TB-Profiler result

Run: SRR18913742
Summary

Run ID: SRR18913742

Sample name:

Date: 2024-10-04T22:16:48.347576

Number of reads: 720773

Percentage reads mapped: 57.49

Median coverage: 26.0

Strain: lineage3.1.3

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 1.0
lineage3.1.3 East-African-Indian RD750 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
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
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 8894 c.1593C>G synonymous_variant 0.24 levofloxacin
moxifloxacin
gyrA 8897 c.1596T>C synonymous_variant 0.24 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8903 c.1602T>C synonymous_variant 0.24 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8915 c.1614A>G synonymous_variant 0.31 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
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 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
nusG 734261 p.Thr3Asn missense_variant 1.0 rifampicin Not assoc w R
rpoB 760460 c.654G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 760475 c.669A>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 760478 c.672C>T synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 760481 c.675G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 760484 c.678A>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 760487 c.681G>C synonymous_variant 0.3 rifampicin
rpoB 760511 c.705G>C synonymous_variant 0.32 rifampicin
rpoB 760532 c.726T>C synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoB 760533 p.Val243Leu missense_variant 0.42 rifampicin
rpoB 760541 c.735G>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 760547 c.741G>C synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoB 760553 c.747C>G synonymous_variant 0.33 rifampicin
rpoB 760565 c.759A>G synonymous_variant 0.32 rifampicin
rpoB 760568 c.762G>C synonymous_variant 0.32 rifampicin
rpoB 760571 c.765G>C synonymous_variant 0.3 rifampicin
rpoB 760589 c.783C>G synonymous_variant 0.29 rifampicin
rpoB 760591 p.Val262Ala missense_variant 0.28 rifampicin
rpoB 760611 c.805_807delTTGinsCTC synonymous_variant 0.27 rifampicin
rpoB 760634 c.828T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 761006 c.1200C>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 761015 c.1209G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 761150 c.1344A>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoB 761162 c.1356G>C synonymous_variant 0.37 rifampicin
rpoB 761165 c.1359G>C synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoB 761171 c.1365C>T synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoB 761180 c.1374A>G synonymous_variant 0.38 rifampicin
rpoB 761189 c.1383T>C synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoB 761195 c.1389G>C synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoB 761198 c.1392G>C synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoB 761213 c.1407G>C synonymous_variant 0.44 rifampicin
rpoB 761234 c.1428G>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoB 761249 c.1443A>G synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoB 761273 c.1467T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 762014 c.2208C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762017 c.2211A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 762167 c.2361T>C synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoB 762176 c.2370T>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 762185 c.2379G>C synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoB 762218 c.2412T>C synonymous_variant 0.39 rifampicin
rpoB 762233 c.2427G>C synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoB 762245 c.2439G>C synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoB 762251 c.2445G>C synonymous_variant 0.37 rifampicin
rpoB 762254 c.2448T>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 762257 c.2451C>G synonymous_variant 0.37 rifampicin
rpoB 762275 c.2469C>G synonymous_variant 0.23 rifampicin
rpoB 762284 c.2478G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 762434 c.2628T>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 762947 c.-423C>G upstream_gene_variant 0.24 rifampicin
rpoB 762962 c.3156C>T synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 762989 c.-381G>C upstream_gene_variant 0.28 rifampicin
rpoB 762995 c.3189G>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 763013 c.-357C>G upstream_gene_variant 0.22 rifampicin
rpoC 763022 c.-348C>G upstream_gene_variant 0.22 rifampicin
rpoB 763028 c.3222T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763052 c.-318G>C upstream_gene_variant 0.21 rifampicin
rpoC 763053 c.-317_-315delTTGinsCTC upstream_gene_variant 0.21 rifampicin
rpoB 763088 c.3282C>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 763507 c.138G>C synonymous_variant 0.23 rifampicin
rpoC 763528 c.159G>C synonymous_variant 0.2 rifampicin
rpoC 764239 c.870T>C synonymous_variant 0.24 rifampicin
rpoC 764257 c.888G>C synonymous_variant 0.29 rifampicin
rpoC 764263 c.894G>C synonymous_variant 0.32 rifampicin
rpoC 764266 c.897T>C synonymous_variant 0.32 rifampicin
rpoC 764278 c.909A>G synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 764297 p.Met310Leu missense_variant 0.3 rifampicin
rpoC 764308 c.939G>C synonymous_variant 0.32 rifampicin
rpoC 764320 c.951C>G synonymous_variant 0.32 rifampicin
rpoC 764353 c.984G>C synonymous_variant 0.32 rifampicin
rpoC 764365 c.996C>T synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 764387 c.1018T>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 764398 c.1029G>C synonymous_variant 0.26 rifampicin
rpoC 764404 c.1035C>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 764428 c.1059G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764431 c.1062G>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764434 c.1065A>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764435 c.1066_1068delAGGinsCGA synonymous_variant 0.22 rifampicin
rpoC 764446 c.1077T>C synonymous_variant 0.21 rifampicin
rpoC 764449 c.1080G>C synonymous_variant 0.21 rifampicin
rpoC 764452 c.1083T>C synonymous_variant 0.21 rifampicin
rpoC 764458 c.1089G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764461 c.1092A>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764497 c.1128A>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764503 c.1134G>C synonymous_variant 0.35 rifampicin
rpoC 764521 c.1152T>C synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoC 764536 c.1167G>T synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 764539 c.1170C>G synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 764548 c.1179G>A synonymous_variant 0.37 rifampicin
rpoC 764560 c.1191T>C synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>C synonymous_variant 0.36 rifampicin
rpoC 764632 c.1263T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764635 c.1266C>G synonymous_variant 0.34 rifampicin
