TB-Profiler result

Run: ERR4769427
Summary

Run ID: ERR4769427

Sample name:

Date: 2024-04-14T21:12:56.580275

Number of reads: 2175083

Percentage reads mapped: 84.36

Median coverage: 63.0

Strain: La1.2

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
La1.2 M.bovis None 1.0
La1 M.bovis None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide pncA p.His57Asp Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
pncA 2289073 p.His57Asp missense_variant 1.0 pyrazinamide Assoc w R
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
dnaA 467 p.His156Arg missense_variant 1.0 isoniazid Not assoc w R
gyrB 5752 c.513G>A synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6406 c.1167C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6446 p.Ala403Ser missense_variant 0.98 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
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 7710 c.409T>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 7821 c.520C>T synonymous_variant 0.93 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8285 c.984C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8741 c.1440C>T synonymous_variant 0.96 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9143 c.1842T>C synonymous_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Glu missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 9323 c.2022C>G synonymous_variant 0.18 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9335 c.2034G>C synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 9377 c.2076A>G synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0010c 13197 p.Thr121Ser missense_variant 1.0 isoniazid Not assoc w R
Rv0010c 13228 c.330delG frameshift_variant 1.0 isoniazid Uncertain significance
Rv0010c 13280 c.279C>A synonymous_variant 1.0 isoniazid Not assoc w R - Interim
Rv0010c 13460 c.99T>C synonymous_variant 1.0 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.98 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
nusG 734502 c.249G>A synonymous_variant 0.13 rifampicin
nusG 734532 c.279A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
nusG 734541 c.288A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 761606 c.1800C>G synonymous_variant 0.14 rifampicin
rpoB 761612 c.1806G>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761615 c.1809A>C synonymous_variant 0.14 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 0.13 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763076 c.-294C>G upstream_gene_variant 0.12 rifampicin
rpoC 763528 c.159G>A synonymous_variant 0.13 rifampicin Not assoc w R - Interim
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 763594 c.225C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763660 c.291T>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763702 c.333C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764188 c.819A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764257 c.888G>C synonymous_variant 0.13 rifampicin
rpoC 764365 c.996C>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764383 c.1014C>G synonymous_variant 0.15 rifampicin
rpoC 764387 c.1018T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764405 c.1036A>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764410 c.1041G>C synonymous_variant 0.16 rifampicin
rpoC 764650 c.1281G>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764791 c.1422C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764809 c.1440C>T synonymous_variant 0.16 rifampicin Not assoc w R
rpoC 764815 c.1446A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764824 c.1455T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764878 c.1509C>G synonymous_variant 0.12 rifampicin
rpoC 764887 c.1518G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764888 c.1519T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764911 c.1542A>G synonymous_variant 0.12 rifampicin
rpoC 765871 c.2502T>C synonymous_variant 0.14 rifampicin
rpoC 765875 p.Val836Ile missense_variant 0.2 rifampicin Uncertain significance
rpoC 765904 c.2535C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 765934 c.2565C>T synonymous_variant 0.2 rifampicin
rpoC 765967 c.2598C>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 765973 c.2604C>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 765979 c.2610C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 765982 c.2613C>T synonymous_variant 0.16 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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781832 c.273T>G synonymous_variant 0.12 streptomycin
rpsL 781859 c.300T>C synonymous_variant 0.14 streptomycin Not assoc w R - Interim
rpsL 781868 c.309T>C synonymous_variant 0.15 streptomycin
rpsL 781871 c.312G>C synonymous_variant 0.14 streptomycin
rpsL 781877 c.318T>A synonymous_variant 0.15 streptomycin
rpsL 781892 c.333A>G synonymous_variant 0.17 streptomycin
rpsL 781898 c.339A>C synonymous_variant 0.15 streptomycin
rpsL 781907 c.348T>C synonymous_variant 0.17 streptomycin
rpsL 781916 c.357T>G synonymous_variant 0.16 streptomycin
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1129c 1254582 c.-48A>G upstream_gene_variant 1.0 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
sigE 1364961 c.549A>C synonymous_variant 0.98 pyrazinamide Not assoc w R - Interim
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 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 0.18 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472028 n.183A>G non_coding_transcript_exon_variant 0.17 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472030 n.185G>A non_coding_transcript_exon_variant 0.17 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472031 n.186G>T non_coding_transcript_exon_variant 0.16 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472033 n.188A>C non_coding_transcript_exon_variant 0.16 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472040 n.195T>G non_coding_transcript_exon_variant 0.16 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472041 n.196C>T non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472042 n.197T>G non_coding_transcript_exon_variant 0.16 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472053 n.211_212delGC non_coding_transcript_exon_variant 0.21 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.22 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.24 