TB-Profiler result

Run: ERR2514821
Summary

Run ID: ERR2514821

Sample name:

Date: 2024-10-04T21:41:18.916383

Number of reads: 556988

Percentage reads mapped: 70.38

Median coverage: 16.0

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 0.97
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
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 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 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575659 c.312A>G synonymous_variant 0.23 isoniazid
ethionamide
mshA 575907 p.Ala187Val missense_variant 0.93 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 1.0 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
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 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 1.0 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 bedaquiline
clofazimine
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 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1303686 c.756C>G synonymous_variant 0.27 pretomanid
delamanid
clofazimine
fbiC 1303695 c.765T>C synonymous_variant 0.24 pretomanid
delamanid
clofazimine
fbiC 1303704 c.774T>G synonymous_variant 0.25 pretomanid
delamanid
clofazimine
fbiC 1303708 c.778T>C synonymous_variant 0.24 pretomanid
delamanid
clofazimine
fbiC 1303728 c.798G>A synonymous_variant 0.25 pretomanid
delamanid
clofazimine
fbiC 1303785 c.855G>T synonymous_variant 0.32 pretomanid
delamanid
clofazimine
fbiC 1303789 p.Ile287Val missense_variant 0.3 pretomanid
delamanid
clofazimine
fbiC 1303818 c.888C>G synonymous_variant 0.29 pretomanid
delamanid
clofazimine
fbiC 1303860 c.930A>C synonymous_variant 0.29 pretomanid
delamanid
clofazimine
fbiC 1303884 c.954T>G synonymous_variant 0.29 pretomanid
delamanid
clofazimine
fbiC 1304004 c.1074A>G synonymous_variant 0.27 pretomanid
delamanid
clofazimine
fbiC 1304727 c.1797A>G synonymous_variant 0.25 pretomanid
delamanid
clofazimine
fbiC 1304742 c.1812T>C synonymous_variant 0.31 pretomanid
delamanid
clofazimine
fbiC 1304748 c.1818T>C synonymous_variant 0.3 pretomanid
delamanid
clofazimine
fbiC 1304757 c.1827A>G synonymous_variant 0.31 pretomanid
delamanid
clofazimine
fbiC 1304760 c.1830G>C synonymous_variant 0.31 pretomanid
delamanid
clofazimine
fbiC 1304769 c.1839C>T synonymous_variant 0.32 pretomanid
delamanid
clofazimine
fbiC 1304778 c.1848T>C synonymous_variant 0.33 pretomanid
delamanid
clofazimine
fbiC 1304784 c.1854T>C synonymous_variant 0.34 pretomanid
delamanid
clofazimine
fbiC 1304787 c.1857T>C synonymous_variant 0.39 pretomanid
delamanid
clofazimine
fbiC 1304808 c.1878C>G synonymous_variant 0.37 pretomanid
delamanid
clofazimine
fbiC 1304811 c.1881C>G synonymous_variant 0.37 pretomanid
delamanid
clofazimine
fbiC 1304817 c.1887T>C synonymous_variant 0.4 pretomanid
delamanid
clofazimine
fbiC 1304829 c.1899T>C synonymous_variant 0.5 pretomanid
delamanid
clofazimine
fbiC 1304832 c.1902C>T synonymous_variant 0.48 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fbiC 1304853 c.1923C>G synonymous_variant 0.43 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fbiC 1304856 c.1926C>G synonymous_variant 0.38 pretomanid
delamanid
clofazimine
fbiC 1304869 c.1939C>T synonymous_variant 0.37 pretomanid
delamanid
clofazimine
fbiC 1304875 p.Ile649Val missense_variant 0.37 pretomanid
delamanid
clofazimine
fbiC 1304928 c.1998T>C synonymous_variant 0.35 pretomanid
delamanid
clofazimine
fbiC 1304937 c.2007G>C synonymous_variant 0.38 pretomanid
delamanid
clofazimine
fbiC 1304940 c.2010A>G synonymous_variant 0.43 pretomanid
delamanid
clofazimine
fbiC 1304946 c.2016G>C synonymous_variant 0.5 pretomanid
delamanid
clofazimine
fbiC 1304955 c.2025G>A synonymous_variant 0.46 pretomanid
delamanid
clofazimine
fbiC 1304958 c.2028T>G synonymous_variant 0.46 pretomanid
delamanid
clofazimine
fbiC 1305150 c.2220C>G synonymous_variant 0.6 pretomanid
delamanid
clofazimine
sigE 1364706 c.294G>A synonymous_variant 0.95 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
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_-234delGCAinsTCG 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 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
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 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783278 c.765A>G synonymous_variant 0.45 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783287 c.756C>G synonymous_variant 0.54 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783293 c.750G>A synonymous_variant 0.62 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783299 c.744A>G synonymous_variant 0.59 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783302 c.741A>G synonymous_variant 0.59 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783311 c.732T>C synonymous_variant 0.59 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783314 c.729C>G synonymous_variant 0.59 kanamycin
levofloxacin
moxifloxacin
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
amikacin
