TB-Profiler result

Run: ERR4813263
Summary

Run ID: ERR4813263

Sample name:

Date: 2024-04-16T02:29:41.401599

Number of reads: 2671239

Percentage reads mapped: 69.56

Median coverage: 83.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 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.Ser428Thr Assoc w R - Interim
p.Ser441Ala Assoc w R - Interim
p.Leu464Met Mutation from literature
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol
pyrazinamide
streptomycin rrs n.799C>T Uncertain significance Mutation from literature
gid p.Gln127* Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1402C>A Uncertain significance Mutation from literature
capreomycin rrs n.1402C>A Uncertain significance Mutation from literature
kanamycin rrs n.1402C>A Uncertain significance Mutation from literature
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
rpoB 761089 p.Ser428Thr missense_variant 0.11 rifampicin Assoc w R - Interim
rpoB 761127 p.Ser441Ala missense_variant 0.18 rifampicin Assoc w R - Interim
rpoB 761196 p.Leu464Met missense_variant 0.17 rifampicin Mutation from literature
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.45 streptomycin Uncertain significance Mutation from literature
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.3 amikacin Uncertain significance Mutation from literature
kanamycin Uncertain significance Mutation from literature
capreomycin Uncertain significance Mutation from literature
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)
gid 4407824 p.Gln127* stop_gained 1.0 streptomycin 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 371 p.Pro124Leu missense_variant 1.0 isoniazid Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoB 761027 c.1221A>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 761037 c.1231_1233delTTGinsCC frameshift_variant&missense_variant 0.13 rifampicin
rpoB 761051 c.1245G>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761054 c.1248G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761057 c.1251G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761084 c.1278C>A synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.11 rifampicin
rpoB 761102 c.1296A>G synonymous_variant 0.12 rifampicin
rpoB 761111 c.1305C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761126 c.1320G>C synonymous_variant 0.18 rifampicin
rpoB 761132 c.1326G>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761133 c.1327T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761150 c.1344A>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761153 c.1347G>C synonymous_variant 0.19 rifampicin
rpoB 761165 c.1359G>A synonymous_variant 0.18 rifampicin
rpoB 761174 c.1368T>C synonymous_variant 0.15 rifampicin
rpoB 761177 c.1371G>C synonymous_variant 0.14 rifampicin
rpoB 761180 c.1374A>G synonymous_variant 0.14 rifampicin
rpoB 761183 c.1377T>C synonymous_variant 0.14 rifampicin
rpoB 761186 p.Glu460Asp missense_variant 0.14 rifampicin Uncertain significance
rpoB 761189 c.1383T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761192 c.1386C>G synonymous_variant 0.15 rifampicin
rpoB 761194 p.Gly463Ala missense_variant 0.15 rifampicin
rpoB 761207 c.1401C>A synonymous_variant 0.24 rifampicin
rpoB 761213 c.1407G>C synonymous_variant 0.25 rifampicin
rpoB 761234 c.1428G>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 761249 c.1443A>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 761255 c.1449T>C synonymous_variant 0.22 rifampicin
rpoB 761261 c.1455G>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761264 c.1458C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761276 c.1470G>C synonymous_variant 0.16 rifampicin
rpoB 761973 p.His723Tyr missense_variant 0.14 rifampicin
rpoB 761980 p.Tyr725Phe missense_variant 0.15 rifampicin
rpoB 761999 c.2193G>C synonymous_variant 0.14 rifampicin
rpoB 762002 c.2196C>G synonymous_variant 0.15 rifampicin
rpoB 762003 c.2197_2199delAACinsCG frameshift_variant&missense_variant 0.15 rifampicin
rpoB 762011 c.2205G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762015 c.2209_2211delGAAinsCG frameshift_variant&missense_variant 0.15 rifampicin
rpoB 762020 p.Glu738Asp missense_variant 0.15 rifampicin
rpoB 762026 c.2220G>C synonymous_variant 0.15 rifampicin
rpoB 762030 p.Thr742Ser missense_variant 0.15 rifampicin
rpoB 762053 c.2247T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762057 p.Ile751Val missense_variant 0.16 rifampicin Uncertain significance
rpoB 762062 c.2256T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762065 c.2259T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762074 c.2268C>G synonymous_variant 0.17 rifampicin
rpoB 762080 c.2274G>C synonymous_variant 0.17 rifampicin
rpoB 762086 c.2280G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 762101 c.2295C>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 762119 c.2313C>G synonymous_variant 0.14 rifampicin
rpoB 762120 p.Asp772Pro missense_variant 0.14 rifampicin
rpoB 762125 p.Glu773Asp missense_variant 0.14 rifampicin
rpoB 762127 p.Val774Ala missense_variant 0.14 rifampicin
rpoB 762131 c.2325C>G synonymous_variant 0.14 rifampicin
rpoB 762140 c.2334G>C synonymous_variant 0.14 rifampicin
rpoB 762143 c.2337T>C synonymous_variant 0.14 rifampicin
rpoB 762146 p.Glu780Asp missense_variant 0.14 rifampicin
rpoB 762149 c.2343G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762156 c.2350_2352delGTGinsAC frameshift_variant&missense_variant 0.15 rifampicin
