TB-Profiler result

Run: SRR7240476

Summary

Run ID: SRR7240476

Sample name:

Date: 2024-04-14T06:27:59.460832

Number of reads: 1503726

Percentage reads mapped: 91.56

Median coverage: 76.0

Strain: La1.8.1

Spoligotype:

Drug-resistance: Other


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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
La1.8 M.bovis None 1.0
La1.8.1 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 rrs n.462C>T Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid fbiC c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Assoc w R - Interim
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
fbiC 1305494 c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN frameshift_variant&stop_lost&splice_region_variant 1.0 delamanid Assoc w R - Interim
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance Mutation from literature
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 0.99 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6446 p.Ala403Ser missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
gyrA 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 8285 c.984C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8471 c.1170T>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 9143 c.1842T>C synonymous_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9217 p.Asp639Ala missense_variant 0.97 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13197 p.Thr121Ser missense_variant 1.0 isoniazid Not assoc w R
Rv0010c 13228 c.330delG frameshift_variant 1.0 isoniazid Uncertain significance
Rv0010c 13460 c.99T>C synonymous_variant 1.0 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
rpoB 762101 c.2295C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762114 p.Ile770Val missense_variant 0.16 rifampicin Uncertain significance
rpoB 762122 c.2316C>T synonymous_variant 0.17 rifampicin
rpoB 762131 c.2325C>G synonymous_variant 0.18 rifampicin
rpoB 762134 c.2328C>A synonymous_variant 0.18 rifampicin
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 0.19 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 0.19 rifampicin Not assoc w R - Interim
rpoB 762176 c.2370T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 762185 c.2379G>T synonymous_variant 0.18 rifampicin
rpoB 762209 c.2403C>T synonymous_variant 0.2 rifampicin
rpoB 762212 c.2406G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 762233 c.2427G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 762236 c.2430G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 762254 c.2448T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 762257 c.2451C>G synonymous_variant 0.2 rifampicin
rpoB 762281 c.2475G>A synonymous_variant 0.19 rifampicin
rpoB 762284 c.2478G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 762293 c.2487T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 762296 c.2490G>A synonymous_variant 0.18 rifampicin
rpoB 762317 c.2511A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762329 c.2523G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 762338 c.2532T>C synonymous_variant 0.17 rifampicin
rpoB 762347 c.2541T>C synonymous_variant 0.19 rifampicin
rpoB 762362 p.Glu852Asp missense_variant 0.17 rifampicin
rpoB 762369 c.2563T>C synonymous_variant 0.15 rifampicin
rpoC 762374 c.-996G>C upstream_gene_variant 0.15 rifampicin
rpoC 762380 c.-990T>G upstream_gene_variant 0.15 rifampicin
rpoC 762398 c.-972T>C upstream_gene_variant 0.15 rifampicin
rpoC 762401 c.-969G>C upstream_gene_variant 0.14 rifampicin
rpoC 762407 c.-963G>C upstream_gene_variant 0.15 rifampicin
rpoB 762410 c.2604T>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762416 c.2610A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762857 c.3051C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762860 c.3054G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762863 c.3057T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>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
rpoC 764116 c.747C>T synonymous_variant 0.97 rifampicin Not assoc w R - Interim
rpoC 764365 c.996C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764539 c.1170C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764548 c.1179G>C synonymous_variant 0.16 rifampicin
rpoC 764566 c.1197C>G 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
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
Rv1258c 1406243 c.1098G>A synonymous_variant 0.99 streptomycin
isoniazid
pyrazinamide
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 1471923 n.78T>C non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471925 n.80T>C non_coding_transcript_exon_variant 0.15 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471932 n.87A>G non_coding_transcript_exon_variant 0.16 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471934 n.89A>G non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471936 n.91A>G non_coding_transcript_exon_variant 0.16 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471985 n.140T>C non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471986 n.141C>T non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471996 n.151C>T non_coding_transcript_exon_variant 0.21 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472029 n.184C>T non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472041 n.196C>T non_coding_transcript_exon_variant 0.25 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472042 n.197T>C non_coding_transcript_exon_variant 0.25 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472053 n.211_212delGC non_coding_transcript_exon_variant 0.27 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.27 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.28 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.27 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472286 n.441C>G non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472287 n.442C>T non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472292 n.447A>G non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472298 n.453G>C non_coding_transcript_exon_variant 0.17 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472302 n.457_458insT non_coding_transcript_exon_variant 0.17 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472310 n.465_466insG non_coding_transcript_exon_variant 0.17 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472314 n.469A>G non_coding_transcript_exon_variant 0.17 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472315 n.470T>G non_coding_transcript_exon_variant 0.17 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472327 n.482G>A non_coding_transcript_exon_variant 0.19 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472328 n.483G>C non_coding_transcript_exon_variant 0.2 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472438 n.593T>C non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.21 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.21 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472456 n.611T>C non_coding_transcript_exon_variant 0.21 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.23 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472489 n.644A>G non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.2 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472847 