TB-Profiler result

Run: SRR7898221
Summary

Run ID: SRR7898221

Sample name:

Date: 2024-04-15T13:12:10.297871

Number of reads: 4505764

Percentage reads mapped: 86.62

Median coverage: 72.0

Strain: lineage1.1.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.2 Indo-Oceanic RD239 0.99
lineage1.1 Indo-Oceanic RD239 0.98
lineage1 Indo-Oceanic RD239 0.99
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-10G>A Assoc w R Can only confer resistance if genetically linked to a functional Eis
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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 761155 p.Ser450Leu missense_variant 0.98 rifampicin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 1.0 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
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
gyrB 6112 p.Met291Ile missense_variant 0.98 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.97 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 7841 c.540C>G synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 7847 c.546G>T synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 8324 c.1023T>C synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 8452 p.Ala384Val missense_variant 0.95 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8489 c.1188A>G synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 8516 c.1215T>C synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 8537 c.1236G>A synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 8540 c.1239C>G synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8546 c.1245T>C synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8552 c.1251C>A synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8555 c.1254G>C synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 8561 c.1260A>C synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8603 c.1302A>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8609 c.1308G>C synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8619 c.1318T>C synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8636 c.1335A>C synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8642 c.1341A>G synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 8672 c.1371A>G synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8678 c.1377G>A synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 8903 c.1602T>C synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8933 c.1632G>A synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9047 c.1746C>T synonymous_variant 0.95 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_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
gyrA 9443 c.2142G>A synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 1.0 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 1.0 isoniazid Not assoc w R
fgd1 491583 c.801G>A synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fgd1 491589 c.807G>A synonymous_variant 0.16 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 575935 c.588G>A synonymous_variant 0.16 ethionamide
isoniazid
mshA 575944 c.597T>G synonymous_variant 0.15 ethionamide
isoniazid
mshA 575953 c.606G>C synonymous_variant 0.13 ethionamide
isoniazid
mshA 576000 p.Asp218Ala missense_variant 0.91 ethionamide Uncertain significance
isoniazid Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
hadA 732250 c.321C>G synonymous_variant 0.16 isoniazid
hadA 732253 c.324T>C synonymous_variant 0.14 isoniazid
hadA 732256 c.327G>C synonymous_variant 0.14 isoniazid
hadA 732280 c.351C>T synonymous_variant 0.16 isoniazid
hadA 732283 c.354C>G synonymous_variant 0.17 isoniazid
nusG 734111 c.-143A>G upstream_gene_variant 0.13 rifampicin
nusG 734116 c.-138T>C upstream_gene_variant 0.86 rifampicin Not assoc w R
nusG 734120 c.-134T>C upstream_gene_variant 0.14 rifampicin Uncertain significance
nusG 734532 c.279A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
nusG 734541 c.288A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
nusG 734559 c.306T>C synonymous_variant 0.18 rifampicin
nusG 734853 c.600A>G synonymous_variant 0.15 rifampicin
nusG 734865 c.612G>C synonymous_variant 0.13 rifampicin
rpoB 759546 c.-261A>G upstream_gene_variant 1.0 rifampicin Not assoc w R
rpoB 760106 c.300G>T synonymous_variant 0.13 rifampicin