rpoB 762167 c.2361T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762176 c.2370T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762177 p.Arg791Thr missense_variant 0.13 rifampicin
rpoB 762185 c.2379G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762194 c.2388G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762233 c.2427G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762959 c.3153G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762962 c.3156C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 762980 c.-390T>C upstream_gene_variant 0.16 rifampicin
rpoC 762983 c.-387C>T upstream_gene_variant 0.16 rifampicin
rpoC 762989 c.-381G>C upstream_gene_variant 0.17 rifampicin
rpoB 762995 c.3189G>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 763004 c.3198G>A synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 763005 p.Cys1067Val missense_variant 0.16 rifampicin
rpoB 763014 c.3208_3210delATGinsCC frameshift_variant&missense_variant 0.16 rifampicin
rpoB 763017 p.Gln1071Glu missense_variant 0.16 rifampicin
rpoB 763028 c.3222T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 763034 c.3228C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 763040 c.3234C>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763043 c.-327G>C upstream_gene_variant 0.21 rifampicin
rpoB 763053 c.3247T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763058 c.-312C>G upstream_gene_variant 0.19 rifampicin
rpoC 763528 c.159G>T synonymous_variant 0.22 rifampicin
rpoC 763531 c.162G>C synonymous_variant 0.22 rifampicin Not assoc w R
rpoC 763534 c.165T>C synonymous_variant 0.21 rifampicin
rpoC 763537 c.168C>T synonymous_variant 0.21 rifampicin
rpoC 763546 c.177A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763550 p.Tyr61Ala missense_variant 0.19 rifampicin
rpoC 763558 c.189C>A synonymous_variant 0.21 rifampicin
rpoC 763570 c.201G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763597 c.228G>A synonymous_variant 0.21 rifampicin
rpoC 763621 c.252C>T synonymous_variant 0.21 rifampicin
rpoC 763633 c.264T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763642 c.273G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763660 c.291T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 763666 c.297G>T synonymous_variant 0.23 rifampicin
rpoC 763672 c.303C>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763696 c.327T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 763699 c.330G>C synonymous_variant 0.22 rifampicin
rpoC 763708 c.339G>C synonymous_variant 0.21 rifampicin
rpoC 763709 c.340C>T synonymous_variant 0.2 rifampicin
rpoC 763714 c.345G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763723 c.354G>C synonymous_variant 0.21 rifampicin
rpoC 763729 c.360G>C synonymous_variant 0.21 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.21 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.19 rifampicin
rpoC 763747 c.378G>A synonymous_variant 0.18 rifampicin
rpoC 763751 p.Ile128Val missense_variant 0.18 rifampicin
rpoC 764521 c.1152T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764527 c.1158C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764533 c.1164C>A synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764536 c.1167G>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764539 c.1170C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764542 c.1173C>G synonymous_variant 0.12 rifampicin
rpoC 764548 c.1179G>A synonymous_variant 0.12 rifampicin
rpoC 764560 c.1191T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>C synonymous_variant 0.14 rifampicin
rpoC 764581 c.1212T>C synonymous_variant 0.14 rifampicin
rpoC 764582 p.Leu405Met missense_variant 0.15 rifampicin
rpoC 764611 c.1242G>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764662 c.1293G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764668 c.1299C>T synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764679 p.Lys437Ser missense_variant 0.22 rifampicin
rpoC 764683 c.1314G>C synonymous_variant 0.22 rifampicin
rpoC 764690 p.Cys441Ala missense_variant 0.22 rifampicin
rpoC 764705 p.Leu446Thr missense_variant 0.22 rifampicin
rpoC 764713 c.1344G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764746 c.1377G>C synonymous_variant 0.27 rifampicin
rpoC 764752 c.1383G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764755 c.1386C>T synonymous_variant 0.23 rifampicin
rpoC 764780 c.1411_1413delAGCinsTCG synonymous_variant 0.17 rifampicin
rpoC 764791 c.1422C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764797 c.1428G>C synonymous_variant 0.15 rifampicin
rpoC 764803 c.1434C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764808 p.Arg480His missense_variant 0.14 rifampicin
rpoC 764812 c.1443C>G synonymous_variant 0.14 rifampicin
rpoC 764815 c.1446A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764824 c.1455T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764827 c.1458G>C synonymous_variant 0.12 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
