Rv2681 2997325 p.Ala196Val missense_variant 0.93 capreomycin Uncertain significance
Rv2752c 3066555 c.-364C>T upstream_gene_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086728 c.-92C>T upstream_gene_variant 1.0 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087084 c.266delA frameshift_variant 1.0 cycloserine
Rv3083 3448783 p.Val94Ile missense_variant 1.0 ethionamide Uncertain significance
lpqB 3623372 c.1539G>C synonymous_variant 1.0 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
lpqB 3623730 p.Ser394Leu missense_variant 0.94 rifampicin Not assoc w R
bedaquiline Uncertain significance
lpqB 3624350 c.561G>T synonymous_variant 0.93 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
lpqB 3624593 c.318G>A synonymous_variant 0.88 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
lpqB 3624710 c.201G>A synonymous_variant 0.95 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
lpqB 3625161 c.-251T>C upstream_gene_variant 0.33 rifampicin
bedaquiline
lpqB 3625195 c.-285A>G upstream_gene_variant 0.35 rifampicin
bedaquiline
mtrB 3625222 c.1392T>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
bedaquiline
rpoA 3877668 c.840A>G synonymous_variant 0.53 rifampicin
rpoA 3877677 c.831G>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoA 3877686 c.822A>G synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoA 3877704 c.804G>T synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoA 3877728 c.780C>G synonymous_variant 0.35 rifampicin
rpoA 3877743 c.765T>C synonymous_variant 0.56 rifampicin Not assoc w R - Interim
rpoA 3877758 c.750G>C synonymous_variant 0.33 rifampicin
rpoA 3877770 c.738A>G synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoA 3877776 c.732T>C synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoA 3878217 c.291A>G synonymous_variant 0.6 rifampicin Not assoc w R - Interim
rpoA 3878264 p.Ser82Gly missense_variant 0.4 rifampicin
rpoA 3878271 c.237T>C synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoA 3879073 c.-566A>G upstream_gene_variant 0.41 rifampicin
rpoA 3879088 c.-582_-581delCAinsGC upstream_gene_variant 0.41 rifampicin
rpoA 3879094 c.-587T>C upstream_gene_variant 0.41 rifampicin
clpC1 4038403 c.2302T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4039865 c.840T>C synonymous_variant 0.29 pyrazinamide
clpC1 4040021 c.684A>C synonymous_variant 0.37 pyrazinamide Not assoc w R - Interim
clpC1 4040024 c.681A>G synonymous_variant 0.35 pyrazinamide
clpC1 4040141 c.564C>T synonymous_variant 0.32 pyrazinamide
clpC1 4040171 c.534C>G synonymous_variant 0.37 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Not assoc w R
embC 4242642 p.Arg927His missense_variant 0.94 ethambutol Uncertain significance
embC 4242970 c.3108C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246551 p.Asn13Ser missense_variant 1.0 ethambutol Not assoc w R
embB 4246864 c.351C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
aftB 4267167 p.Gln557Pro missense_variant 1.0 ethambutol Uncertain significance
ubiA 4269351 c.483C>T synonymous_variant 0.95 ethambutol Not assoc w R
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 4326024 p.Pro484Ser missense_variant 1.0 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R