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.25 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472286 n.441C>G non_coding_transcript_exon_variant 0.2 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472287 n.442C>T non_coding_transcript_exon_variant 0.2 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472292 n.447A>G non_coding_transcript_exon_variant 0.12 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472327 n.482G>A non_coding_transcript_exon_variant 0.2 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472328 n.483G>C non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472431 n.586G>A non_coding_transcript_exon_variant 0.15 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472438 n.593T>C non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.22 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.23 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472489 n.644A>G non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472683 n.838_839insTA non_coding_transcript_exon_variant 0.26 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472847 n.1002G>C non_coding_transcript_exon_variant 0.15 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472848 n.1003T>G non_coding_transcript_exon_variant 0.15 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472849 n.1004C>G non_coding_transcript_exon_variant 0.15 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472858 n.1013G>T non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472859 n.1014G>C non_coding_transcript_exon_variant 0.16 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472860 n.1015C>G non_coding_transcript_exon_variant 0.15 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.2 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473100 n.1255G>C non_coding_transcript_exon_variant 0.21 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.27 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473109 n.1264T>G non_coding_transcript_exon_variant 0.22 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473111 n.1266A>T non_coding_transcript_exon_variant 0.21 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.22 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.23 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.16 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473291 n.1446_1447insT non_coding_transcript_exon_variant 0.16 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1473770 n.113T>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473788 n.131A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1474045 n.388C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1474054 n.397T>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
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 0.19 capreomycin Uncertain significance
linezolid
rrl 1474100 n.443C>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474106 n.449A>G non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474108 n.451C>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474109 n.452A>G non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474110 n.453A>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474174 n.517A>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474263 n.606G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1474284 n.629dupC non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474290 n.633T>C non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474292 n.636_644delTCCTCTCCG non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474303 n.646A>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474306 n.649A>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474308 n.653_654delTG non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474350 n.693G>C non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474351 n.694G>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1474353 n.696A>G non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474413 n.756_757delACinsTAT non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474452 n.795C>G non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid
rrl 1474638 n.981C>A non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474708 n.1052dupG non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid
rrl 1474711 n.1054_1055insA non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1474715 n.1061delA non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.41 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>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475031 n.1374G>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid
rrl 1475120 n.1463G>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475460 n.1803A>G non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475659 n.2002G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1475764 n.2107A>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.17 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 1475995 n.2338G>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1475997 n.2340A>G non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1476033 n.2376T>C non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1476034 n.2377C>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1476035 n.2378G>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1476044 n.2387T>G non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1476045 n.2388G>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476088 n.2431A>C non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476095 n.2438C>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1476103 n.2446C>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1476108 n.2451T>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1476110 n.2453G>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.3 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 1476245 n.2588C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476246 n.2589G>A non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476256 n.2599A>C non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1476262 n.2605G>A non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476529 n.2872A>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.28 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.28 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.24 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476665 n.3008T>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1476674 n.3017T>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476679 n.3022T>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
