TB-Profiler result

Run: ERR3797073
Summary

Run ID: ERR3797073

Sample name:

Date: 2024-04-15T04:26:14.144600

Number of reads: 695829

Percentage reads mapped: 41.57

Median coverage: 21.0

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 0.99
La1.8.1 M.bovis None 0.95
La1 M.bovis None 0.96
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
gyrB 5752 c.513G>A synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6406 c.1167C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6446 p.Ala403Ser missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
gyrA 6610 c.-692C>G upstream_gene_variant 0.39 levofloxacin
moxifloxacin
gyrA 6613 c.-689A>G upstream_gene_variant 0.37 levofloxacin
moxifloxacin
gyrA 6616 c.-686A>G upstream_gene_variant 0.37 levofloxacin
moxifloxacin
gyrA 6637 c.-665T>G upstream_gene_variant 0.39 levofloxacin
moxifloxacin
gyrB 7093 c.1854T>C synonymous_variant 0.38 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7114 c.-188C>G upstream_gene_variant 0.3 levofloxacin
moxifloxacin
gyrA 7123 c.-179C>G upstream_gene_variant 0.3 levofloxacin
moxifloxacin
gyrA 7129 c.-173T>G upstream_gene_variant 0.42 levofloxacin
moxifloxacin
gyrA 7132 c.-170T>G upstream_gene_variant 0.45 levofloxacin
moxifloxacin
gyrA 7136 c.-166T>C upstream_gene_variant 0.35 levofloxacin
moxifloxacin
gyrA 7141 c.-161T>A upstream_gene_variant 0.41 levofloxacin
moxifloxacin
gyrA 7144 c.-158A>G upstream_gene_variant 0.47 levofloxacin
moxifloxacin
gyrA 7147 c.-155G>C upstream_gene_variant 0.37 levofloxacin
moxifloxacin
gyrA 7150 c.-152G>C upstream_gene_variant 0.35 levofloxacin
moxifloxacin
gyrB 7153 c.1914G>C synonymous_variant 0.45 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7168 c.-134C>G upstream_gene_variant 0.4 levofloxacin
moxifloxacin
gyrA 7177 c.-125G>A upstream_gene_variant 0.4 levofloxacin
moxifloxacin
gyrA 7178 c.-124T>C upstream_gene_variant 0.4 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7457 c.156T>C synonymous_variant 0.27 levofloxacin
moxifloxacin
gyrA 7475 c.174A>G synonymous_variant 0.28 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7480 p.Phe60Tyr missense_variant 0.35 levofloxacin
moxifloxacin
gyrA 7484 c.183T>C synonymous_variant 0.33 levofloxacin
moxifloxacin
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7679 c.378G>C synonymous_variant 0.22 levofloxacin
moxifloxacin
gyrA 7683 c.382_384delAGGinsCT frameshift_variant&missense_variant 0.26 levofloxacin
moxifloxacin
gyrA 7697 c.396C>G synonymous_variant 0.23 levofloxacin
moxifloxacin
gyrA 7706 c.405C>T synonymous_variant 0.26 levofloxacin
moxifloxacin
gyrA 7728 c.427_429delAGGinsCT frameshift_variant&missense_variant 0.25 levofloxacin
moxifloxacin
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 0.8 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Glu missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 9335 c.2034G>C synonymous_variant 0.33 levofloxacin
moxifloxacin
gyrA 9345 c.2044_2046delAGGinsCC frameshift_variant&missense_variant 0.37 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
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575803 c.456C>T synonymous_variant 0.21 ethionamide
isoniazid Not assoc w R - Interim
mshA 575821 c.474G>C synonymous_variant 0.21 ethionamide
isoniazid
mshA 575824 c.477T>C synonymous_variant 0.19 ethionamide
isoniazid
mshA 575833 c.486C>G synonymous_variant 0.18 ethionamide
isoniazid
mshA 575857 c.510G>C synonymous_variant 0.22 ethionamide
isoniazid
ccsA 620688 c.798G>C synonymous_variant 0.36 capreomycin
amikacin
kanamycin
ccsA 620694 c.804C>G synonymous_variant 0.38 capreomycin
amikacin
kanamycin
ccsA 620698 p.Val270Ile missense_variant 0.38 capreomycin
amikacin
kanamycin
ccsA 620709 c.819G>C synonymous_variant 0.38 capreomycin
amikacin
kanamycin
ccsA 620733 c.843G>C synonymous_variant 0.33 capreomycin
amikacin
kanamycin
ccsA 620736 c.846G>C synonymous_variant 0.33 capreomycin
amikacin
kanamycin
ccsA 620739 c.849A>G synonymous_variant 0.3 capreomycin
amikacin
kanamycin
ccsA 620742 c.852G>C synonymous_variant 0.29 capreomycin
amikacin
kanamycin
ccsA 620748 c.858T>G synonymous_variant 0.29 capreomycin
amikacin
kanamycin
ccsA 620754 c.864G>T synonymous_variant 0.29 capreomycin
amikacin
kanamycin
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
nusG 734329 p.Ala26Thr missense_variant 1.0 rifampicin Uncertain significance
rpoB 760522 p.Ser239Asn missense_variant 0.23 rifampicin Uncertain significance