n.1002G>C non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472848 n.1003T>G non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472849 n.1004C>G non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472858 n.1013G>T non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472859 n.1014G>C non_coding_transcript_exon_variant 0.19 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472860 n.1015C>G non_coding_transcript_exon_variant 0.19 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.26 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>T non_coding_transcript_exon_variant 0.15 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475573 n.1916G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475602 n.1945G>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1475603 n.1946G>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1475604 n.1947A>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1475612 n.1955G>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1475615 n.1958C>G non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475616 n.1959A>G non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475619 n.1962C>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475621 n.1964T>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1475626 n.1969delTinsCC non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475629 n.1972G>C non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475637 n.1980T>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475638 n.1981C>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475639 n.1982C>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475659 n.2002G>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1475764 n.2107A>C non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475995 n.2338G>A non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid
rrl 1475997 n.2340A>G non_coding_transcript_exon_variant 0.34 capreomycin
linezolid
rrl 1476033 n.2376T>C non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid
rrl 1476034 n.2377C>G non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid
rrl 1476035 n.2378G>C non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid
rrl 1476044 n.2387T>G non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid
rrl 1476045 n.2388G>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476088 n.2431A>C non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476103 n.2446C>A non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid
rrl 1476108 n.2451T>G non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid
rrl 1476110 n.2453G>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476256 n.2599A>C non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1476262 n.2605G>A non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476529 n.2872A>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.16 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.17 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476616 n.2959A>G non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833979 c.438T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834222 c.681T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834225 c.684C>G synonymous_variant 0.14 pyrazinamide
rpsA 1834231 c.690T>G synonymous_variant 0.13 pyrazinamide
rpsA 1834240 c.699T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834249 c.708T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834261 c.720A>G synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
rpsA 1834264 c.723G>C synonymous_variant 0.14 pyrazinamide
rpsA 1834411 c.870T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834423 c.882G>T synonymous_variant 0.16 pyrazinamide
rpsA 1834451 c.910T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834456 c.915T>G synonymous_variant 0.16 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.17 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834522 c.981C>T synonymous_variant 0.15 pyrazinamide
rpsA 1834527 p.Arg329Gln missense_variant 0.15 pyrazinamide
rpsA 1834546 c.1005T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834555 c.1014T>C synonymous_variant 0.17 pyrazinamide
rpsA 1834558 c.1017C>G synonymous_variant 0.18 pyrazinamide
rpsA 1834603 p.Glu354Asp missense_variant 0.14 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
ndh 2102193 p.Arg284Trp missense_variant 1.0 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Uncertain significance
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
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2168011 p.Ser868Arg missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2168319 p.Thr765Ile missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2168814 c.1798dupA frameshift_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
eis 2715125 p.Thr70Ala missense_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
Rv2477c 2782927 c.1116A>G synonymous_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R
amikacin Not assoc w R - Interim
Rv2681 2997325 p.Ala196Val missense_variant 1.0 capreomycin Uncertain significance
ald 3086728 c.-92C>T upstream_gene_variant 1.0 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087084 c.266delA frameshift_variant 1.0 cycloserine
Rv3083 3448783 p.Val94Ile missense_variant 1.0 ethionamide Uncertain significance
lpqB 3623372 c.1539G>C synonymous_variant 1.0 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
lpqB 3623730 p.Ser394Leu missense_variant 1.0 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 1.0 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
mtrB 3626995 c.-382C>A upstream_gene_variant 0.12 bedaquiline
rifampicin
rpoA 3877968 c.540C>G synonymous_variant 0.13 rifampicin
rpoA 3877971 p.Asp179Glu missense_variant 0.13 rifampicin Uncertain significance
rpoA 3877974 c.534G>C synonymous_variant 0.13 rifampicin
rpoA 3878842 c.-335G>T upstream_gene_variant 0.14 rifampicin
rpoA 3878853 c.-346G>A upstream_gene_variant 0.14 rifampicin
rpoA 3878873 c.-366G>A upstream_gene_variant 0.13 rifampicin
rpoA 3878878 c.-371T>C upstream_gene_variant 0.13 rifampicin Uncertain significance
rpoA 3878938 c.-431T>C upstream_gene_variant 0.13 rifampicin
rpoA 3878947 c.-440G>T upstream_gene_variant 0.14 rifampicin
rpoA 3879154 c.-647T>C upstream_gene_variant 1.0 rifampicin
clpC1 4038403 c.2302T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4038896 c.1809C>T synonymous_variant 0.14 pyrazinamide
clpC1 4038908 c.1797C>G synonymous_variant 0.14 pyrazinamide
clpC1 4038911 c.1794G>T synonymous_variant 0.12 pyrazinamide
clpC1 4038917 c.1788C>T synonymous_variant 0.12 pyrazinamide
clpC1 4038923 c.1782A>G synonymous_variant 0.13 pyrazinamide
clpC1 4038926 c.1779G>A synonymous_variant 0.13 pyrazinamide
clpC1 4040480 c.225T>C synonymous_variant 0.13 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
glpK 4138977 p.Gly260Ala missense_variant 1.0 ethambutol Not assoc w R
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242970 c.3108C>T synonymous_variant 0.98 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246551 p.Asn13Ser missense_variant 1.0 ethambutol Not assoc w R
embB 4246864 c.351C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
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