TB-Profiler result

Run: SRR15315797
Summary

Run ID: SRR15315797

Sample name:

Date: 2024-10-04T23:35:29.531766

Number of reads: 9578057

Percentage reads mapped: 76.34

Median coverage: 252.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: RR-TB

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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 0.96
lineage2.2 East-Asian (Beijing) RD105;RD207 0.96
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Leu464Met Mutation from literature
isoniazid
ethambutol
pyrazinamide
streptomycin rrs n.799C>T Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1402C>A Uncertain significance Mutation from literature
n.1484G>T Assoc w R
capreomycin rrs n.1402C>A Uncertain significance Mutation from literature
n.1484G>T Assoc w R
kanamycin rrs n.1402C>A Uncertain significance Mutation from literature
n.1484G>T Assoc w R
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
rpoB 761196 p.Leu464Met missense_variant 0.15 rifampicin Mutation from literature
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance Mutation from literature
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.37 amikacin Uncertain significance Mutation from literature
capreomycin Uncertain significance Mutation from literature
kanamycin Uncertain significance Mutation from literature
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.22 amikacin Assoc w R
capreomycin Assoc w R
kanamycin 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.95 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.97 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.95 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.99 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.98 ethionamide Uncertain significance
rpoB 761027 c.1221A>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761036 c.1230G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761037 c.1231T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761051 c.1245G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761054 c.1248G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761060 c.1254C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761064 p.Ala420Ser missense_variant 0.15 rifampicin Uncertain significance
rpoB 761088 c.1282_1284delAGCinsTCG synonymous_variant 0.16 rifampicin
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.16 rifampicin
rpoB 761102 c.1296A>G synonymous_variant 0.17 rifampicin
rpoB 761123 c.1317G>C synonymous_variant 0.21 rifampicin
rpoB 761129 c.1323G>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 761132 c.1326G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 761133 c.1327T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 761138 c.1332C>G synonymous_variant 0.22 rifampicin
rpoB 761147 c.1341C>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 761150 c.1344A>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 761156 c.1350G>C synonymous_variant 0.21 rifampicin
rpoB 761165 c.1359G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761168 c.1362C>G synonymous_variant 0.19 rifampicin
rpoB 761171 c.1365C>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761180 c.1374A>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761186 p.Glu460Asp missense_variant 0.18 rifampicin Uncertain significance
rpoB 761195 c.1389G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761204 c.1398C>T synonymous_variant 0.14 rifampicin
rpoB 761207 c.1401C>T synonymous_variant 0.14 rifampicin
rpoB 761213 c.1407G>C synonymous_variant 0.13 rifampicin
rpoB 761234 c.1428G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 762098 c.2292C>G synonymous_variant 0.12 rifampicin
rpoB 762101 c.2295C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 762110 c.2304G>C synonymous_variant 0.12 rifampicin
rpoB 762114 p.Ile770Val missense_variant 0.11 rifampicin Uncertain significance
rpoB 762122 p.Asp772Glu missense_variant 0.12 rifampicin
rpoB 762128 c.2322G>C synonymous_variant 0.12 rifampicin
rpoB 762131 c.2325C>G synonymous_variant 0.12 rifampicin
rpoB 762134 c.2328C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762143 c.2337T>C synonymous_variant 0.13 rifampicin
rpoB 762149 c.2343G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762152 c.2346C>G synonymous_variant 0.14 rifampicin
rpoB 762156 p.Val784Ile missense_variant 0.13 rifampicin
rpoB 762176 c.2370T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762185 c.2379G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762189 p.Ile795Leu missense_variant 0.14 rifampicin
rpoB 762209 c.2403C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762212 c.2406G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762233 c.2427G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762959 c.3153G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762962 c.3156C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 762971 c.-399G>C upstream_gene_variant 0.15 rifampicin
rpoC 762989 c.-381G>C upstream_gene_variant 0.14 rifampicin
rpoB 762995 c.3189G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 763005 p.Cys1067Val missense_variant 0.13 rifampicin
rpoB 763014 p.Met1070Leu missense_variant 0.14 rifampicin
rpoB 763017 p.Gln1071Glu missense_variant 0.14 rifampicin
rpoB 763028 c.3222T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.96 rifampicin Not assoc w R
rpoB 763040 c.3234C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763053 c.-317_-315delTTGinsCTC upstream_gene_variant 0.14 rifampicin
rpoC 763064 c.-306G>A upstream_gene_variant 0.14 rifampicin
rpoB 763070 c.3264T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 763074 p.Thr1090Val missense_variant 0.11 rifampicin
rpoB 763077 p.Val1091Pro missense_variant 0.11 rifampicin
rpoB 763094 c.3288G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 763528 c.159G>C synonymous_variant 0.11 rifampicin
rpoC 763531 c.162G>C synonymous_variant 0.11 rifampicin Not assoc w R
rpoC 763534 c.165T>C synonymous_variant 0.12 rifampicin
rpoC 763537 c.168C>T synonymous_variant 0.12 rifampicin
rpoC 763546 c.177A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763633 c.264T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763636 c.267T>C synonymous_variant 0.14 rifampicin