rpoB 760532 c.726T>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 760547 c.741G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 760611 c.805T>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 761036 c.1230G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.3 rifampicin
rpoB 761102 c.1296A>G synonymous_variant 0.39 rifampicin
rpoB 761132 c.1326G>T synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoB 761133 c.1327T>C synonymous_variant 0.53 rifampicin Not assoc w R - Interim
rpoB 761147 c.1341C>T synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoB 761150 c.1344A>T synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoB 761153 c.1347G>T synonymous_variant 0.34 rifampicin
rpoB 761165 c.1359G>C synonymous_variant 0.45 rifampicin Not assoc w R - Interim
rpoB 761180 c.1374A>C synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoB 761189 c.1383T>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 761195 c.1389G>C synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoB 761198 c.1392G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 761249 c.1443A>G synonymous_variant 0.48 rifampicin Not assoc w R - Interim
rpoB 761261 c.1455G>T synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 761306 c.1500C>G synonymous_variant 0.28 rifampicin
rpoB 761318 c.1512G>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 761327 c.1521A>G synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoB 761354 c.1548C>T synonymous_variant 0.21 rifampicin
rpoB 761362 p.Ser519Thr missense_variant 0.23 rifampicin
rpoB 761606 c.1800C>G synonymous_variant 0.28 rifampicin
rpoB 761612 c.1806G>T synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 761615 c.1809A>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 761636 c.1830G>T synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoB 761645 c.1839C>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 761657 c.1851C>A synonymous_variant 0.22 rifampicin
rpoB 761954 c.2148C>G synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 761969 c.2163G>A synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 761999 c.2193G>C synonymous_variant 0.35 rifampicin
rpoB 762002 c.2196C>G synonymous_variant 0.37 rifampicin
rpoB 762053 c.2247T>C synonymous_variant 0.58 rifampicin Not assoc w R - Interim
rpoB 762065 c.2259T>C synonymous_variant 0.58 rifampicin Not assoc w R - Interim
rpoB 762083 c.2277T>C synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoB 762086 c.2280G>C synonymous_variant 0.48 rifampicin Not assoc w R - Interim
rpoB 762101 c.2295C>G synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoB 762114 p.Ile770Val missense_variant 0.43 rifampicin Uncertain significance
rpoB 762167 c.2361T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoB 762176 c.2370T>C synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoB 762185 c.2379G>T synonymous_variant 0.38 rifampicin
rpoB 762218 c.2412T>C synonymous_variant 0.26 rifampicin
rpoB 762233 c.2427G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 762251 c.2445G>C synonymous_variant 0.24 rifampicin
rpoB 762254 c.2448T>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 762257 c.2451C>G synonymous_variant 0.3 rifampicin
rpoB 762275 c.2469C>G synonymous_variant 0.23 rifampicin
rpoB 762284 c.2478G>C synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoB 762293 c.2487T>G synonymous_variant 0.31 rifampicin
rpoB 762305 c.2499G>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 762314 c.2508C>T synonymous_variant 0.25 rifampicin
rpoB 762317 c.2511A>G synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoB 762320 c.2514C>G synonymous_variant 0.24 rifampicin
rpoC 762443 c.-927G>C upstream_gene_variant 0.17 rifampicin
rpoB 762470 c.2664G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 762509 c.-861T>G upstream_gene_variant 0.18 rifampicin
rpoB 762510 c.2704_2706delGCCinsCG frameshift_variant&missense_variant 0.18 rifampicin
rpoC 762533 c.-837T>C upstream_gene_variant 0.22 rifampicin
rpoC 762536 c.-834T>C upstream_gene_variant 0.23 rifampicin
rpoC 762537 c.-833T>C upstream_gene_variant 0.24 rifampicin
rpoC 762551 c.-819C>T upstream_gene_variant 0.25 rifampicin
rpoB 763028 c.3222T>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.81 rifampicin Not assoc w R
rpoB 763040 c.3234C>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 763076 c.-294C>G upstream_gene_variant 0.2 rifampicin
