TB-Profiler result

Run: ERR2514821
Summary

Run ID: ERR2514821

Sample name:

Date: 2024-04-13T23:46:09.028635

Number of reads: 556988

Percentage reads mapped: 70.38

Median coverage: 16.0

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 0.97
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 1.0
lineage2.2 East-Asian (Beijing) RD105;RD207 0.95
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 fbiC c.859_861delATCinsGG Assoc w R - Interim Confers DLM-PMD cross-resistance
c.1945_1947delATTinsGG Assoc w R - Interim Confers DLM-PMD cross-resistance
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
fbiC 1303789 c.859_861delATCinsGG frameshift_variant&missense_variant 0.3 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiC 1304875 c.1945_1947delATTinsGG frameshift_variant&missense_variant 0.37 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
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 1137 c.1137C>G synonymous_variant 0.4 isoniazid
dnaA 1152 c.1152A>G synonymous_variant 0.32 isoniazid
dnaA 1153 c.1153T>C synonymous_variant 0.32 isoniazid
dnaA 1158 c.1158C>T synonymous_variant 0.32 isoniazid
dnaA 1164 c.1164A>C synonymous_variant 0.32 isoniazid
dnaA 1167 c.1167A>G synonymous_variant 0.32 isoniazid Not assoc w R - Interim
dnaA 1176 c.1176A>G synonymous_variant 0.32 isoniazid
dnaA 1185 c.1185C>G synonymous_variant 0.3 isoniazid Not assoc w R - Interim
dnaA 1188 c.1188G>A synonymous_variant 0.27 isoniazid
dnaA 1191 c.1191T>C synonymous_variant 0.26 isoniazid
dnaA 1204 c.1204C>T synonymous_variant 0.24 isoniazid
dnaA 1218 c.1218C>G synonymous_variant 0.21 isoniazid
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7475 c.174A>G synonymous_variant 0.3 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7480 p.Phe60Tyr missense_variant 0.32 levofloxacin
moxifloxacin
gyrA 7484 c.183T>C synonymous_variant 0.32 levofloxacin
moxifloxacin
gyrA 7490 c.189C>G synonymous_variant 0.32 levofloxacin
moxifloxacin
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8111 c.810G>C synonymous_variant 0.27 levofloxacin
moxifloxacin
gyrA 8121 c.820T>C synonymous_variant 0.23 levofloxacin
moxifloxacin
gyrA 8129 c.828T>C synonymous_variant 0.28 levofloxacin
moxifloxacin
gyrA 8135 c.834C>G synonymous_variant 0.29 levofloxacin
moxifloxacin
gyrA 8156 c.855T>C synonymous_variant 0.39 levofloxacin
moxifloxacin
gyrA 8168 c.867A>G synonymous_variant 0.29 levofloxacin
moxifloxacin
gyrA 8177 c.876A>C synonymous_variant 0.25 levofloxacin
moxifloxacin
gyrA 8189 c.888G>C synonymous_variant 0.27 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8198 c.897T>C synonymous_variant 0.27 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8207 c.906T>C synonymous_variant 0.28 levofloxacin
moxifloxacin
gyrA 8480 c.1179C>T synonymous_variant 0.47 levofloxacin
moxifloxacin
gyrA 8486 c.1185T>C synonymous_variant 0.47 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8516 c.1215T>C synonymous_variant 0.58 levofloxacin
moxifloxacin
gyrA 8519 c.1218A>G synonymous_variant 0.47 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9284 c.1983T>C synonymous_variant 0.33 levofloxacin
moxifloxacin
gyrA 9296 c.1995T>C synonymous_variant 0.27 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9299 c.1998G>C synonymous_variant 0.27 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9300 p.Ala667Ser missense_variant 0.27 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Glu missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 9308 p.Asp669Glu missense_variant 0.29 levofloxacin
moxifloxacin
gyrA 9323 c.2022C>G synonymous_variant 0.26 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9329 c.2028C>G synonymous_variant 0.26 levofloxacin
moxifloxacin
gyrA 9335 c.2034G>C synonymous_variant 0.26 levofloxacin
moxifloxacin
gyrA 9365 c.2064G>A synonymous_variant 0.29 levofloxacin
moxifloxacin
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575659 c.312A>G synonymous_variant 0.23 ethionamide
isoniazid
mshA 575907 p.Ala187Val missense_variant 0.93 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