inhA 1674703 c.502T>C synonymous_variant 0.14 ethionamide
isoniazid
rpsA 1833709 c.168C>T synonymous_variant 0.14 pyrazinamide
rpsA 1833724 c.183C>T synonymous_variant 0.14 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.14 pyrazinamide
rpsA 1833734 p.Ala65Ser missense_variant 0.14 pyrazinamide
rpsA 1833770 p.Asn77His missense_variant 0.16 pyrazinamide
rpsA 1833778 c.237C>G synonymous_variant 0.15 pyrazinamide
rpsA 1833811 c.270G>C synonymous_variant 0.13 pyrazinamide
rpsA 1833838 c.297G>C synonymous_variant 0.15 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.14 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.15 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.14 pyrazinamide
rpsA 1833862 c.321G>C synonymous_variant 0.13 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.16 pyrazinamide
rpsA 1833949 c.408T>C synonymous_variant 0.14 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.14 pyrazinamide
rpsA 1833988 c.447C>G synonymous_variant 0.14 pyrazinamide
rpsA 1834015 c.474G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834105 c.564C>T synonymous_variant 0.15 pyrazinamide
rpsA 1834225 c.684C>G synonymous_variant 0.14 pyrazinamide
rpsA 1834240 c.699T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
rpsA 1834543 c.1002C>G synonymous_variant 0.13 pyrazinamide
rpsA 1834859 p.Ala440Thr missense_variant 1.0 pyrazinamide Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 1.0 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2062946 p.Ser595Gly missense_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
ndh 2102106 p.Gly313Arg missense_variant 1.0 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R - Interim
ndh 2103173 c.-132delG upstream_gene_variant 1.0 ethionamide
delamanid
isoniazid
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155503 c.609C>T synonymous_variant 1.0 isoniazid Not assoc w R
katG 2156025 c.87C>A synonymous_variant 1.0 isoniazid Not assoc w R
katG 2156465 c.-354C>T upstream_gene_variant 1.0 isoniazid Not assoc w R - Interim
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2168011 p.Ser868Arg missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2168814 c.1798dupA frameshift_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2517917 c.-198G>T upstream_gene_variant 0.18 isoniazid
kasA 2517941 c.-174C>G upstream_gene_variant 0.16 isoniazid
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
Rv2477c 2782927 c.1116A>G synonymous_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R
amikacin Not assoc w R - Interim
Rv2681 2997325 p.Ala196Val missense_variant 1.0 capreomycin Uncertain significance
Rv2752c 3065888 p.Val102Ile missense_variant 0.98 ethambutol Uncertain significance
moxifloxacin
levofloxacin
rifampicin Uncertain significance
isoniazid Uncertain significance
thyX 3067786 p.Thr54Ala missense_variant 0.96 para-aminosalicylic_acid
ald 3086728 c.-92C>T upstream_gene_variant 0.99 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087084 c.266delA frameshift_variant 1.0 cycloserine
fbiD 3339154 p.Ile13Leu missense_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
Rv3083 3448745 p.Ile81Ser missense_variant 1.0 ethionamide Uncertain significance
Rv3083 3448783 p.Val94Ile missense_variant 1.0 ethionamide Uncertain significance
lpqB 3623730 p.Ser394Leu missense_variant 0.98 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3624350 c.561G>T synonymous_variant 1.0 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3624593 c.318G>A synonymous_variant 1.0 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
lpqB 3624710 c.201G>A synonymous_variant 0.98 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3625678 c.-768C>G upstream_gene_variant 0.13 bedaquiline
rifampicin
rpoA 3877737 c.771G>C synonymous_variant 0.15 rifampicin
rpoA 3877743 c.765T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877764 c.744C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877770 c.738A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3877776 c.732T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3877782 c.726T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3877785 c.723C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3877827 c.681C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3877836 c.672A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877842 c.666A>G synonymous_variant 0.14 rifampicin
rpoA 3877848 c.660C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3877856 c.652T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877866 c.642G>C synonymous_variant 0.17 rifampicin
rpoA 3877872 c.636C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877875 c.633T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3878310 c.198G>C synonymous_variant 0.15 rifampicin
rpoA 3878322 c.186A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878331 c.177A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878346 c.162T>C synonymous_variant 0.15 rifampicin
rpoA 3878358 c.150C>G synonymous_variant 0.15 rifampicin
rpoA 3878364 c.144A>C synonymous_variant 0.17 rifampicin
rpoA 3878394 c.114G>T synonymous_variant 0.17 rifampicin
rpoA 3878400 c.108T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3878415 c.93C>T synonymous_variant 0.15 rifampicin
rpoA 3878442 c.66G>C synonymous_variant 0.15 rifampicin
rpoA 3878630 c.-124delC upstream_gene_variant 1.0 rifampicin Not assoc w R
clpC1 4038403 c.2302T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4239487 c.-376T>C upstream_gene_variant 1.0 ethambutol Uncertain significance
embC 4240671 p.Thr270Ile missense_variant 0.98 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242970 c.3108C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246551 p.Asn13Ser missense_variant 1.0 ethambutol Not assoc w R
embB 4246864 c.351C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247173 c.660G>A synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
aftB 4267858 p.Ile327Val missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269351 c.483C>T synonymous_variant 1.0 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407743 p.Arg154Trp missense_variant 0.99 streptomycin Uncertain significance