rpoB 763115 c.3309T>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 763136 c.3330C>T synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoC 763158 c.-212C>T upstream_gene_variant 0.31 rifampicin
rpoB 763166 c.3360A>G synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoC 763468 c.99G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 763486 c.117T>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.45 rifampicin Not assoc w R - Interim
rpoC 763660 c.291T>G synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoC 763702 c.333C>G synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 763714 c.345G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 764131 c.762T>C synonymous_variant 0.28 rifampicin
rpoC 764153 p.Gln262Lys missense_variant 0.23 rifampicin
rpoC 764188 c.819A>G synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 764206 p.Asp279Glu missense_variant 0.28 rifampicin
rpoC 764215 c.846A>C synonymous_variant 0.29 rifampicin
rpoC 764217 p.Asn283Ser missense_variant 0.29 rifampicin
rpoC 764227 c.858G>C synonymous_variant 0.29 rifampicin
rpoC 764239 c.870T>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 764242 c.873C>T synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 764245 c.876C>G synonymous_variant 0.28 rifampicin
rpoC 764254 c.885G>C synonymous_variant 0.3 rifampicin
rpoC 764263 c.894G>C synonymous_variant 0.26 rifampicin
rpoC 764266 c.897T>C synonymous_variant 0.3 rifampicin
rpoC 764272 c.903G>C synonymous_variant 0.31 rifampicin
rpoC 764278 c.909A>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764296 c.927G>C synonymous_variant 0.31 rifampicin
rpoC 764320 c.951C>T synonymous_variant 0.38 rifampicin
rpoC 764353 c.984G>C synonymous_variant 0.33 rifampicin
rpoC 764365 c.996C>T synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoC 764371 c.1002G>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 764377 c.1008C>G synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 764380 c.1011G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 764387 c.1018T>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 764405 c.1036_1038delAGGinsCC frameshift_variant&missense_variant 0.37 rifampicin
rpoC 764429 c.1060C>T synonymous_variant 0.3 rifampicin
rpoC 764434 c.1065A>G synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 764435 c.1066_1068delAGGinsCA frameshift_variant&missense_variant 0.29 rifampicin
rpoC 764446 c.1077T>C synonymous_variant 0.33 rifampicin
rpoC 764449 c.1080G>C synonymous_variant 0.32 rifampicin
rpoC 764458 c.1089G>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 764461 c.1092A>G synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 764485 c.1116G>C synonymous_variant 0.22 rifampicin
rpoC 764611 c.1242G>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764626 c.1257C>T synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 764716 c.1347G>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 765357 p.Met663Thr missense_variant 0.35 rifampicin
rpoC 765367 c.1998C>G synonymous_variant 0.27 rifampicin
rpoC 765370 c.2001G>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 765373 c.2004G>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 765404 p.Leu679Lys missense_variant 0.29 rifampicin
rpoC 765407 c.2038_2040delGGTinsAC frameshift_variant&missense_variant 0.29 rifampicin
rpoC 765425 p.Lys686Glu missense_variant 0.32 rifampicin
rpoC 765445 c.2076G>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 765452 p.Ala695Arg missense_variant 0.29 rifampicin
rpoC 765499 c.2130C>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 765886 c.2517C>G synonymous_variant 0.28 rifampicin
rpoC 765937 c.2568T>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 765979 c.2610C>G synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 765982 c.2613C>T synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 765994 c.2625A>T synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 766021 c.2652G>C synonymous_variant 0.34 rifampicin
rpoC 766027 c.2658G>C synonymous_variant 0.28 rifampicin
rpoC 766043 p.Gln892Glu missense_variant 0.25 rifampicin
rpoC 766996 c.3627C>T synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoC 767098 c.3729T>C synonymous_variant 0.37 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 775865 c.2616T>C synonymous_variant 0.22 clofazimine
bedaquiline
mmpL5 775910 c.2571G>C synonymous_variant 0.31 clofazimine