nusG 734532 c.279A>G synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoB 760091 c.285G>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 760101 c.295T>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 760112 c.306T>C synonymous_variant 0.42 rifampicin
rpoB 760118 c.312T>G synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoB 760121 c.315T>C synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoB 760130 p.Asp108Glu missense_variant 0.47 rifampicin Uncertain significance
rpoB 760139 c.333A>C synonymous_variant 0.45 rifampicin
rpoB 760142 c.336C>G synonymous_variant 0.45 rifampicin
rpoB 760181 c.375T>C synonymous_variant 0.55 rifampicin Not assoc w R - Interim
rpoB 760184 c.378A>G synonymous_variant 0.52 rifampicin Not assoc w R - Interim
rpoB 760196 c.390C>G synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoB 760223 c.417T>C synonymous_variant 0.46 rifampicin
rpoB 760235 c.429T>C synonymous_variant 0.52 rifampicin Not assoc w R - Interim
rpoB 760283 c.477G>C synonymous_variant 0.53 rifampicin Not assoc w R - Interim
rpoB 760298 c.492G>C synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoB 760307 c.501T>C synonymous_variant 0.35 rifampicin
rpoB 760328 c.522G>C synonymous_variant 0.47 rifampicin
rpoB 760331 c.525G>C synonymous_variant 0.42 rifampicin
rpoB 760340 c.534G>T synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoB 760361 c.555T>C synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoB 760370 c.564C>G synonymous_variant 0.33 rifampicin
rpoB 760376 p.Asp190Glu missense_variant 0.35 rifampicin Uncertain significance
rpoB 760380 p.Thr192Leu missense_variant 0.33 rifampicin
rpoB 760655 c.849A>G synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoB 760946 c.1140A>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 760982 c.1176G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 760985 c.1179G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 760991 c.1185G>C synonymous_variant 0.27 rifampicin
rpoB 761102 c.1296A>G synonymous_variant 0.25 rifampicin
rpoB 761234 c.1428G>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 761249 c.1443A>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 761255 c.1449T>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 761261 c.1455G>T synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoB 761306 c.1500C>G synonymous_variant 0.3 rifampicin
rpoB 761318 c.1512G>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 761867 c.2061C>T synonymous_variant 0.22 rifampicin
rpoB 761873 c.2067A>C synonymous_variant 0.19 rifampicin
rpoB 761885 c.2079T>C synonymous_variant 0.2 rifampicin
rpoB 761909 c.2103T>C synonymous_variant 0.21 rifampicin
rpoB 761912 c.2106T>C synonymous_variant 0.22 rifampicin
rpoB 761915 p.Asp703Glu missense_variant 0.23 rifampicin
rpoB 761916 p.Asp704Asn missense_variant 0.23 rifampicin
rpoB 763028 c.3222T>C synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.59 rifampicin Not assoc w R
rpoB 763031 c.3225T>G synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoB 763034 c.3228C>G synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoB 763040 c.3234C>G synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoB 763085 c.3279C>G synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.45 rifampicin Not assoc w R - Interim
rpoB 763145 c.3339G>A synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoC 763148 c.-222G>C upstream_gene_variant 0.45 rifampicin
rpoC 763158 c.-212C>T upstream_gene_variant 0.42 rifampicin
rpoB 763166 c.3360A>G synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoC 763441 c.72C>T synonymous_variant 0.4 rifampicin
rpoC 763444 c.75T>C synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 763456 c.87A>G synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 763576 c.207C>G synonymous_variant 0.31 rifampicin
rpoC 763594 c.225C>T synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 764215 c.846A>G synonymous_variant 0.3 rifampicin
rpoC 764236 c.867G>A synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 764237 p.Leu290Ile missense_variant 0.3 rifampicin
rpoC 764266 c.897T>C synonymous_variant 0.29 rifampicin
rpoC 764269 c.900G>C synonymous_variant 0.29 rifampicin
rpoC 764272 c.903G>C synonymous_variant 0.29 rifampicin