Rv2477c 2783317 c.726G>C synonymous_variant 0.54 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783332 c.711T>C synonymous_variant 0.5 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783335 c.708C>G synonymous_variant 0.5 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783350 c.693T>C synonymous_variant 0.53 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783353 c.690T>C synonymous_variant 0.5 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783356 c.687C>G synonymous_variant 0.47 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783359 c.684G>A synonymous_variant 0.47 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783374 c.669G>C synonymous_variant 0.43 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783656 c.387G>C synonymous_variant 0.32 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783659 c.384A>G synonymous_variant 0.32 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783665 c.378A>G synonymous_variant 0.35 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783673 c.370C>A synonymous_variant 0.35 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783674 c.369T>C synonymous_variant 0.35 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783683 c.360A>G synonymous_variant 0.35 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783691 c.352C>T synonymous_variant 0.35 kanamycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2477c 2783695 c.348C>T synonymous_variant 0.27 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783700 p.Thr115Ser missense_variant 0.29 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783716 c.327G>A synonymous_variant 0.33 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783751 p.Ile98Val missense_variant 0.58 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783758 p.Asp95Glu missense_variant 0.64 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
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 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3064974 c.1218T>C synonymous_variant 0.3 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3064995 c.1197C>G synonymous_variant 0.31 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3064998 c.1194A>G synonymous_variant 0.3 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3065007 c.1185G>C synonymous_variant 0.29 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3065013 c.1179G>C synonymous_variant 0.29 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3065018 p.Asn392His missense_variant 0.3 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3065022 c.1170G>C synonymous_variant 0.3 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3065028 p.Val388Ile missense_variant 0.33 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3065040 c.1152C>G synonymous_variant 0.32 levofloxacin
moxifloxacin
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
Rv2752c 3065048 c.1144C>T synonymous_variant 0.32 levofloxacin
moxifloxacin
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
Rv2752c 3065064 c.1128G>C synonymous_variant 0.22 levofloxacin
moxifloxacin
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
Rv2752c 3066603 c.-412A>G upstream_gene_variant 0.38 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3066612 c.-421G>A upstream_gene_variant 0.32 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3066617 c.-426G>A upstream_gene_variant 0.32 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3066618 c.-427A>C upstream_gene_variant 0.32 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3066633 c.-442T>C upstream_gene_variant 0.29 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
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 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625222 c.1392T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3626562 p.Pro18Ser missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626876 c.-263A>G upstream_gene_variant 0.35 rifampicin
bedaquiline
mtrB 3627167 c.-554T>C upstream_gene_variant 0.5 rifampicin
bedaquiline
mtrA 3627175 c.175C>T synonymous_variant 0.55 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3627181 c.-568T>C upstream_gene_variant 0.55 rifampicin
bedaquiline
mtrB 3627182 c.-569T>C upstream_gene_variant 0.55 rifampicin
bedaquiline
mtrA 3627188 c.162A>G synonymous_variant 0.55 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3627196 c.-583C>T upstream_gene_variant 0.5 rifampicin
bedaquiline
mtrB 3627209 c.-596G>A upstream_gene_variant 0.43 rifampicin
bedaquiline
mtrA 3627221 c.129C>T synonymous_variant 0.35 rifampicin Not assoc w R - Interim
bedaquiline
mtrA 3627227 c.123T>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3627296 c.-683T>C upstream_gene_variant 0.33 rifampicin
bedaquiline
mtrB 3627299 c.-688_-686delTTGinsCTA upstream_gene_variant 0.32 rifampicin
bedaquiline
mtrB 3627314 c.-701C>T upstream_gene_variant 0.3 rifampicin
bedaquiline
mtrB 3627317 c.-704T>C upstream_gene_variant 0.3 rifampicin
bedaquiline
mtrA 3627343 p.Thr3Ser missense_variant 0.26 rifampicin
bedaquiline
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_1782delCTAinsTTG 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 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138451 c.1305T>C synonymous_variant 0.2 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
glpK 4138606 c.1150T>C synonymous_variant 0.42 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138622 c.1134C>G synonymous_variant 0.38 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138625 c.1131G>C synonymous_variant 0.35 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138628 c.1128T>C synonymous_variant 0.33 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138634 c.1122G>A synonymous_variant 0.27 levofloxacin
moxifloxacin
isoniazid Not assoc w R - Interim
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
glpK 4138643 c.1113A>C synonymous_variant 0.29 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138670 c.1086G>C synonymous_variant 0.32 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
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 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin 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