mmpS5 779588 c.-683C>T upstream_gene_variant 1.0 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471997 n.152T>C non_coding_transcript_exon_variant 0.16 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472023 n.178G>C non_coding_transcript_exon_variant 0.26 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472027 n.182C>T non_coding_transcript_exon_variant 0.17 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472028 n.183A>G non_coding_transcript_exon_variant 0.27 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472030 n.185G>C non_coding_transcript_exon_variant 0.28 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472034 n.189T>C non_coding_transcript_exon_variant 0.27 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472043 n.198T>G non_coding_transcript_exon_variant 0.26 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472053 n.211_212delGC non_coding_transcript_exon_variant 0.25 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472057 n.212C>T non_coding_transcript_exon_variant 0.25 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.25 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472062 n.217G>T non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472067 n.222G>T non_coding_transcript_exon_variant 0.25 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472068 n.223T>G non_coding_transcript_exon_variant 0.25 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.27 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.27 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472092 n.247C>T non_coding_transcript_exon_variant 0.31 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.33 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.31 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472120 n.275G>A non_coding_transcript_exon_variant 0.38 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.31 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.29 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Uncertain significance
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.29 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472245 n.400C>A non_coding_transcript_exon_variant 0.28 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.28 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472279 n.434T>G non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472286 n.441C>G non_coding_transcript_exon_variant 0.13 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472484 n.639A>T non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472496 n.651T>A non_coding_transcript_exon_variant 0.15 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472506 n.661A>T non_coding_transcript_exon_variant 0.27 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472572 n.727T>A non_coding_transcript_exon_variant 0.4 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.43 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472591 n.746G>A non_coding_transcript_exon_variant 0.43 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.32 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.39 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473047 n.1202C>T non_coding_transcript_exon_variant 0.36 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.29 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.26 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473091 n.1246G>A non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473093 n.1248C>A non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473094 n.1249T>G non_coding_transcript_exon_variant 0.24 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473099 n.1254T>A non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473100 n.1255G>C non_coding_transcript_exon_variant 0.25 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.25 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473109 n.1264T>G non_coding_transcript_exon_variant 0.25 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473110 n.1265T>C non_coding_transcript_exon_variant 0.25 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.3 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 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.34 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.34 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473157 n.1312C>T non_coding_transcript_exon_variant 0.32 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.31 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.29 streptomycin Uncertain significance
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473298 n.1453A>G non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473305 n.1460G>T non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1474263 n.606G>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474286 n.629_630delCTinsACC non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474289 n.632C>G non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474291 n.634T>G non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474293 n.637_650delCCTCTCCGGAGGAG non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474310 n.655delG non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474351 n.694G>C non_coding_transcript_exon_variant 0.1 capreomycin Uncertain significance
linezolid
rrl 1474359 n.702C>G non_coding_transcript_exon_variant 0.1 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474476 n.819C>G non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474483 n.826C>G non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474495 n.838G>A non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474496 n.839C>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474498 n.841G>A non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474505 n.848C>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474508 n.851C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474520 n.863A>C non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1474551 n.894G>C non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474558 n.901G>T non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474584 n.927C>T non_coding_transcript_exon_variant 0.51 capreomycin