rpoC 764278 c.909A>G synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 764293 c.924G>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 764626 c.1257C>T synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 764668 c.1299C>T synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 764752 c.1383G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764803 c.1434C>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764809 c.1440C>T synonymous_variant 0.24 rifampicin Not assoc w R
rpoC 764815 c.1446A>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 765404 p.Leu679Val missense_variant 0.32 rifampicin
rpoC 765409 c.2040T>C synonymous_variant 0.27 rifampicin
rpoC 765454 c.2085C>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 765499 c.2130C>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 765508 c.2139C>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 765541 c.2172C>G synonymous_variant 0.32 rifampicin
rpoC 765658 c.2289C>T synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 765700 c.2331T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 765883 c.2514C>G synonymous_variant 0.37 rifampicin
rpoC 765886 c.2517C>G synonymous_variant 0.37 rifampicin
rpoC 765892 c.2523T>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 765937 c.2568T>C synonymous_variant 0.48 rifampicin Not assoc w R - Interim
rpoC 765967 c.2598C>T synonymous_variant 0.56 rifampicin Not assoc w R - Interim
rpoC 766312 c.2943T>G synonymous_variant 0.25 rifampicin
rpoC 766327 c.2958C>A synonymous_variant 0.26 rifampicin
rpoC 766345 c.2976T>C synonymous_variant 0.35 rifampicin
rpoC 766348 c.2979A>G synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 766357 c.2988C>T synonymous_variant 0.38 rifampicin
rpoC 766363 c.2994G>C synonymous_variant 0.39 rifampicin
rpoC 766366 c.2997C>G synonymous_variant 0.39 rifampicin
rpoC 766381 c.3012C>T synonymous_variant 0.42 rifampicin
rpoC 766384 c.3015A>G synonymous_variant 0.44 rifampicin
rpoC 766408 c.3039C>G synonymous_variant 0.5 rifampicin
rpoC 766411 c.3042C>G synonymous_variant 0.5 rifampicin
rpoC 766522 c.3153C>G synonymous_variant 0.57 rifampicin
rpoC 766528 c.3159T>C synonymous_variant 0.53 rifampicin
rpoC 766531 c.3162G>C synonymous_variant 0.53 rifampicin
rpoC 766645 p.Glu1092Asp missense_variant 0.87 rifampicin Not assoc w R
rpoC 766843 c.3474T>C synonymous_variant 0.26 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 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781700 c.141G>C synonymous_variant 0.3 streptomycin
rpsL 781715 c.156T>C synonymous_variant 0.29 streptomycin
rpsL 781728 c.169T>C synonymous_variant 0.27 streptomycin
rpsL 781736 c.177T>C synonymous_variant 0.31 streptomycin
rpsL 781742 c.183C>T synonymous_variant 0.31 streptomycin
rpsL 781748 c.189C>G synonymous_variant 0.31 streptomycin
rpsL 781754 c.195G>C synonymous_variant 0.33 streptomycin
rpsL 781760 c.201T>C synonymous_variant 0.31 streptomycin
rpsL 781769 c.210G>A synonymous_variant 0.33 streptomycin
rpsL 781772 c.213C>G synonymous_variant 0.33 streptomycin
rpsL 781808 c.249C>T synonymous_variant 0.29 streptomycin
rpsL 781811 c.252C>T synonymous_variant 0.29 streptomycin
rpsL 781832 c.273T>C synonymous_variant 0.29 streptomycin
rpsL 781838 c.279G>C synonymous_variant 0.29 streptomycin
rpsL 781841 c.282C>G synonymous_variant 0.23 streptomycin
rplC 801246 c.438C>T synonymous_variant 0.21 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1303686 c.756C>G synonymous_variant 0.27 clofazimine
pretomanid
delamanid
fbiC 1303695 c.765T>C synonymous_variant 0.24 clofazimine
pretomanid
delamanid
fbiC 1303704 c.774T>G synonymous_variant 0.25 clofazimine
pretomanid
delamanid
fbiC 1303708 c.778T>C synonymous_variant 0.24 clofazimine
pretomanid
delamanid
fbiC 1303728 c.798G>A synonymous_variant 0.25 clofazimine
pretomanid
delamanid
fbiC 1303785 c.855G>T synonymous_variant 0.32 clofazimine
pretomanid
delamanid
fbiC 1303818 c.888C>G synonymous_variant 0.29 clofazimine
pretomanid
delamanid
fbiC 1303860 c.930A>C synonymous_variant 0.29 clofazimine
pretomanid
delamanid
fbiC 1303884 c.954T>G synonymous_variant 0.29 clofazimine
pretomanid
delamanid
fbiC 1304004 c.1074A>G synonymous_variant 0.27 clofazimine