rpoB 760424 c.618C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760430 c.624T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760434 p.Val210Ile missense_variant 0.15 rifampicin
rpoB 760475 c.669A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760490 c.684C>T synonymous_variant 0.89 rifampicin Not assoc w R
rpoB 760591 p.Val262Ala missense_variant 0.14 rifampicin
rpoB 760611 c.805T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760661 c.855A>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760670 c.864G>C synonymous_variant 0.15 rifampicin
rpoB 760674 c.868T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760679 c.873A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760683 c.877T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760716 c.910_912delCGCinsAG frameshift_variant&missense_variant 0.19 rifampicin
rpoB 760727 c.921C>T synonymous_variant 0.18 rifampicin
rpoB 760730 c.924T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760757 c.951T>C synonymous_variant 0.13 rifampicin
rpoB 760769 c.963C>G synonymous_variant 0.13 rifampicin
rpoB 760946 c.1140A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760970 c.1164G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760971 c.1165_1167delCGGinsAA frameshift_variant&missense_variant 0.14 rifampicin
rpoB 760982 c.1176G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760985 c.1179G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760991 c.1185G>C synonymous_variant 0.18 rifampicin
rpoB 761006 c.1200C>T synonymous_variant 0.17 rifampicin
rpoB 761537 c.1731C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761601 p.Ala599Thr missense_variant 0.33 rifampicin Uncertain significance
rpoB 761948 c.2142G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761954 c.2148C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 762284 c.2478G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762317 c.2511A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 762329 c.2523G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 762410 c.-960T>C upstream_gene_variant 0.14 rifampicin
rpoB 762416 c.2610A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762425 c.2619C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 762434 c.-936T>C upstream_gene_variant 0.14 rifampicin
rpoB 762470 c.2664G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762491 c.2685T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762510 c.2704_2706delGCCinsCG frameshift_variant&missense_variant 0.18 rifampicin
rpoC 762533 c.-837T>C upstream_gene_variant 0.15 rifampicin
rpoC 762536 c.-834T>C upstream_gene_variant 0.15 rifampicin
rpoC 762537 c.-833T>C upstream_gene_variant 0.15 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763630 c.261G>T synonymous_variant 0.15 rifampicin
rpoC 763633 c.264T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763636 c.267T>C synonymous_variant 0.15 rifampicin
rpoC 763884 p.Ala172Val missense_variant 0.97 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.97 rifampicin Not assoc w R
rpoC 764236 c.867G>A synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764248 c.879C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764260 c.891G>A synonymous_variant 0.23 rifampicin
rpoC 764266 c.897T>C synonymous_variant 0.23 rifampicin
rpoC 764272 c.903G>T synonymous_variant 0.2 rifampicin
rpoC 764317 c.948C>G synonymous_variant 0.19 rifampicin
rpoC 764668 c.1299C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764791 c.1422C>A synonymous_variant 0.15 rifampicin
rpoC 764809 c.1440C>T synonymous_variant 0.16 rifampicin Not assoc w R
rpoC 764824 c.1455T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764872 c.1503A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764893 c.1524T>C synonymous_variant 0.22 rifampicin
rpoC 764932 c.1563C>G synonymous_variant 0.19 rifampicin
rpoC 764953 c.1584G>C synonymous_variant 0.15 rifampicin
rpoC 764968 c.1599T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 765171 p.Pro601Leu missense_variant 1.0 rifampicin Not assoc w R
rpoC 765454 c.2085C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765688 c.2319G>C synonymous_variant 0.17 rifampicin
rpoC 765689 c.2320C>T synonymous_variant 0.17 rifampicin
rpoC 765700 c.2331T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765734 c.2365T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765742 c.2373G>A synonymous_variant 0.14 rifampicin
