TB-Profiler result

Run: SRR10315466
Summary

Run ID: SRR10315466

Sample name:

Date: 2024-04-15T00:23:58.994528

Number of reads: 4299337

Percentage reads mapped: 79.08

Median coverage: 123.0

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 0.99
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 1.0
lineage2.2 East-Asian (Beijing) RD105;RD207 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Leu430Pro Assoc w R
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide ethA c.-191_*1642del Assoc w R
clofazimine
para-aminosalicylic_acid
delamanid fgd1 c.730_732delAACinsGG Assoc w R - Interim Confers DLM-PMD cross-resistance
c.766_768delGCTinsCC Assoc w R - Interim Confers DLM-PMD cross-resistance
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
fgd1 491512 c.730_732delAACinsGG frameshift_variant&missense_variant 0.15 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fgd1 491548 c.766_768delGCTinsCC frameshift_variant&missense_variant 0.13 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
rpoB 761095 p.Leu430Pro missense_variant 0.99 rifampicin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.5 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
ethA 4324361 c.-191_*1642del transcript_ablation 0.93 ethionamide 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 7472 c.171T>C synonymous_variant 0.12 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrA 7475 c.174A>G synonymous_variant 0.12 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7480 p.Phe60Tyr missense_variant 0.13 levofloxacin
moxifloxacin
gyrA 7484 c.183T>C synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 7499 c.198G>C synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 7526 c.225G>C synonymous_variant 0.17 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7532 c.231T>G synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7541 c.240C>G synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7547 c.246C>T synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7565 c.264C>T synonymous_variant 0.12 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7569 p.Ala90Ser missense_variant 0.12 levofloxacin
moxifloxacin
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7592 c.291G>C synonymous_variant 0.12 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7595 c.294C>G synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 8571 c.1270C>T synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491490 c.708C>T synonymous_variant 0.13 clofazimine
pretomanid
delamanid
fgd1 491499 c.717G>C synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fgd1 491508 c.726A>C synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fgd1 491536 c.754C>T synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fgd1 491542 c.760T>C synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fgd1 491547 c.765A>T synonymous_variant 0.13 clofazimine
pretomanid
delamanid
fgd1 491562 c.780C>T synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fgd1 491563 c.781_783delAGCinsTCG synonymous_variant 0.13 clofazimine
pretomanid
delamanid
fgd1 491571 c.789C>T synonymous_variant 0.18 clofazimine
pretomanid
delamanid
fgd1 491595 c.813C>T synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fgd1 491610 c.828A>G synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fgd1 491616 c.834A>G synonymous_variant 0.13 clofazimine
pretomanid
delamanid
fgd1 491620 p.Ile280Val missense_variant 0.12 clofazimine
pretomanid
delamanid
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.98 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 1.0 ethionamide Uncertain significance
rpoB 760298 c.492G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760310 c.504G>C synonymous_variant 0.12 rifampicin
rpoB 760316 c.510C>G synonymous_variant 0.12 rifampicin
rpoB 760357 p.Thr184Ser missense_variant 0.15 rifampicin Uncertain significance
rpoB 760361 c.555T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760376 p.Asp190Glu missense_variant 0.15 rifampicin Uncertain significance
rpoB 760406 c.600G>T synonymous_variant 0.13 rifampicin
rpoB 760407 p.Ser201Gly missense_variant 0.13 rifampicin Uncertain significance
rpoB 760415 c.609C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760424 c.618C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760430 c.624T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 760457 c.651C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760463 c.657C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760475 c.669A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760478 c.672C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760481 c.675G>T synonymous_variant 0.14 rifampicin
rpoB 760484 c.678A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760764 p.Glu320Gln missense_variant 0.12 rifampicin
rpoB 760784 c.978G>T synonymous_variant 0.13 rifampicin
rpoB 760793 c.987A>G synonymous_variant 0.14 rifampicin
rpoB 760805 c.999G>C synonymous_variant 0.14 rifampicin
rpoB 760817 c.1011A>G synonymous_variant 0.15 rifampicin