pretomanid
delamanid
fbiC 1304727 c.1797A>G synonymous_variant 0.25 clofazimine
pretomanid
delamanid
fbiC 1304742 c.1812T>C synonymous_variant 0.31 clofazimine
pretomanid
delamanid
fbiC 1304748 c.1818T>C synonymous_variant 0.3 clofazimine
pretomanid
delamanid
fbiC 1304757 c.1827A>G synonymous_variant 0.31 clofazimine
pretomanid
delamanid
fbiC 1304760 c.1830G>C synonymous_variant 0.31 clofazimine
pretomanid
delamanid
fbiC 1304769 c.1839C>T synonymous_variant 0.32 clofazimine
pretomanid
delamanid
fbiC 1304778 c.1848T>C synonymous_variant 0.33 clofazimine
pretomanid
delamanid
fbiC 1304784 c.1854T>C synonymous_variant 0.34 clofazimine
pretomanid
delamanid
fbiC 1304787 c.1857T>C synonymous_variant 0.39 clofazimine
pretomanid
delamanid
fbiC 1304808 c.1878C>G synonymous_variant 0.37 clofazimine
pretomanid
delamanid
fbiC 1304811 c.1881C>G synonymous_variant 0.37 clofazimine
pretomanid
delamanid
fbiC 1304817 c.1887T>C synonymous_variant 0.4 clofazimine
pretomanid
delamanid
fbiC 1304829 c.1899T>C synonymous_variant 0.5 clofazimine
pretomanid
delamanid
fbiC 1304832 c.1902C>T synonymous_variant 0.48 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fbiC 1304853 c.1923C>G synonymous_variant 0.43 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fbiC 1304856 c.1926C>G synonymous_variant 0.38 clofazimine
pretomanid
delamanid
fbiC 1304869 c.1939C>T synonymous_variant 0.37 clofazimine
pretomanid
delamanid
fbiC 1304928 c.1998T>C synonymous_variant 0.35 clofazimine
pretomanid
delamanid
fbiC 1304937 c.2007G>C synonymous_variant 0.38 clofazimine
pretomanid
delamanid
fbiC 1304940 c.2010A>G synonymous_variant 0.43 clofazimine
pretomanid
delamanid
fbiC 1304946 c.2016G>C synonymous_variant 0.5 clofazimine
pretomanid
delamanid
fbiC 1304955 c.2025G>A synonymous_variant 0.46 clofazimine
pretomanid
delamanid
fbiC 1304958 c.2028T>G synonymous_variant 0.46 clofazimine
pretomanid
delamanid
fbiC 1305150 c.2220C>G synonymous_variant 0.6 clofazimine
pretomanid
delamanid
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
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rpsA 1833874 c.333T>C synonymous_variant 0.32 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.24 pyrazinamide
rpsA 1833931 c.390C>T synonymous_variant 0.22 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.17 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.23 pyrazinamide
rpsA 1834099 c.558C>G synonymous_variant 0.29 pyrazinamide
rpsA 1834105 c.564C>G synonymous_variant 0.27 pyrazinamide
rpsA 1834108 c.567C>G synonymous_variant 0.29 pyrazinamide
rpsA 1834123 c.582C>G synonymous_variant 0.39 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
rpsA 1834189 c.648G>C synonymous_variant 0.43 pyrazinamide
rpsA 1834195 c.654G>C synonymous_variant 0.45 pyrazinamide
rpsA 1834222 c.681T>C synonymous_variant 0.41 pyrazinamide
rpsA 1834249 c.708T>C synonymous_variant 0.37 pyrazinamide
rpsA 1834261 c.720A>G synonymous_variant 0.36 pyrazinamide Not assoc w R - Interim
rpsA 1834262 c.721_723delTCGinsAGT synonymous_variant 0.36 pyrazinamide
rpsA 1834303 c.762T>C synonymous_variant 0.3 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.29 pyrazinamide
rpsA 1834654 p.Glu371Asp missense_variant 0.27 pyrazinamide
rpsA 1834690 c.1149T>C synonymous_variant 0.32 pyrazinamide
rpsA 1834732 c.1191T>C synonymous_variant 0.28 pyrazinamide
rpsA 1834733 p.Ala398Ser missense_variant 0.29 pyrazinamide
rpsA 1834753 c.1212T>C synonymous_variant 0.29 pyrazinamide
rpsA 1834765 p.Glu408Asp missense_variant 0.35 pyrazinamide
rpsA 1834775 p.Ala412Thr missense_variant 0.33 pyrazinamide
rpsA 1834780 c.1239A>G synonymous_variant 0.33 pyrazinamide
tsnR 1853361 c.-245T>C upstream_gene_variant 0.32 linezolid
tsnR 1853370 c.-236_-234delGCAinsTG upstream_gene_variant 0.35 linezolid
tsnR 1853375 c.-231G>C upstream_gene_variant 0.33 linezolid
tsnR 1853387 c.-219T>G upstream_gene_variant 0.36 linezolid
tsnR 1853394 c.-212_-211delCTinsGC upstream_gene_variant 0.35 linezolid
tsnR 1853420 c.-186T>G upstream_gene_variant 0.38 linezolid
tsnR 1853429 c.-177G>C upstream_gene_variant 0.39 linezolid
tsnR 1853432 c.-174G>C upstream_gene_variant 0.39 linezolid