bedaquiline
mmpL5 775913 c.2566_2568delGCCinsTA frameshift_variant&missense_variant 0.3 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781871 c.312G>C synonymous_variant 0.4 streptomycin
rpsL 781880 c.321C>G synonymous_variant 0.38 streptomycin
rpsL 781892 c.333A>G synonymous_variant 0.36 streptomycin
rpsL 781898 c.339A>C synonymous_variant 0.35 streptomycin
rpsL 781907 c.348T>C synonymous_variant 0.32 streptomycin
rpsL 781910 c.351C>T synonymous_variant 0.29 streptomycin
rpsL 781916 c.357T>G synonymous_variant 0.35 streptomycin
rpsL 781929 p.Gly124Ser missense_variant 0.41 streptomycin Uncertain significance
rpsL 781933 c.374G>A splice_region_variant&stop_retained_variant 0.3 streptomycin
rplC 800618 c.-191T>C upstream_gene_variant 0.26 linezolid
rplC 800633 c.-176T>C upstream_gene_variant 0.33 linezolid
rplC 800645 c.-164C>G upstream_gene_variant 0.33 linezolid
rplC 800715 c.-94A>C upstream_gene_variant 0.37 linezolid
rplC 800720 c.-89T>C upstream_gene_variant 0.32 linezolid
rplC 800723 c.-86C>G upstream_gene_variant 0.33 linezolid
rplC 800759 c.-50C>T upstream_gene_variant 0.46 linezolid
rplC 801454 p.Glu216Gln missense_variant 0.95 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
Rv1129c 1254582 c.-48A>G upstream_gene_variant 1.0 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
fbiC 1303881 c.951G>C synonymous_variant 0.28 clofazimine
pretomanid
delamanid
fbiC 1303884 c.954T>C synonymous_variant 0.27 clofazimine
pretomanid
delamanid
fbiC 1303891 p.Ala321Thr missense_variant 0.27 clofazimine
pretomanid
delamanid
fbiC 1304559 p.Glu543Asp missense_variant 0.38 clofazimine
pretomanid
delamanid
fbiC 1304565 c.1635C>G synonymous_variant 0.32 clofazimine
pretomanid
delamanid
fbiC 1304568 c.1638T>C synonymous_variant 0.39 clofazimine
pretomanid
delamanid
fbiC 1304580 c.1650T>C synonymous_variant 0.4 clofazimine
pretomanid
delamanid
fbiC 1304613 c.1683T>C synonymous_variant 0.39 clofazimine
pretomanid
delamanid
fbiC 1304634 c.1704C>G synonymous_variant 0.32 clofazimine
pretomanid
delamanid
fbiC 1304640 c.1710A>C synonymous_variant 0.32 clofazimine
pretomanid
delamanid
fbiC 1304646 c.1716T>C synonymous_variant 0.29 clofazimine
pretomanid
delamanid
sigE 1364950 c.538_540delGCAinsTG frameshift_variant&stop_gained 0.22 pyrazinamide Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471935 n.90T>C non_coding_transcript_exon_variant 0.7 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.26 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.39 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.33 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.35 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.41 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472848 n.1003T>G non_coding_transcript_exon_variant 0.45 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472849 n.1004C>G non_coding_transcript_exon_variant 0.45 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472858 n.1013G>T non_coding_transcript_exon_variant 0.43 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472859 n.1014G>C non_coding_transcript_exon_variant 0.43 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473123 n.1278delAinsTC non_coding_transcript_exon_variant 0.48 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.47 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.41 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475995 n.2338G>A non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.47 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
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 0.65 capreomycin Uncertain significance
linezolid
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.61 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476665 n.3008T>C non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid
rrl 1476674 n.3017T>C non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476679 n.3022T>C non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid
rrl 1476689 n.3032A>T non_coding_transcript_exon_variant 0.4 capreomycin
linezolid
rrl 1476692 n.3035T>A non_coding_transcript_exon_variant 0.64 capreomycin
linezolid
inhA 1673715 c.-487C>G upstream_gene_variant 0.96 ethionamide Uncertain significance
isoniazid Uncertain significance
inhA 1674703 c.502_504delTTGinsCC frameshift_variant&missense_variant 0.36 ethionamide
isoniazid
inhA 1674718 c.517A>C synonymous_variant 0.28 ethionamide
