TB-Profiler result

Run: ERR9992784
Summary

Run ID: ERR9992784

Sample name:

Date: 2024-04-15T07:21:42.150036

Number of reads: 3086396

Percentage reads mapped: 67.8

Median coverage: 95.0

Strain: lineage2.2.2

Spoligotype:

Drug-resistance: XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 1.0
lineage2.2.2 East-Asian (Beijing) RD105;RD207 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.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)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Cys14Arg Assoc w R
streptomycin rrs n.514A>C Assoc w R
gid p.Leu79Ser Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
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 inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
ethA p.Ala381Pro Uncertain significance Mutation from literature
clofazimine mmpR5 p.Cys46Arg Assoc w R - Interim Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 p.Cys46Arg Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV. Can only confer resistance if genetically linked to a functional MmpL5
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
gyrA 7582 p.Asp94Gly missense_variant 1.0 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
mmpR5 779125 p.Cys46Arg missense_variant 1.0 bedaquiline Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV. Can only confer resistance if genetically linked to a functional MmpL5
clofazimine Assoc w R - Interim Can only confer resistance if genetically linked to a functional MmpL5
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.64 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.52 amikacin Assoc w R
kanamycin Assoc w R
capreomycin 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)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289202 p.Cys14Arg missense_variant 1.0 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol Assoc w R
ethA 4326333 p.Ala381Pro missense_variant 1.0 ethionamide Uncertain significance Mutation from literature
gid 4407967 p.Leu79Ser missense_variant 1.0 streptomycin Uncertain significance Mutation from literature
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
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 760953 p.Ile383Val missense_variant 0.1 rifampicin
rpoB 760965 c.1159_1161delATGinsCC frameshift_variant&missense_variant 0.11 rifampicin
rpoB 760968 c.1162_1164delTCGinsGC frameshift_variant&missense_variant 0.11 rifampicin
rpoB 760973 c.1167G>C synonymous_variant 0.11 rifampicin
rpoB 761015 c.1209G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761027 c.1221A>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 761037 c.1231T>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763504 c.135C>G synonymous_variant 0.1 rifampicin
rpoC 763528 c.159G>C synonymous_variant 0.12 rifampicin
rpoC 763534 c.165T>C synonymous_variant 0.12 rifampicin
rpoC 763546 c.177A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763576 c.207C>G synonymous_variant 0.13 rifampicin
rpoC 763594 c.225C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763633 c.264T>G synonymous_variant 0.16 rifampicin
rpoC 763660 c.291T>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764498 p.Ser377Ala missense_variant 0.11 rifampicin
rpoC 764539 c.1170C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764581 c.1212T>C synonymous_variant 0.14 rifampicin
rpoC 764582 p.Leu405Met missense_variant 0.15 rifampicin
rpoC 764611 c.1242G>C synonymous_variant 0.19 rifampicin
rpoC 764623 c.1254C>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764644 c.1275G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764662 c.1293G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764695 c.1326T>C synonymous_variant 0.15 rifampicin
rpoC 764706 p.Leu446Gln missense_variant 0.18 rifampicin Uncertain significance
rpoC 764737 c.1368G>C synonymous_variant 0.17 rifampicin
rpoC 764749 c.1380G>C synonymous_variant 0.14 rifampicin
rpoC 764752 c.1383G>C synonymous_variant 0.14 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 764780 c.1411_1412delAGinsTC synonymous_variant 0.12 rifampicin
rpoC 764791 c.1422C>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764797 c.1428G>C synonymous_variant 0.12 rifampicin
rpoC 764817 p.Val483Gly missense_variant 0.92 rifampicin Uncertain significance
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
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
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.12 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.16 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472133 n.288G>A non_coding_transcript_exon_variant 0.49 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.51 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.51 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.52 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.51 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.49 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.52 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.52 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.51 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472286 n.441C>G non_coding_transcript_exon_variant 0.35 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472289 n.444T>G non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472290 n.445C>G non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472298 n.453_468delGTCCGGGTTCTCTCGGinsCGAA non_coding_transcript_exon_variant 0.25 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472315 n.470T>G non_coding_transcript_exon_variant 0.33 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472324 n.479G>C non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472325 n.480G>C non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472328 n.483G>C non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472338 n.493A>G non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472379 n.534T>C non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.28 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.28 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Uncertain significance
rrs 1472435 n.590T>C non_coding_transcript_exon_variant 0.29 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472436 n.591G>T non_coding_transcript_exon_variant 0.29 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472437 n.592T>G non_coding_transcript_exon_variant 0.29 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472446 n.601T>G non_coding_transcript_exon_variant 0.28 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472448 n.603T>C non_coding_transcript_exon_variant 0.28 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472460 n.615T>C non_coding_transcript_exon_variant 0.29 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.29 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472466 n.621C>T non_coding_transcript_exon_variant 0.28 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472467 n.622G>C non_coding_transcript_exon_variant 0.29 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472473 n.628G>T non_coding_transcript_exon_variant 0.31 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472474 n.629C>G non_coding_transcript_exon_variant 0.31 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472492 n.648_651delTACT non_coding_transcript_exon_variant 0.23 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472498 n.656_657insTAGG non_coding_transcript_exon_variant 0.23 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472507 n.662C>A non_coding_transcript_exon_variant 0.35 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472517 n.672T>C non_coding_transcript_exon_variant 0.37 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.4 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472545 n.700A>G non_coding_transcript_exon_variant 0.39 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472571 n.726G>T non_coding_transcript_exon_variant 0.33 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472582 n.737G>T non_coding_transcript_exon_variant 0.32 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472583 n.738T>G non_coding_transcript_exon_variant 0.32 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.54 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.51 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472673 n.828_829delTTinsG non_coding_transcript_exon_variant 0.46 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472686 n.841G>A non_coding_transcript_exon_variant 0.44 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.44 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.43 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.41 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.41 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.27 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.26 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.26 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.31 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.39 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.47 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473062 n.1217T>G non_coding_transcript_exon_variant 0.49 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473065 n.1220C>A non_coding_transcript_exon_variant 0.5 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.49 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.51 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.49 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.49 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.49 streptomycin Uncertain significance