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ahpC 2726591 c.399C>G synonymous_variant 0.35 isoniazid
ahpC 2726593 p.Val134Ala missense_variant 0.35 isoniazid
ahpC 2726600 c.408T>C synonymous_variant 0.37 isoniazid
ahpC 2726601 p.Ile137Leu missense_variant 0.35 isoniazid
ahpC 2726693 c.501C>A synonymous_variant 0.25 isoniazid
ahpC 2726696 c.504C>G synonymous_variant 0.24 isoniazid
Rv2477c 2783275 c.768C>G synonymous_variant 0.45 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783278 c.765A>G synonymous_variant 0.45 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783287 c.756C>G synonymous_variant 0.54 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783293 c.750G>A synonymous_variant 0.62 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783299 c.744A>G synonymous_variant 0.59 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783302 c.741A>G synonymous_variant 0.59 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783311 c.732T>C synonymous_variant 0.59 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783314 c.729C>G synonymous_variant 0.59 ethambutol Not assoc w R - Interim
moxifloxacin
streptomycin Not assoc w R - Interim
levofloxacin
kanamycin
rifampicin Not assoc w R - Interim
amikacin
Rv2477c 2783317 c.726G>C synonymous_variant 0.54 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783332 c.711T>C synonymous_variant 0.5 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783335 c.708C>G synonymous_variant 0.5 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783350 c.693T>C synonymous_variant 0.53 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783353 c.690T>C synonymous_variant 0.5 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783356 c.687C>G synonymous_variant 0.47 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783359 c.684G>A synonymous_variant 0.47 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783374 c.669G>C synonymous_variant 0.43 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783656 c.387G>C synonymous_variant 0.32 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783659 c.384A>G synonymous_variant 0.32 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783665 c.378A>G synonymous_variant 0.35 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783673 c.370C>A synonymous_variant 0.35 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783674 c.369T>C synonymous_variant 0.35 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783683 c.360A>G synonymous_variant 0.35 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783691 c.352C>T synonymous_variant 0.35 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2477c 2783695 c.348C>T synonymous_variant 0.27 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783700 p.Thr115Ser missense_variant 0.29 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783716 c.327G>A synonymous_variant 0.33 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783751 p.Ile98Val missense_variant 0.58 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783758 p.Asp95Glu missense_variant 0.64 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2681 2997128 c.390A>G synonymous_variant 0.24 capreomycin
Rv2681 2997129 p.Ala131Thr missense_variant 0.23 capreomycin
Rv2681 2997134 c.396A>G synonymous_variant 0.23 capreomycin
Rv2681 2997137 c.399C>T synonymous_variant 0.23 capreomycin
Rv2681 2997149 c.411T>C synonymous_variant 0.24 capreomycin
Rv2681 2997158 c.420C>G synonymous_variant 0.24 capreomycin
Rv2681 2997173 p.Asp145Glu missense_variant 0.23 capreomycin
Rv2681 2997176 c.438A>C synonymous_variant 0.22 capreomycin
Rv2681 2997188 c.450G>C synonymous_variant 0.22 capreomycin
Rv2681 2997189 p.Ala151Thr missense_variant 0.22 capreomycin