rpoB 760820 c.1014T>C synonymous_variant 0.15 rifampicin
rpoB 760826 c.1020C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760830 c.1024T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760841 c.1035T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760859 c.1053T>C synonymous_variant 0.12 rifampicin
rpoB 760862 c.1056G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761213 c.1407G>C synonymous_variant 0.15 rifampicin
rpoB 761217 p.Pro471Ser missense_variant 0.16 rifampicin
rpoB 761234 c.1428G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761249 c.1443A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 761261 c.1455G>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761264 c.1458C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761282 c.1476C>T synonymous_variant 0.18 rifampicin
rpoB 761288 c.1482G>T synonymous_variant 0.17 rifampicin
rpoB 761318 c.1512G>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761327 c.1521A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761330 c.1524G>C synonymous_variant 0.13 rifampicin
rpoB 761345 c.1539G>C synonymous_variant 0.13 rifampicin
rpoB 762008 c.2202C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762014 c.2208C>T synonymous_variant 0.16 rifampicin
rpoB 762047 c.2241G>A synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 762053 c.2247T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 762062 c.2256T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 762065 c.2259T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 762083 c.2277T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 762086 c.2280G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 762101 c.2295C>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 762114 p.Ile770Val missense_variant 0.21 rifampicin Uncertain significance
rpoB 762131 c.2325C>G synonymous_variant 0.2 rifampicin
rpoB 762137 c.2331C>T synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 762140 c.2334G>C synonymous_variant 0.19 rifampicin
rpoB 762143 c.2337T>C synonymous_variant 0.19 rifampicin
rpoB 762149 c.2343G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 762158 c.2352G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 762167 c.2361T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762176 c.2370T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762185 c.2379G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 762233 c.2427G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 762245 c.2439G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 762284 c.2478G>T synonymous_variant 0.23 rifampicin
rpoB 762293 c.2487T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 762308 c.2502G>C synonymous_variant 0.25 rifampicin
rpoB 762317 c.2511A>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 762329 c.2523G>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 762338 c.2532T>C synonymous_variant 0.24 rifampicin
rpoB 762341 c.2535G>C synonymous_variant 0.23 rifampicin
rpoB 762347 c.2541T>C synonymous_variant 0.23 rifampicin
rpoB 762350 c.2544C>T synonymous_variant 0.24 rifampicin
rpoB 762362 p.Glu852Asp missense_variant 0.22 rifampicin
rpoB 762369 c.2563T>C synonymous_variant 0.21 rifampicin
rpoC 762374 c.-996G>C upstream_gene_variant 0.21 rifampicin
rpoC 762395 c.-975G>C upstream_gene_variant 0.2 rifampicin
rpoC 762398 c.-972T>C upstream_gene_variant 0.21 rifampicin
rpoC 762401 c.-969G>C upstream_gene_variant 0.22 rifampicin
rpoB 762404 c.2598T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 762410 c.-960T>C upstream_gene_variant 0.24 rifampicin
rpoB 762416 c.2610A>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 762434 c.-936T>C upstream_gene_variant 0.2 rifampicin
rpoC 762443 c.-927G>C upstream_gene_variant 0.21 rifampicin
rpoB 762449 c.2643C>A synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 762452 c.2646G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 762470 c.2664G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762491 c.2685T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 762509 c.-861T>G upstream_gene_variant 0.12 rifampicin
rpoB 762510 p.Ala902Pro missense_variant 0.12 rifampicin Uncertain significance
rpoB 762929 c.3123G>C synonymous_variant 0.12 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
rpoB 762995 c.3189G>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 763004 c.3198G>A synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 763007 c.3201C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 763028 c.3222T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 763053 c.3247T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 763085 c.3279C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763103 c.-267G>C upstream_gene_variant 0.12 rifampicin
rpoC 763618 c.249C>T synonymous_variant 0.13 rifampicin
rpoC 763633 c.264T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763660 c.291T>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763666 c.297G>A synonymous_variant 0.14 rifampicin