isoniazid
inhA 1674756 c.555T>C synonymous_variant 0.31 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
inhA 1674771 c.570C>G synonymous_variant 0.26 ethionamide
isoniazid
inhA 1674780 c.579T>G synonymous_variant 0.31 ethionamide
isoniazid
inhA 1674801 c.600T>C synonymous_variant 0.24 ethionamide
isoniazid
rpsA 1833979 c.438T>C synonymous_variant 0.31 pyrazinamide
rpsA 1833988 c.447C>T synonymous_variant 0.27 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.32 pyrazinamide
rpsA 1834012 c.471G>C synonymous_variant 0.32 pyrazinamide
rpsA 1834423 c.882G>C synonymous_variant 0.37 pyrazinamide
rpsA 1834451 c.910T>C synonymous_variant 0.32 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.3 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.36 pyrazinamide
rpsA 1834513 c.972C>G synonymous_variant 0.34 pyrazinamide
rpsA 1834520 p.Ala327Ser missense_variant 0.26 pyrazinamide
rpsA 1834528 c.987T>C synonymous_variant 0.3 pyrazinamide
rpsA 1834540 c.999G>C synonymous_variant 0.23 pyrazinamide
rpsA 1834690 c.1149T>C synonymous_variant 0.35 pyrazinamide
rpsA 1834859 p.Ala440Thr missense_variant 1.0 pyrazinamide Uncertain significance
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 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063157 c.1572C>G synonymous_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
ndh 2103173 c.-132delG upstream_gene_variant 1.0 ethionamide
delamanid
isoniazid
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
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 2222308 p.Asp286Gly missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
kasA 2518687 c.573C>T synonymous_variant 0.23 isoniazid
kasA 2518702 c.588C>T synonymous_variant 0.21 isoniazid
kasA 2518714 c.600A>C synonymous_variant 0.25 isoniazid
kasA 2518747 c.633C>G synonymous_variant 0.25 isoniazid
kasA 2518795 c.681C>G synonymous_variant 0.18 isoniazid
eis 2715125 p.Thr70Ala missense_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
Rv2477c 2782927 c.1116A>G synonymous_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R
amikacin Not assoc w R - Interim
Rv2681 2997325 p.Ala196Val missense_variant 1.0 capreomycin Uncertain significance
Rv2752c 3066555 c.-364C>T upstream_gene_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
thyA 3074037 c.435C>G synonymous_variant 0.21 para-aminosalicylic_acid
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 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
lpqB 3623730 p.Ser394Leu missense_variant 0.95 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3624350 c.561G>T synonymous_variant 0.87 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3624593 c.318G>A synonymous_variant 0.82 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
lpqB 3624710 c.201G>A synonymous_variant 0.78 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3625663 c.-753G>C upstream_gene_variant 0.26 bedaquiline
rifampicin
lpqB 3625669 c.-759G>C upstream_gene_variant 0.25 bedaquiline
rifampicin
lpqB 3625690 c.-780T>C upstream_gene_variant 0.32 bedaquiline
rifampicin
mtrB 3625705 c.909C>G synonymous_variant 0.33 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625711 c.903C>T synonymous_variant 0.27 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625720 c.894G>C synonymous_variant 0.31 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625729 c.885A>G synonymous_variant 0.32 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3625735 c.-825C>T upstream_gene_variant 0.32 bedaquiline
rifampicin
mtrB 3625744 c.870G>A synonymous_variant 0.31 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625747 c.867G>C synonymous_variant 0.28 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625753 p.Ala287Gln missense_variant 0.28 bedaquiline
rifampicin
mtrB 3625762 c.852A>T synonymous_variant 0.26 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3625765 c.-855C>A upstream_gene_variant 0.24 bedaquiline
rifampicin
mtrB 3625774 c.840G>A synonymous_variant 0.24 bedaquiline
rifampicin Not assoc w R - Interim
rpoA 3877647 c.861C>T synonymous_variant 0.27 rifampicin
rpoA 3877668 c.840A>G synonymous_variant 0.32 rifampicin