Rv2752c 3064973 p.Ala407Ser missense_variant 0.24 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3064974 c.1218T>C synonymous_variant 0.3 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3064995 c.1197C>G synonymous_variant 0.31 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3064998 c.1194A>G synonymous_variant 0.3 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3065007 c.1185G>C synonymous_variant 0.29 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3065013 c.1179G>C synonymous_variant 0.29 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3065018 p.Asn392His missense_variant 0.3 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3065022 c.1170G>C synonymous_variant 0.3 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3065028 c.1162_1164delGTGinsAT frameshift_variant&missense_variant 0.33 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv2752c 3065040 c.1152C>G synonymous_variant 0.32 ethambutol Not assoc w R - Interim
moxifloxacin
levofloxacin
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
Rv2752c 3065048 c.1144C>T synonymous_variant 0.32 ethambutol Not assoc w R - Interim
moxifloxacin
levofloxacin
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
Rv2752c 3065064 c.1128G>C synonymous_variant 0.22 ethambutol Not assoc w R - Interim
moxifloxacin
levofloxacin
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
Rv2752c 3066603 c.-412A>G upstream_gene_variant 0.38 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066612 c.-421G>A upstream_gene_variant 0.32 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066617 c.-426G>A upstream_gene_variant 0.32 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066618 c.-427A>C upstream_gene_variant 0.32 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066633 c.-442T>C upstream_gene_variant 0.29 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
thyX 3067793 c.153T>C synonymous_variant 0.28 para-aminosalicylic_acid
thyX 3067802 c.144C>G synonymous_variant 0.28 para-aminosalicylic_acid
thyA 3074045 c.427C>T synonymous_variant 0.41 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625222 c.1392T>C synonymous_variant 0.23 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626562 p.Pro18Ser missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626876 c.-263A>G upstream_gene_variant 0.35 bedaquiline
rifampicin
mtrB 3627167 c.-554T>C upstream_gene_variant 0.5 bedaquiline
rifampicin
mtrA 3627175 c.175C>T synonymous_variant 0.55 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627181 c.-568T>C upstream_gene_variant 0.55 bedaquiline
rifampicin
mtrB 3627182 c.-569T>C upstream_gene_variant 0.55 bedaquiline
rifampicin
mtrA 3627188 c.162A>G synonymous_variant 0.55 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627196 c.-583C>T upstream_gene_variant 0.5 bedaquiline
rifampicin
mtrB 3627209 c.-596G>A upstream_gene_variant 0.43 bedaquiline
rifampicin
mtrA 3627221 c.129C>T synonymous_variant 0.35 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3627227 c.123T>C synonymous_variant 0.35 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627296 c.-683T>C upstream_gene_variant 0.33 bedaquiline
rifampicin
mtrA 3627299 c.49_51delTTGinsCA frameshift_variant&missense_variant 0.32 bedaquiline
rifampicin
mtrB 3627314 c.-701C>T upstream_gene_variant 0.3 bedaquiline
rifampicin
mtrB 3627317 c.-704T>C upstream_gene_variant 0.3 bedaquiline
rifampicin
mtrA 3627343 p.Thr3Ser missense_variant 0.26 bedaquiline
rifampicin
rpoA 3877613 p.Ile299Val missense_variant 0.22 rifampicin
rpoA 3877656 c.852T>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoA 3877962 c.546G>T synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoA 3878022 c.486T>C synonymous_variant 0.29 rifampicin
rpoA 3878205 c.303T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3878217 c.291A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3878226 c.282C>G synonymous_variant 0.31 rifampicin
rpoA 3878232 c.276G>C synonymous_variant 0.39 rifampicin
rpoA 3878247 c.261G>C synonymous_variant 0.42 rifampicin
rpoA 3878271 c.237T>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoA 3878276 c.232C>T synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoA 3878283 p.Glu75Ala missense_variant 0.39 rifampicin
rpoA 3878292 c.216T>C synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoA 3878304 c.204G>C synonymous_variant 0.27 rifampicin
rpoA 3878313 c.195G>T synonymous_variant 0.28 rifampicin
rpoA 3878415 c.93C>T synonymous_variant 0.27 rifampicin
clpC1 4038486 p.Gly740Asn missense_variant 0.53 pyrazinamide
clpC1 4038489 p.Ala739Gly missense_variant 0.53 pyrazinamide