rpoC 763675 c.306C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763702 c.333C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763709 c.340C>T synonymous_variant 0.15 rifampicin
rpoC 763714 c.345G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763723 c.354G>C synonymous_variant 0.17 rifampicin
rpoC 763732 c.363C>T synonymous_variant 0.17 rifampicin
rpoC 763741 c.372C>T synonymous_variant 0.16 rifampicin
rpoC 763747 c.378G>A synonymous_variant 0.18 rifampicin
rpoC 763765 c.396T>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763792 p.Glu141Asp missense_variant 0.15 rifampicin
rpoC 763807 c.438T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763813 c.444C>G synonymous_variant 0.13 rifampicin
rpoC 764153 p.Gln262Lys missense_variant 0.12 rifampicin
rpoC 764161 c.792G>C synonymous_variant 0.12 rifampicin
rpoC 764278 c.909A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764293 c.924G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764297 p.Met310Leu missense_variant 0.15 rifampicin
rpoC 764344 c.975C>T synonymous_variant 0.21 rifampicin
rpoC 764353 c.984G>T synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764365 c.996C>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764371 c.1002G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764380 c.1011G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764387 c.1018T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764405 c.1036_1038delAGGinsCC frameshift_variant&missense_variant 0.2 rifampicin
rpoC 764431 c.1062G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764434 c.1065A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764435 c.1066_1068delAGGinsCA frameshift_variant&missense_variant 0.17 rifampicin
rpoC 764446 c.1077T>C synonymous_variant 0.17 rifampicin
rpoC 764449 c.1080G>C synonymous_variant 0.17 rifampicin
rpoC 764458 c.1089G>C synonymous_variant 0.17 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 0.17 rifampicin
rpoC 764491 c.1122G>T synonymous_variant 0.12 rifampicin
rpoC 764497 c.1128A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764605 c.1236G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764623 c.1254C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764701 c.1332C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764707 c.1338G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764713 c.1344G>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764752 c.1383G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764758 c.1389C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764803 c.1434C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764809 c.1440C>T synonymous_variant 0.15 rifampicin Not assoc w R
rpoC 764815 c.1446A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764824 c.1455T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764827 c.1458G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764858 c.1489T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764869 c.1500C>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764875 c.1506C>T synonymous_variant 0.2 rifampicin
rpoC 764878 c.1509C>G synonymous_variant 0.2 rifampicin
rpoC 764887 c.1518G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764888 c.1519T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764911 c.1542A>G synonymous_variant 0.15 rifampicin
rpoC 764912 p.Met515Gln missense_variant 0.15 rifampicin Uncertain significance
rpoC 764935 c.1566T>C synonymous_variant 0.13 rifampicin
rpoC 764948 c.1579T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 765904 c.2535C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 765908 c.2539C>T synonymous_variant 0.13 rifampicin
rpoC 765934 c.2565C>T synonymous_variant 0.13 rifampicin
rpoC 767162 p.Asn1265Asp missense_variant 0.12 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 775856 c.2625T>C synonymous_variant 0.12 clofazimine
bedaquiline
mmpL5 775904 c.2577G>A synonymous_variant 0.15 clofazimine
bedaquiline
mmpL5 775951 c.2530C>T synonymous_variant 0.16 clofazimine
bedaquiline
mmpL5 775966 p.Ala839Ser missense_variant 0.14 clofazimine
bedaquiline
mmpL5 775970 c.2511G>C synonymous_variant 0.14 clofazimine
bedaquiline
mmpL5 775975 c.2506T>C synonymous_variant 0.15 clofazimine
bedaquiline
mmpL5 775981 p.Leu834Met missense_variant 0.15 clofazimine
bedaquiline
mmpL5 775994 c.2485_2487delATCinsCG frameshift_variant&missense_variant 0.13 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 775997 c.2484T>G synonymous_variant 0.12 clofazimine
bedaquiline
mmpL5 776000 c.2481G>C synonymous_variant 0.12 clofazimine
bedaquiline
mmpL5 776005 p.Ile826Leu missense_variant 0.12 clofazimine
bedaquiline
mmpL5 776009 c.2472A>G synonymous_variant 0.12 clofazimine
bedaquiline
mmpL5 776030 c.2451G>C synonymous_variant 0.14 clofazimine
bedaquiline
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781682 c.123T>C synonymous_variant 0.12 streptomycin
rpsL 781709 c.150G>C synonymous_variant 0.13 streptomycin Not assoc w R - Interim
rpsL 781715 c.156T>C synonymous_variant 0.12 streptomycin