linezolid
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474692 n.1035G>A non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474694 n.1037C>T non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1474709 n.1053_1056delTGGT non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474717 n.1060_1061insGGTTC non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1474734 n.1077G>A non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1474736 n.1079C>T non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.17 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.17 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474783 n.1126G>A non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474806 n.1149A>G non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1474822 n.1165G>T non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474905 n.1248T>A non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1475637 n.1980T>G non_coding_transcript_exon_variant 0.1 capreomycin Uncertain significance
linezolid
rrl 1475638 n.1981C>G non_coding_transcript_exon_variant 0.1 capreomycin Uncertain significance
linezolid
rrl 1475649 n.1992A>G non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475650 n.1993A>G non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1475655 n.1998T>A non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475659 n.2002G>A non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475672 n.2015C>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475696 n.2039T>A non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid
rrl 1475697 n.2040C>T non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475703 n.2046A>T non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 0.51 capreomycin
linezolid
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475963 n.2306G>A non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.44 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.51 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.38 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rpsA 1834327 c.786G>C synonymous_variant 0.14 pyrazinamide
rpsA 1834378 c.837T>G synonymous_variant 0.1 pyrazinamide
rpsA 1834387 c.846C>T synonymous_variant 0.1 pyrazinamide
rpsA 1834395 p.Arg285Gln missense_variant 0.14 pyrazinamide
rpsA 1834405 c.864C>G synonymous_variant 0.14 pyrazinamide
rpsA 1834411 c.870T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834416 p.Ala292Val missense_variant 0.15 pyrazinamide
rpsA 1834423 c.882G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834435 c.894G>C synonymous_variant 0.16 pyrazinamide
rpsA 1834451 c.910_912delTTGinsCC frameshift_variant&missense_variant 0.15 pyrazinamide Uncertain significance
rpsA 1834465 c.924T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.14 pyrazinamide
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2752c 3065926 p.Ala89Glu missense_variant 1.0 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
alr 3840764 c.657G>C synonymous_variant 1.0 cycloserine
clpC1 4039757 c.948A>G synonymous_variant 0.12 pyrazinamide
clpC1 4039766 c.939T>C synonymous_variant 0.14 pyrazinamide
clpC1 4039773 p.Lys311Met missense_variant 0.14 pyrazinamide
clpC1 4039778 c.927A>G synonymous_variant 0.14 pyrazinamide
clpC1 4039781 c.924G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039805 c.900C>T synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
clpC1 4039808 c.897G>A synonymous_variant 0.14 pyrazinamide
clpC1 4039817 c.888A>T synonymous_variant 0.12 pyrazinamide
clpC1 4039820 c.885T>G synonymous_variant 0.11 pyrazinamide
clpC1 4039826 c.879C>G synonymous_variant 0.11 pyrazinamide
clpC1 4039829 c.874_876delTTGinsCC frameshift_variant&missense_variant 0.11 pyrazinamide
clpC1 4039838 c.865_867delCTGinsAC frameshift_variant&missense_variant 0.11 pyrazinamide
clpC1 4039850 c.855T>C synonymous_variant 0.11 pyrazinamide
clpC1 4039853 c.852G>C synonymous_variant 0.11 pyrazinamide
clpC1 4039865 c.840T>A synonymous_variant 0.1 pyrazinamide
clpC1 4039875 p.Asn277Arg missense_variant 0.12 pyrazinamide
clpC1 4039898 c.807C>G synonymous_variant 0.17 pyrazinamide
clpC1 4039913 c.792C>T synonymous_variant 0.14 pyrazinamide
clpC1 4039929 c.775_776delAGinsTC synonymous_variant 0.13 pyrazinamide
clpC1 4039931 c.774T>G synonymous_variant 0.13 pyrazinamide
clpC1 4039934 c.771G>C synonymous_variant 0.13 pyrazinamide
clpC1 4039937 c.768G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039940 c.765G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039946 c.759A>G synonymous_variant 0.14 pyrazinamide
clpC1 4039949 c.756G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039952 c.753T>C synonymous_variant 0.15 pyrazinamide
clpC1 4039955 c.750G>C synonymous_variant 0.15 pyrazinamide
clpC1 4039976 p.Lys243Thr missense_variant 0.13 pyrazinamide
clpC1 4039982 p.Thr241Ile missense_variant 0.13 pyrazinamide
clpC1 4039991 c.714G>C synonymous_variant 0.13 pyrazinamide
clpC1 4040002 p.His235Asn missense_variant 0.14 pyrazinamide
clpC1 4040003 c.702G>C synonymous_variant 0.14 pyrazinamide
clpC1 4040015 c.690G>C synonymous_variant 0.12 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338214 p.Gly103Val missense_variant 1.0 capreomycin
amikacin
kanamycin
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R