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473262 n.1417T>C non_coding_transcript_exon_variant 0.48 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.45 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473283 n.1438T>C non_coding_transcript_exon_variant 0.44 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473292 n.1447_1449delGGAinsTGGG non_coding_transcript_exon_variant 0.37 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.38 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473314 n.1469A>G non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.31 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474483 n.826C>G non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474508 n.851C>T non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 0.11 capreomycin
linezolid
rrl 1474529 n.872A>G non_coding_transcript_exon_variant 0.11 capreomycin
linezolid
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474540 n.883T>C non_coding_transcript_exon_variant 0.11 capreomycin
linezolid
rrl 1474541 n.884G>T non_coding_transcript_exon_variant 0.11 capreomycin
linezolid
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 0.11 capreomycin
linezolid
rrl 1474551 n.894G>C non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474558 n.901G>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
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 0.31 capreomycin Uncertain significance
linezolid
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.49 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474709 n.1053_1056delTGGT non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474717 n.1060_1061insGTGAG non_coding_transcript_exon_variant 0.4 capreomycin
linezolid
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.51 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>T non_coding_transcript_exon_variant 0.48 capreomycin
linezolid
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>C non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.37 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475550 n.1893A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475571 n.1914A>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475586 n.1929C>T non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475706 n.2049A>C non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475782 n.2125T>C non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1475788 n.2131C>G non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.37 capreomycin
linezolid
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475983 n.2326T>C non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.18 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475989 n.2332T>C non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1475991 n.2334T>C non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1475993 n.2336C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475996 n.2339T>A non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475997 n.2340A>G non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1476000 n.2343G>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1476001 n.2344T>C non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid
rrl 1476032 n.2375C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid
rrl 1476033 n.2376T>C non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid
rrl 1476034 n.2377C>G non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid
rrl 1476045 n.2388G>C non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476060 n.2403T>G non_coding_transcript_exon_variant 0.34 capreomycin
linezolid
rrl 1476076 n.2419A>G non_coding_transcript_exon_variant 0.34 capreomycin
linezolid
rrl 1476081 n.2424A>T non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1476085 n.2428G>A non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid
rrl 1476088 n.2431A>G non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1476095 n.2439delT non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1476099 n.2442A>C non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476255 n.2598A>G non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.39 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476267 n.2610G>T non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1476268 n.2611A>G non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1476275 n.2618T>C non_coding_transcript_exon_variant 0.39 capreomycin
linezolid
rrl 1476276 n.2619C>A non_coding_transcript_exon_variant 0.39 capreomycin
linezolid
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476298 n.2641C>A non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476309 n.2652G>T non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1476325 n.2668A>C non_coding_transcript_exon_variant 0.52 capreomycin
linezolid
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.51 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.47 capreomycin
linezolid
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.4 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid
rrl 1476524 n.2867delCinsAGG non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1476529 n.2872A>T non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476531 n.2874T>G non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1476537 n.2880_2883delAAACinsGT non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1476573 n.2916A>G non_coding_transcript_exon_variant 0.3 capreomycin
linezolid Uncertain significance
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.2 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476596 n.2939C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833721 c.180A>G synonymous_variant 0.13 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.13 pyrazinamide
rpsA 1833733 c.192C>G synonymous_variant 0.13 pyrazinamide
rpsA 1833734 p.Ala65Ser missense_variant 0.13 pyrazinamide
rpsA 1833739 c.198C>G synonymous_variant 0.15 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.15 pyrazinamide
rpsA 1833748 c.207C>G synonymous_variant 0.15 pyrazinamide
rpsA 1833769 c.228C>G synonymous_variant 0.15 pyrazinamide
rpsA 1833781 c.240T>C synonymous_variant 0.11 pyrazinamide
rpsA 1833782 p.Ser81Ala missense_variant 0.11 pyrazinamide
rpsA 1833835 c.294C>T synonymous_variant 0.11 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.11 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
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 2063078 c.1650dupG frameshift_variant 0.84 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
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 2221939 p.Arg409Gln missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
thyX 3067964 c.-19C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
thyA 3074243 c.228dupA frameshift_variant 1.0 para-aminosalicylic_acid
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
clpC1 4040976 c.-272T>G upstream_gene_variant 1.0 pyrazinamide
glpK 4139947 c.-192C>A upstream_gene_variant 1.0 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
aftB 4267647 p.Asp397Gly missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269089 p.Ala249Thr missense_variant 1.0 ethambutol Uncertain significance
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
whiB6 4338794 c.-273A>G upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R