rpoC 766043 p.Gln892Glu missense_variant 0.14 rifampicin
rpoC 766054 c.2685C>T synonymous_variant 0.13 rifampicin
rpoC 766082 p.Ala905Gln missense_variant 0.14 rifampicin
rpoC 766312 c.2943T>G synonymous_variant 0.12 rifampicin
rpoC 766357 c.2988C>T synonymous_variant 0.16 rifampicin
rpoC 766366 c.2997C>G synonymous_variant 0.15 rifampicin
rpoC 766381 c.3012C>T synonymous_variant 0.14 rifampicin
rpoC 766384 c.3015A>G synonymous_variant 0.13 rifampicin
rpoC 766483 c.3114G>C synonymous_variant 0.13 rifampicin
rpoC 766486 c.3117A>C synonymous_variant 0.14 rifampicin
rpoC 766492 c.3123T>C synonymous_variant 0.14 rifampicin
rpoC 766607 p.Ile1080Leu missense_variant 0.14 rifampicin
rpoC 766630 c.3261G>C synonymous_variant 0.14 rifampicin
rpoC 766666 c.3297C>G synonymous_variant 0.17 rifampicin
rpoC 766672 c.3303T>C synonymous_variant 0.17 rifampicin
rpoC 766726 c.3357T>C synonymous_variant 0.2 rifampicin
rpoC 766735 c.3366G>T synonymous_variant 0.22 rifampicin
rpoC 766738 c.3369G>C synonymous_variant 0.18 rifampicin
rpoC 766747 c.3378C>G synonymous_variant 0.19 rifampicin
rpoC 766750 c.3381C>G synonymous_variant 0.19 rifampicin
rpoC 766765 c.3396A>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 766804 c.3435A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766933 c.3564A>G synonymous_variant 0.12 rifampicin
rpoC 766945 c.3576A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766963 c.3594T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776395 p.Phe696Leu missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Uncertain significance
mmpS5 778740 p.Val56Met missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781841 c.282C>G synonymous_variant 0.13 streptomycin
rplC 800357 c.-452C>A upstream_gene_variant 1.0 linezolid Not assoc w R
rplC 800546 c.-263T>A upstream_gene_variant 0.17 linezolid
rplC 800567 c.-242A>G upstream_gene_variant 0.16 linezolid
rplC 800582 c.-227C>G upstream_gene_variant 0.16 linezolid
rplC 800600 c.-209G>T upstream_gene_variant 0.16 linezolid
Rv1129c 1254527 p.Arg3Pro missense_variant 1.0 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin
isoniazid
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 1304991 c.2061G>C synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fbiC 1304994 c.2064A>G synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fbiC 1304995 p.Leu689Met missense_variant 0.14 clofazimine
pretomanid
delamanid
fbiC 1305006 c.2076A>G synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fbiC 1305021 c.2091C>G synonymous_variant 0.13 clofazimine
pretomanid
delamanid
embR 1417019 p.Cys110Tyr missense_variant 1.0 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 1.0 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474083 n.426C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1474093 n.436G>A non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1474717 n.1060A>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1475028 n.1371G>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475430 n.1773T>C non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475532 n.1875A>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475617 n.1960C>G non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475620 n.1964delT non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475625 n.1968G>C non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rpsA 1833541 c.-1T>C upstream_gene_variant 0.13 pyrazinamide
rpsA 1833554 p.Thr5Ala missense_variant 0.14 pyrazinamide Uncertain significance
rpsA 1833557 p.Val6Ile missense_variant 0.14 pyrazinamide
rpsA 1833742 c.201A>G synonymous_variant 0.16 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.16 pyrazinamide
rpsA 1833790 c.249T>C synonymous_variant 0.13 pyrazinamide
rpsA 1833793 c.252C>T synonymous_variant 0.13 pyrazinamide
rpsA 1833802 c.261A>G synonymous_variant 0.14 pyrazinamide
rpsA 1833811 c.270G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834051 c.510G>A synonymous_variant 0.15 pyrazinamide
rpsA 1834099 c.558C>G synonymous_variant 0.14 pyrazinamide
rpsA 1834102 c.561T>G synonymous_variant 0.13 pyrazinamide
rpsA 1834105 c.564C>G synonymous_variant 0.13 pyrazinamide
rpsA 1834336 c.795C>G synonymous_variant 0.12 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
rpsA 1834366 c.825A>G synonymous_variant 0.18 pyrazinamide Not assoc w R - Interim