rpoC 763660 c.291T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763666 c.297G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763669 c.300C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763696 c.327T>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764371 c.1002G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764377 c.1008C>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764383 c.1014C>G synonymous_variant 0.11 rifampicin
rpoC 764387 c.1018_1020delTTGinsCTC synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764398 c.1029G>C synonymous_variant 0.12 rifampicin
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764410 c.1041G>C synonymous_variant 0.11 rifampicin
rpoC 764428 c.1059G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764434 c.1065A>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764435 c.1066_1068delAGGinsCGC synonymous_variant 0.11 rifampicin
rpoC 764440 c.1071G>C synonymous_variant 0.12 rifampicin
rpoC 764441 p.Ile358Leu missense_variant 0.12 rifampicin
rpoC 764446 c.1077T>C synonymous_variant 0.13 rifampicin
rpoC 764449 c.1080G>C synonymous_variant 0.14 rifampicin
rpoC 764458 c.1089G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764461 c.1092A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764485 c.1116G>C synonymous_variant 0.19 rifampicin
rpoC 764491 c.1122G>C synonymous_variant 0.18 rifampicin
rpoC 764497 c.1128A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764498 p.Ser377Ala missense_variant 0.17 rifampicin
rpoC 764521 c.1152T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764524 c.1155C>T synonymous_variant 0.19 rifampicin
rpoC 764530 c.1161C>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764533 c.1164C>T synonymous_variant 0.18 rifampicin
rpoC 764536 c.1167G>C synonymous_variant 0.18 rifampicin
rpoC 764539 c.1170C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764545 c.1176C>G synonymous_variant 0.18 rifampicin
rpoC 764548 c.1179G>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764551 c.1182G>T synonymous_variant 0.19 rifampicin
rpoC 764566 c.1197C>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 764581 c.1212T>C synonymous_variant 0.25 rifampicin
rpoC 764582 p.Leu405Met missense_variant 0.25 rifampicin
rpoC 764605 c.1236G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>T synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 764620 c.1251G>C synonymous_variant 0.24 rifampicin
rpoC 764632 c.1263T>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764644 c.1275G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 764662 c.1293G>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 764706 p.Leu446Gln missense_variant 0.22 rifampicin Uncertain significance
rpoC 764716 c.1347G>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764746 c.1377G>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764752 c.1383G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764759 p.Asn464Asp missense_variant 0.16 rifampicin
rpoC 764764 c.1395T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764780 c.1411_1413delAGCinsTCG synonymous_variant 0.12 rifampicin
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 0.98 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.98 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.98 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.97 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.99 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.2 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.2 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472582 n.737G>A non_coding_transcript_exon_variant 0.23 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472591 n.746G>A non_coding_transcript_exon_variant 0.26 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.27 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.29 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.29 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.28 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.28 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.24 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472674 n.829T>C non_coding_transcript_exon_variant 0.24 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.23 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472685 n.840G>A non_coding_transcript_exon_variant 0.24 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.25 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.25 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.23 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.25 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.26 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.25 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.25 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.25 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.33 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.35 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.35 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.36 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473127 n.1282G>A non_coding_transcript_exon_variant 0.36 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.38 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.36 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.35 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.3 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.26 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473292 n.1447_1449delGGAinsTGGG non_coding_transcript_exon_variant 0.27 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.26 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.23 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.23 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.1 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.1 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474253 n.596A>T non_coding_transcript_exon_variant 0.1 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474583 n.926C>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474636 n.979_982delACCGinsTTAC non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474664 n.1007G>A non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1474672 