rpsL 781728 c.169T>C synonymous_variant 0.13 streptomycin
rpsL 781732 c.174_177delGAGT frameshift_variant 0.14 streptomycin Uncertain significance
rpsL 781739 c.180_181insCGGC frameshift_variant 0.13 streptomycin Uncertain significance
rpsL 781742 c.183C>T synonymous_variant 0.13 streptomycin
rpsL 781751 c.192G>C synonymous_variant 0.13 streptomycin
rpsL 781760 c.201T>C synonymous_variant 0.14 streptomycin
rpsL 781772 c.213C>T synonymous_variant 0.15 streptomycin Not assoc w R - Interim
rpsL 781808 c.249C>T synonymous_variant 0.14 streptomycin
rpsL 781829 c.270G>C synonymous_variant 0.16 streptomycin
rpsL 781832 c.273T>C synonymous_variant 0.16 streptomycin
rpsL 781838 c.279G>C synonymous_variant 0.14 streptomycin
rpsL 781841 c.282C>T synonymous_variant 0.14 streptomycin
rpsL 781859 c.300T>G synonymous_variant 0.14 streptomycin
rpsL 781865 c.306G>C synonymous_variant 0.15 streptomycin
rpsL 781868 c.309T>C synonymous_variant 0.14 streptomycin
rpsL 781871 c.312G>C synonymous_variant 0.14 streptomycin
rpsL 781892 c.333A>G synonymous_variant 0.14 streptomycin
rpsL 781898 c.339A>C synonymous_variant 0.14 streptomycin
rpsL 781901 c.342C>T synonymous_variant 0.15 streptomycin
rpsL 781907 c.348T>C synonymous_variant 0.14 streptomycin
rpsL 781916 c.357T>C synonymous_variant 0.14 streptomycin
rpsL 781929 p.Gly124Ser missense_variant 0.16 streptomycin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1304613 c.1683T>C synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fbiC 1304634 c.1704C>G synonymous_variant 0.13 clofazimine
pretomanid
delamanid
fbiC 1304640 c.1710A>C synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fbiC 1304646 c.1716T>C synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fbiC 1304649 c.1719C>T synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fbiC 1304672 p.Val581Ala missense_variant 0.12 clofazimine
pretomanid
delamanid
fbiC 1304675 p.Gly582Glu missense_variant 0.12 clofazimine
pretomanid
delamanid
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471986 n.141C>T non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472019 n.174G>A non_coding_transcript_exon_variant 0.23 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472023 n.178G>T non_coding_transcript_exon_variant 0.21 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.2 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472380 n.535G>C non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.26 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.37 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473123 n.1278delAinsTC non_coding_transcript_exon_variant 0.32 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.45 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.43 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473291 n.1446_1447insT non_coding_transcript_exon_variant 0.42 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.4 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid
rrl 1475775 n.2118G>A non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.3 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476664 n.3007T>C non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1476665 n.3008T>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rpsA 1833928 c.387G>C synonymous_variant 0.13 pyrazinamide
rpsA 1833949 c.408T>C synonymous_variant 0.13 pyrazinamide
rpsA 1833976 c.435C>T synonymous_variant 0.13 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.13 pyrazinamide
rpsA 1833991 c.450C>A synonymous_variant 0.13 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.13 pyrazinamide
rpsA 1834009 c.468C>T synonymous_variant 0.13 pyrazinamide
rpsA 1834012 c.471G>T synonymous_variant 0.13 pyrazinamide
rpsA 1834015 c.474G>C synonymous_variant 0.14 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.13 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 0.99 pyrazinamide Not assoc w R - Interim
rpsA 1834279 c.738C>T synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
rpsA 1834297 c.756C>T synonymous_variant 0.14 pyrazinamide
rpsA 1834303 c.762T>G synonymous_variant 0.14 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834345 c.804C>T synonymous_variant 0.14 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
rpsA 1834361 c.820T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834366 c.825A>G synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
rpsA 1834396 c.855G>C synonymous_variant 0.16 pyrazinamide
rpsA 1834411 c.870T>C synonymous_variant 0.13 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 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2517941 c.-174C>G upstream_gene_variant 0.14 isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3877848 c.660C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877866 c.642G>C synonymous_variant 0.15 rifampicin
rpoA 3877875 c.633T>A synonymous_variant 0.14 rifampicin
rpoA 3877878 c.630G>C synonymous_variant 0.14 rifampicin
rpoA 3877887 c.621G>C synonymous_variant 0.13 rifampicin