rpoA 3877677 c.831G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoA 3877680 c.828G>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoA 3877686 c.822A>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoA 3877692 c.816G>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoA 3877704 c.804G>T synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoA 3877743 c.765T>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoA 3877818 c.690A>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoA 3877839 c.669G>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoA 3877896 c.612G>C synonymous_variant 0.21 rifampicin
rpoA 3877905 c.603A>G synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoA 3877908 p.Asn200Ser missense_variant 0.3 rifampicin
rpoA 3877962 c.546G>T synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoA 3877986 c.522G>C synonymous_variant 0.37 rifampicin
rpoA 3877989 c.519A>G synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoA 3878169 c.339G>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoA 3878193 c.315T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoA 3878217 c.291A>G synonymous_variant 0.28 rifampicin Not assoc w R - Interim
clpC1 4038403 c.2302T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4038908 c.1797C>G synonymous_variant 0.28 pyrazinamide
clpC1 4038914 c.1791G>C synonymous_variant 0.25 pyrazinamide
clpC1 4038923 c.1782A>G synonymous_variant 0.26 pyrazinamide
clpC1 4038953 c.1752A>G synonymous_variant 0.3 pyrazinamide
clpC1 4038956 c.1749T>C synonymous_variant 0.32 pyrazinamide
clpC1 4038965 c.1740T>C synonymous_variant 0.29 pyrazinamide
clpC1 4038989 c.1716T>C synonymous_variant 0.29 pyrazinamide
clpC1 4038997 c.1708T>C synonymous_variant 0.3 pyrazinamide Not assoc w R - Interim
clpC1 4039067 c.1638G>C synonymous_variant 0.23 pyrazinamide
clpC1 4039082 c.1623C>T synonymous_variant 0.23 pyrazinamide
clpC1 4039085 c.1620A>G synonymous_variant 0.3 pyrazinamide
clpC1 4039091 c.1614G>C synonymous_variant 0.2 pyrazinamide
clpC1 4039097 c.1608G>T synonymous_variant 0.23 pyrazinamide
clpC1 4039100 c.1605C>G synonymous_variant 0.21 pyrazinamide
clpC1 4039103 c.1602T>C synonymous_variant 0.27 pyrazinamide
clpC1 4039106 c.1599G>C synonymous_variant 0.26 pyrazinamide
clpC1 4039119 c.1585_1586delTCinsAG synonymous_variant 0.19 pyrazinamide
clpC1 4039121 c.1584T>C synonymous_variant 0.26 pyrazinamide
clpC1 4039124 c.1581C>G synonymous_variant 0.19 pyrazinamide
clpC1 4039142 c.1563A>G synonymous_variant 0.35 pyrazinamide
clpC1 4039145 c.1560G>C synonymous_variant 0.32 pyrazinamide
clpC1 4039274 c.1431G>C synonymous_variant 0.21 pyrazinamide Not assoc w R - Interim
clpC1 4039298 c.1407T>C synonymous_variant 0.2 pyrazinamide
clpC1 4039391 c.1314T>G synonymous_variant 0.28 pyrazinamide
clpC1 4039577 c.1128T>C synonymous_variant 0.26 pyrazinamide Not assoc w R - Interim
clpC1 4039589 c.1116G>C synonymous_variant 0.21 pyrazinamide
clpC1 4039592 c.1113G>C synonymous_variant 0.22 pyrazinamide
clpC1 4039610 c.1095G>T synonymous_variant 0.24 pyrazinamide
clpC1 4039616 c.1089G>C synonymous_variant 0.35 pyrazinamide
clpC1 4039622 c.1083C>T synonymous_variant 0.32 pyrazinamide
clpC1 4039649 c.1056G>C synonymous_variant 0.28 pyrazinamide
clpC1 4039652 c.1053G>C synonymous_variant 0.23 pyrazinamide
clpC1 4039682 c.1023C>G synonymous_variant 0.27 pyrazinamide
clpC1 4039724 c.981A>G synonymous_variant 0.35 pyrazinamide
clpC1 4039760 c.945T>C synonymous_variant 0.26 pyrazinamide
clpC1 4039769 c.936C>G synonymous_variant 0.26 pyrazinamide
clpC1 4039817 c.888A>T synonymous_variant 0.27 pyrazinamide
clpC1 4039831 c.874T>C synonymous_variant 0.3 pyrazinamide
clpC1 4040024 c.681A>G synonymous_variant 0.24 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
glpK 4138676 c.1080T>C synonymous_variant 0.27 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138681 p.Met359Val missense_variant 0.26 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Not assoc w R
embC 4240726 c.864G>C synonymous_variant 0.3 ethambutol Not assoc w R - Interim
embC 4240819 c.957A>G synonymous_variant 0.29 ethambutol
embC 4240831 c.969T>G synonymous_variant 0.29 ethambutol
embC 4242642 p.Arg927His missense_variant 1.0 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
embB 4248734 p.Arg741Trp missense_variant 1.0 ethambutol Uncertain significance
aftB 4267167 p.Gln557Pro missense_variant 1.0 ethambutol Uncertain significance
aftB 4267858 p.Ile327Val missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269351 c.483C>T synonymous_variant 1.0 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
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R