n.1015C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474709 n.1053_1056delTGGT non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474717 n.1060_1061insGTGAG non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.3 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>A non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474904 n.1247G>T non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475696 n.2039T>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1475697 n.2040C>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475702 n.2045G>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1475703 n.2046A>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1475740 n.2083G>C non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1475758 n.2101A>G non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1475761 n.2104_2106delCGCinsT non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1475766 n.2109G>C non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid
rrl 1475788 n.2131C>G non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.34 capreomycin
linezolid
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.16 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476001 n.2344T>C non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476032 n.2375C>A non_coding_transcript_exon_variant 0.1 capreomycin
linezolid
rrl 1476034 n.2377C>G non_coding_transcript_exon_variant 0.1 capreomycin Uncertain significance
linezolid
rrl 1476035 n.2378G>C non_coding_transcript_exon_variant 0.1 capreomycin Uncertain significance
linezolid
rrl 1476044 n.2387T>G non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid
rrl 1476045 n.2388G>T non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid
rrl 1476047 n.2390G>T non_coding_transcript_exon_variant 0.11 capreomycin
linezolid
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.1 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.11 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476058 n.2401T>C non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.11 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.11 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.11 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.12 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476213 n.2556G>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476251 n.2594T>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.23 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476288 n.2631T>C non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.34 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.34 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.26 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833410 c.-132G>A upstream_gene_variant 0.97 pyrazinamide
rpsA 1833970 c.429G>T synonymous_variant 0.13 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.13 pyrazinamide
rpsA 1833994 c.453G>C synonymous_variant 0.13 pyrazinamide
rpsA 1833997 c.456G>C synonymous_variant 0.13 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.14 pyrazinamide
rpsA 1834009 c.468C>T synonymous_variant 0.13 pyrazinamide
rpsA 1834012 c.471G>T synonymous_variant 0.13 pyrazinamide
rpsA 1834024 c.483G>C synonymous_variant 0.13 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.13 pyrazinamide
rpsA 1834034 p.Ile165Val missense_variant 0.12 pyrazinamide
rpsA 1834069 c.528G>C synonymous_variant 0.12 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 0.96 pyrazinamide Not assoc w R - Interim
rpsA 1834294 c.753G>C synonymous_variant 0.13 pyrazinamide
rpsA 1834298 p.Gln253Glu missense_variant 0.13 pyrazinamide
rpsA 1834303 c.762T>G synonymous_variant 0.13 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834307 p.Asp256Gln missense_variant 0.13 pyrazinamide
rpsA 1834336 c.795C>G synonymous_variant 0.16 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
rpsA 1834354 c.813G>T synonymous_variant 0.14 pyrazinamide
rpsA 1834357 c.816T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834360 c.819G>C synonymous_variant 0.14 pyrazinamide
rpsA 1834361 c.820T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834366 c.825A>G synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
rpsA 1834369 c.828C>G synonymous_variant 0.16 pyrazinamide
rpsA 1834378 c.837T>G synonymous_variant 0.17 pyrazinamide
rpsA 1834384 c.843A>G synonymous_variant 0.18 pyrazinamide
rpsA 1834395 p.Arg285Gln missense_variant 0.18 pyrazinamide
rpsA 1834411 c.870T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834417 c.876G>C synonymous_variant 0.16 pyrazinamide
rpsA 1834423 c.882G>C synonymous_variant 0.14 pyrazinamide
rpsA 1834427 p.Ile296Val missense_variant 0.14 pyrazinamide Uncertain significance
rpsA 1834451 c.910_912delTTGinsCTC synonymous_variant 0.14 pyrazinamide
rpsA 1834456 c.915T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.12 pyrazinamide
rpsA 1834474 c.933C>G synonymous_variant 0.12 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.94 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.98 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
Rv2477c 2783248 c.795G>C synonymous_variant 0.96 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.97 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.96 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4039610 c.1095G>C synonymous_variant 0.11 pyrazinamide
clpC1 4039616 c.1089G>C synonymous_variant 0.11 pyrazinamide
clpC1 4039982 c.723G>C synonymous_variant 0.1 pyrazinamide
clpC1 4039994 p.Glu237Asp missense_variant 0.11 pyrazinamide
clpC1 4040001 p.His235Arg missense_variant 0.11 pyrazinamide
clpC1 4040010 p.Ala232Asp missense_variant 0.12 pyrazinamide Uncertain significance
clpC1 4040015 c.690G>C synonymous_variant 0.11 pyrazinamide
clpC1 4040021 c.684A>C synonymous_variant 0.11 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.97 ethambutol Not assoc w R
embA 4245680 p.Lys816Asn missense_variant 0.59 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.96 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
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.99 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.96 streptomycin Not assoc w R