rpsA 1834378 c.837T>C synonymous_variant 0.21 pyrazinamide Not assoc w R - Interim
rpsA 1834411 c.870T>G synonymous_variant 0.23 pyrazinamide
rpsA 1834423 c.882G>C synonymous_variant 0.25 pyrazinamide
rpsA 1834450 c.909G>A synonymous_variant 0.23 pyrazinamide
rpsA 1834451 c.910T>C synonymous_variant 0.24 pyrazinamide
rpsA 1834465 c.924T>C synonymous_variant 0.18 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.19 pyrazinamide
rpsA 1834495 c.954G>A synonymous_variant 0.16 pyrazinamide
rpsA 1834522 c.981C>T synonymous_variant 0.16 pyrazinamide
rpsA 1834528 c.987T>G synonymous_variant 0.15 pyrazinamide
rpsA 1834660 c.1119C>T synonymous_variant 0.18 pyrazinamide Not assoc w R - Interim
rpsA 1834669 c.1128G>C synonymous_variant 0.21 pyrazinamide
rpsA 1834687 c.1146C>T synonymous_variant 0.18 pyrazinamide
rpsA 1834720 c.1179C>G synonymous_variant 0.18 pyrazinamide
rpsA 1834753 c.1212T>G synonymous_variant 0.14 pyrazinamide
rpsA 1834774 c.1233C>T synonymous_variant 0.18 pyrazinamide
rpsA 1834780 c.1239A>G synonymous_variant 0.16 pyrazinamide
rpsA 1834786 c.1245A>G synonymous_variant 0.13 pyrazinamide
rpsA 1834789 c.1248T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834792 c.1251G>C synonymous_variant 0.13 pyrazinamide
rpsA 1834798 c.1257C>G synonymous_variant 0.13 pyrazinamide
tsnR 1853974 c.369C>T synonymous_variant 1.0 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.99 linezolid Not assoc w R
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
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
PPE35 2167983 p.Gly877Asp missense_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 2518756 c.642G>C synonymous_variant 0.14 isoniazid
kasA 2518783 c.669T>C synonymous_variant 0.13 isoniazid
kasA 2518789 c.675G>T synonymous_variant 0.15 isoniazid
kasA 2518795 c.681C>G synonymous_variant 0.18 isoniazid
kasA 2518798 c.684G>T synonymous_variant 0.17 isoniazid
kasA 2518825 c.711T>C synonymous_variant 0.16 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0 isoniazid
folC 2746420 c.1179A>G synonymous_variant 0.15 para-aminosalicylic_acid
folC 2746426 c.1173G>C synonymous_variant 0.16 para-aminosalicylic_acid
folC 2746429 c.1170C>A synonymous_variant 0.15 para-aminosalicylic_acid
folC 2746644 p.Arg319Ser missense_variant 1.0 para-aminosalicylic_acid
Rv2477c 2782453 c.1590C>A synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2782480 c.1563G>A synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2782483 c.1560G>C synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783883 c.160T>C synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2681 2996912 c.174C>T synonymous_variant 0.99 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.98 ethambutol Not assoc w R
moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv2752c 3065305 p.Ala296Val missense_variant 0.98 ethambutol Not assoc w R
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R - Interim
Rv2752c 3065901 c.291A>G synonymous_variant 0.13 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3065910 c.282C>G synonymous_variant 0.17 ethambutol Not assoc w R - Interim
moxifloxacin
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
Rv2752c 3065916 c.276T>C synonymous_variant 0.18 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3065919 c.273G>C synonymous_variant 0.19 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066795 c.-604G>C upstream_gene_variant 0.14 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066822 c.-631T>G upstream_gene_variant 0.14 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066839 c.-648A>G upstream_gene_variant 0.14 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066846 c.-655G>C upstream_gene_variant 0.13 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 1.0 ethionamide Uncertain significance
lpqB 3623756 c.1155G>C synonymous_variant 0.14 bedaquiline
rifampicin
lpqB 3623759 c.1152G>C synonymous_variant 0.14 bedaquiline
rifampicin
lpqB 3624486 p.Asp142Gly missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3625069 c.-159T>G upstream_gene_variant 0.13 bedaquiline
rifampicin
mtrB 3626467 c.147G>A synonymous_variant 0.95 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