clpC1 4038494 c.2211G>C synonymous_variant 0.57 pyrazinamide
clpC1 4038497 p.Ser736Gln missense_variant 0.53 pyrazinamide
clpC1 4038530 p.Glu725Asp missense_variant 0.52 pyrazinamide
clpC1 4038551 c.2154C>G synonymous_variant 0.47 pyrazinamide
clpC1 4038596 c.2109A>G synonymous_variant 0.39 pyrazinamide
clpC1 4038623 c.2082A>G synonymous_variant 0.36 pyrazinamide
clpC1 4038755 c.1950G>T synonymous_variant 0.32 pyrazinamide
clpC1 4038770 c.1935C>T synonymous_variant 0.32 pyrazinamide
clpC1 4038773 c.1932T>C synonymous_variant 0.32 pyrazinamide
clpC1 4038782 c.1923G>C synonymous_variant 0.32 pyrazinamide
clpC1 4038790 c.1915C>T synonymous_variant 0.31 pyrazinamide Not assoc w R - Interim
clpC1 4038878 c.1827A>G synonymous_variant 0.29 pyrazinamide Not assoc w R - Interim
clpC1 4038908 c.1797C>G synonymous_variant 0.32 pyrazinamide
clpC1 4038914 c.1791G>C synonymous_variant 0.35 pyrazinamide
clpC1 4038923 c.1780_1782delCTAinsTG frameshift_variant&synonymous_variant 0.37 pyrazinamide
clpC1 4038953 c.1752A>G synonymous_variant 0.44 pyrazinamide
clpC1 4038956 c.1749T>C synonymous_variant 0.41 pyrazinamide
clpC1 4038965 c.1740T>C synonymous_variant 0.4 pyrazinamide
clpC1 4039226 c.1479T>C synonymous_variant 0.3 pyrazinamide Not assoc w R - Interim
clpC1 4039694 c.1011G>C synonymous_variant 0.26 pyrazinamide
clpC1 4039724 c.981A>G synonymous_variant 0.3 pyrazinamide
clpC1 4039826 c.879C>G synonymous_variant 0.24 pyrazinamide
clpC1 4039831 c.874T>C synonymous_variant 0.24 pyrazinamide
clpC1 4039850 c.855T>C synonymous_variant 0.25 pyrazinamide
clpC1 4039865 c.840T>C synonymous_variant 0.28 pyrazinamide
clpC1 4039898 c.807C>G synonymous_variant 0.28 pyrazinamide
clpC1 4039931 c.774T>C synonymous_variant 0.25 pyrazinamide
clpC1 4039958 c.747G>C synonymous_variant 0.3 pyrazinamide
clpC1 4039979 c.726C>G synonymous_variant 0.32 pyrazinamide
clpC1 4039988 c.717C>G synonymous_variant 0.35 pyrazinamide
clpC1 4039991 c.714G>C synonymous_variant 0.35 pyrazinamide
clpC1 4040021 c.684A>C synonymous_variant 0.38 pyrazinamide Not assoc w R - Interim
clpC1 4040024 c.681A>G synonymous_variant 0.38 pyrazinamide
clpC1 4040033 c.672G>C synonymous_variant 0.35 pyrazinamide
glpK 4138442 c.1314C>A synonymous_variant 0.31 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138451 c.1305T>C synonymous_variant 0.2 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
glpK 4138606 c.1150T>C synonymous_variant 0.42 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138622 c.1134C>G synonymous_variant 0.38 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138625 c.1131G>C synonymous_variant 0.35 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138628 c.1128T>C synonymous_variant 0.33 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138634 c.1122G>A synonymous_variant 0.27 ethambutol Not assoc w R - Interim
moxifloxacin
streptomycin Not assoc w R - Interim
levofloxacin
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
glpK 4138643 c.1113A>C synonymous_variant 0.29 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138670 c.1086G>C synonymous_variant 0.32 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4240780 c.918T>C synonymous_variant 0.26 ethambutol
embC 4240783 c.921G>C synonymous_variant 0.26 ethambutol
embC 4240789 c.927T>C synonymous_variant 0.29 ethambutol
embC 4240819 c.957A>G synonymous_variant 0.32 ethambutol
embC 4240828 c.966G>C synonymous_variant 0.33 ethambutol
embC 4240831 c.969T>C synonymous_variant 0.31 ethambutol
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
embA 4245077 c.1845G>C synonymous_variant 0.38 ethambutol
embA 4245083 c.1851A>C synonymous_variant 0.38 ethambutol
embA 4245101 c.1869G>C synonymous_variant 0.33 ethambutol
embA 4245137 c.1905T>C synonymous_variant 0.3 ethambutol
embB 4248130 c.1617G>C synonymous_variant 0.22 ethambutol
embB 4248133 c.1620C>G synonymous_variant 0.22 ethambutol
embB 4248145 p.Leu544Phe missense_variant 0.21 ethambutol
embB 4248157 c.1644A>G synonymous_variant 0.19 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 1.0 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
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R