rpoA 3877899 c.609C>T synonymous_variant 0.11 rifampicin
rpoA 3877905 c.603A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoA 3877920 c.588G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoA 3877962 c.546G>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoA 3878046 c.462T>G synonymous_variant 0.12 rifampicin
rpoA 3878050 p.Arg153Lys missense_variant 0.12 rifampicin
rpoA 3878061 c.447G>A synonymous_variant 0.13 rifampicin
rpoA 3878070 c.438T>C synonymous_variant 0.13 rifampicin
rpoA 3878082 c.426T>C synonymous_variant 0.17 rifampicin
rpoA 3878103 c.405A>G synonymous_variant 0.2 rifampicin
rpoA 3878118 c.390T>C synonymous_variant 0.2 rifampicin
rpoA 3878127 c.381G>C synonymous_variant 0.2 rifampicin
rpoA 3878143 p.Gly122Asp missense_variant 0.13 rifampicin Uncertain significance
rpoA 3878145 c.363C>G synonymous_variant 0.13 rifampicin
rpoA 3878160 c.348C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878163 c.345C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878187 c.321C>A synonymous_variant 0.14 rifampicin
rpoA 3878193 c.315T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878197 p.Glu104Ala missense_variant 0.14 rifampicin Uncertain significance
rpoA 3878205 c.303T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878217 c.291A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3878238 c.270C>T synonymous_variant 0.14 rifampicin
clpC1 4039391 c.1314T>G synonymous_variant 0.12 pyrazinamide
clpC1 4039394 c.1311G>C synonymous_variant 0.12 pyrazinamide
clpC1 4039397 c.1308A>G synonymous_variant 0.12 pyrazinamide
clpC1 4039409 c.1296T>C synonymous_variant 0.14 pyrazinamide
clpC1 4039412 c.1293T>G synonymous_variant 0.15 pyrazinamide
clpC1 4039415 p.Glu430Asp missense_variant 0.13 pyrazinamide Uncertain significance
clpC1 4039430 c.1275T>C synonymous_variant 0.14 pyrazinamide
clpC1 4039442 c.1263A>G synonymous_variant 0.13 pyrazinamide
clpC1 4039454 c.1251A>T synonymous_variant 0.13 pyrazinamide
clpC1 4039649 c.1056G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039652 c.1053G>C synonymous_variant 0.15 pyrazinamide
clpC1 4039670 c.1035G>C synonymous_variant 0.15 pyrazinamide
clpC1 4039682 c.1023C>G synonymous_variant 0.16 pyrazinamide
clpC1 4039694 c.1011G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039724 c.981A>G synonymous_variant 0.14 pyrazinamide
clpC1 4039733 c.972G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039850 c.855T>C synonymous_variant 0.11 pyrazinamide
clpC1 4039865 c.840T>C synonymous_variant 0.11 pyrazinamide
clpC1 4039883 c.822G>A synonymous_variant 0.12 pyrazinamide
clpC1 4039889 c.816G>C synonymous_variant 0.13 pyrazinamide
clpC1 4039898 c.807C>G synonymous_variant 0.15 pyrazinamide
clpC1 4039904 c.801A>G synonymous_variant 0.17 pyrazinamide
clpC1 4039907 c.798G>A synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
clpC1 4039934 c.771G>A synonymous_variant 0.14 pyrazinamide
clpC1 4039937 c.768G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039946 c.759A>T synonymous_variant 0.14 pyrazinamide
clpC1 4039949 c.756G>C synonymous_variant 0.12 pyrazinamide
clpC1 4039952 c.753T>C synonymous_variant 0.14 pyrazinamide
clpC1 4039958 c.747G>C synonymous_variant 0.13 pyrazinamide
clpC1 4040003 c.702G>C synonymous_variant 0.14 pyrazinamide
clpC1 4040021 c.684A>C synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4040024 c.681A>G synonymous_variant 0.15 pyrazinamide
clpC1 4040033 c.672G>C synonymous_variant 0.15 pyrazinamide
glpK 4138670 c.1086G>C synonymous_variant 0.12 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138676 c.1080T>C synonymous_variant 0.12 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138679 c.1075_1077delATGinsGC frameshift_variant&missense_variant 0.12 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4138703 c.1053C>G synonymous_variant 0.12 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138718 c.1038T>C synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138727 c.1029C>G synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138747 c.1009C>T synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138757 c.999A>G synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138763 c.993G>A synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138769 c.987G>A synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138778 c.978C>A synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138781 c.975G>T synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
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
embB 4248118 c.1605T>C synonymous_variant 0.12 ethambutol
embB 4248133 c.1620C>G synonymous_variant 0.12 ethambutol
embB 4248142 c.1629T>C synonymous_variant 0.13 ethambutol
embB 4248167 p.Thr552Ala missense_variant 0.13 ethambutol
embB 4248170 p.Ala553Ser missense_variant 0.13 ethambutol
embB 4248173 p.Val554Leu missense_variant 0.12 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
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
gid 4407620 p.Tyr195His missense_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R