mtrB 3626999 c.-386G>C upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3627008 c.-395G>C upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3627011 c.-398T>C upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3627014 c.-401G>T upstream_gene_variant 0.18 bedaquiline
rifampicin
mtrA 3627068 c.282T>C synonymous_variant 0.15 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3627080 c.270T>C synonymous_variant 0.13 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627296 c.-683T>C upstream_gene_variant 0.18 bedaquiline
rifampicin
mtrB 3627301 c.-688T>C upstream_gene_variant 0.17 bedaquiline
rifampicin
mtrA 3627884 c.-535A>G upstream_gene_variant 0.13 bedaquiline
rifampicin
rpoA 3877557 c.951C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877587 c.921A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877593 c.915C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3877596 c.912G>C synonymous_variant 0.13 rifampicin
rpoA 3877650 c.858C>T synonymous_variant 0.13 rifampicin
rpoA 3877656 c.852T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877668 c.840A>G synonymous_variant 0.18 rifampicin
rpoA 3877679 p.Ala277Ser missense_variant 0.16 rifampicin
rpoA 3877683 c.825G>T synonymous_variant 0.16 rifampicin
rpoA 3877686 c.822A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877692 c.816G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3877704 c.804G>C synonymous_variant 0.16 rifampicin
rpoA 3878355 c.153C>G synonymous_variant 0.12 rifampicin
rpoA 3878364 c.144A>C synonymous_variant 0.13 rifampicin
rpoA 3878367 c.141C>T synonymous_variant 0.14 rifampicin
rpoA 3878370 c.138T>C synonymous_variant 0.14 rifampicin
rpoA 3878385 c.123C>G synonymous_variant 0.14 rifampicin
rpoA 3878764 c.-257A>G upstream_gene_variant 0.14 rifampicin
rpoA 3878785 c.-278T>G upstream_gene_variant 0.13 rifampicin
rpoA 3878788 c.-281G>C upstream_gene_variant 0.14 rifampicin Uncertain significance
rpoA 3878878 c.-371T>C upstream_gene_variant 0.13 rifampicin Uncertain significance
rpoA 3878889 c.-382A>G upstream_gene_variant 0.15 rifampicin
ddn 3987057 p.Arg72Trp missense_variant 0.97 delamanid Uncertain significance
pretomanid
clpC1 4038658 p.Lys683Gln missense_variant 0.18 pyrazinamide
clpC1 4038661 p.Ser682Thr missense_variant 0.16 pyrazinamide
clpC1 4038662 c.2043T>C synonymous_variant 0.16 pyrazinamide
clpC1 4038671 c.2034T>C synonymous_variant 0.17 pyrazinamide
clpC1 4038683 c.2022T>G synonymous_variant 0.21 pyrazinamide
clpC1 4038695 c.2010C>G synonymous_variant 0.21 pyrazinamide
clpC1 4038701 c.2004G>T synonymous_variant 0.23 pyrazinamide
clpC1 4038704 c.2001T>C synonymous_variant 0.22 pyrazinamide
clpC1 4038908 c.1797C>G synonymous_variant 0.2 pyrazinamide
clpC1 4038914 c.1791G>C synonymous_variant 0.18 pyrazinamide
clpC1 4038917 c.1788C>T synonymous_variant 0.19 pyrazinamide
clpC1 4038923 c.1780_1782delCTAinsTG frameshift_variant&synonymous_variant 0.21 pyrazinamide
clpC1 4038956 c.1749T>C synonymous_variant 0.15 pyrazinamide
clpC1 4038965 c.1740T>C synonymous_variant 0.19 pyrazinamide
clpC1 4039243 c.1462C>T synonymous_variant 0.15 pyrazinamide
clpC1 4039661 c.1044T>G synonymous_variant 0.16 pyrazinamide
clpC1 4039664 c.1041G>C synonymous_variant 0.16 pyrazinamide
clpC1 4040165 c.540G>C synonymous_variant 0.13 pyrazinamide
clpC1 4040171 c.534C>G synonymous_variant 0.14 pyrazinamide
clpC1 4040180 c.525C>G synonymous_variant 0.15 pyrazinamide
clpC1 4040201 c.504C>A synonymous_variant 0.15 pyrazinamide
clpC1 4040315 c.390G>A synonymous_variant 0.16 pyrazinamide
clpC1 4040517 p.Val63Ala missense_variant 0.89 pyrazinamide Not assoc w R - Interim
panD 4044740 c.-459C>T upstream_gene_variant 0.99 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.99 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 4139183 c.572dupG frameshift_variant 0.28 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.91 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 1.0 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.98 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
embB 4247991 p.Val493Ala missense_variant 0.98 ethambutol
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.96 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 4338603 c.-82C>T 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 4407873 c.330G>T synonymous_variant 1.0 streptomycin Not assoc w R
gid 4408094 p.Gly37Arg missense_variant 0.99 streptomycin Uncertain significance