rpoC 764650 c.1281G>T synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 764662 c.1293G>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 764665 c.1296C>G synonymous_variant 0.35 rifampicin
rpoC 764695 c.1326T>C synonymous_variant 0.3 rifampicin
rpoC 764701 c.1332C>G synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 764716 c.1347G>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 764780 c.1411_1413delAGCinsTCG synonymous_variant 0.19 rifampicin
rpoC 764791 c.1422C>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764797 c.1428G>C synonymous_variant 0.21 rifampicin
rpoC 764803 c.1434C>G synonymous_variant 0.22 rifampicin
rpoC 764809 c.1440C>G synonymous_variant 0.18 rifampicin
rpoC 764812 c.1443C>G synonymous_variant 0.18 rifampicin
rpoC 764815 c.1446A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764824 c.1455T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764827 c.1458G>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781802 c.243G>C synonymous_variant 0.19 streptomycin
rpsL 781805 c.246G>C synonymous_variant 0.18 streptomycin
rpsL 781808 c.249C>T synonymous_variant 0.18 streptomycin
rpsL 781814 c.255C>T synonymous_variant 0.21 streptomycin
rpsL 781817 c.258G>T synonymous_variant 0.18 streptomycin
rpsL 781829 c.270G>C synonymous_variant 0.2 streptomycin
rpsL 781832 c.273T>G synonymous_variant 0.2 streptomycin
rpsL 781838 c.279G>T synonymous_variant 0.21 streptomycin
rpsL 781865 c.306G>C synonymous_variant 0.21 streptomycin
rpsL 781868 c.309T>C synonymous_variant 0.21 streptomycin
rpsL 781871 c.312G>C synonymous_variant 0.2 streptomycin
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.96 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406613 p.Glu243Ala missense_variant 0.97 streptomycin Uncertain significance
pyrazinamide Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.56 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.59 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.57 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.59 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.59 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.57 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.53 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.41 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473081 n.1236C>G non_coding_transcript_exon_variant 0.46 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473082 n.1237G>C non_coding_transcript_exon_variant 0.5 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.59 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.57 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.55 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.53 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.5 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.49 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.49 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473129 n.1284C>G non_coding_transcript_exon_variant 0.52 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473130 n.1285G>C non_coding_transcript_exon_variant 0.52 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.48 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.52 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474674 n.1017A>C non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1474675 n.1018C>A non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474709 n.1053_1056delTGGT non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474718 n.1061_1062delAGinsGTGAGAA non_coding_transcript_exon_variant 0.67 capreomycin
linezolid
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474822 n.1165G>C non_coding_transcript_exon_variant 0.54 capreomycin
linezolid
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475713 n.2056C>T non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid
rrl 1475758 n.2101_2102delACinsG non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid
rrl 1475768 n.2111_2112delGTinsC non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.54 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476087 n.2430C>T non_coding_transcript_exon_variant 0.48 capreomycin
linezolid
rrl 1476089 n.2432T>C non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1476091 n.2434_2435insC non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1476099 n.2442A>G non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476103 n.2446C>A non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid
rrl 1476105 n.2450delA non_coding_transcript_exon_variant 0.48 capreomycin
linezolid
rrl 1476110 n.2453G>T non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.5 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.52 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.5 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.51 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.54 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476266 n.2609G>A non_coding_transcript_exon_variant 0.41 capreomycin
linezolid
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.63 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476300 n.2643G>A non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.59 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.47 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.48 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476614 n.2957A>T non_coding_transcript_exon_variant 0.47 capreomycin
linezolid
rrl 1476616 n.2959A>G non_coding_transcript_exon_variant 0.43 capreomycin
linezolid
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.43 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833874 c.333T>C synonymous_variant 0.26 pyrazinamide
rpsA 1833886 c.345C>G synonymous_variant 0.24 pyrazinamide
rpsA 1833894 p.Ala118Glu missense_variant 0.24 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.33 pyrazinamide
rpsA 1833940 c.399C>G synonymous_variant 0.33 pyrazinamide
rpsA 1833952 c.411C>T synonymous_variant 0.3 pyrazinamide
rpsA 1833955 c.414G>C synonymous_variant 0.29 pyrazinamide
rpsA 1833961 c.420C>G synonymous_variant 0.29 pyrazinamide
rpsA 1833970 c.429G>C synonymous_variant 0.25 pyrazinamide
rpsA 1833973 c.432G>C synonymous_variant 0.26 pyrazinamide
rpsA 1833985 c.444G>C synonymous_variant 0.28 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.22 pyrazinamide
rpsA 1834054 c.513C>G synonymous_variant 0.31 pyrazinamide
rpsA 1834069 c.528G>C synonymous_variant 0.31 pyrazinamide
rpsA 1834093 c.552G>C synonymous_variant 0.24 pyrazinamide
rpsA 1834099 c.558C>G synonymous_variant 0.23 pyrazinamide
rpsA 1834102 c.561T>C synonymous_variant 0.23 pyrazinamide
rpsA 1834105 c.564C>T synonymous_variant 0.24 pyrazinamide
rpsA 1834108 c.567C>G synonymous_variant 0.24 pyrazinamide
rpsA 1834114 c.573G>C synonymous_variant 0.24 pyrazinamide
rpsA 1834135 c.594G>C synonymous_variant 0.23 pyrazinamide
rpsA 1834159 c.618G>A synonymous_variant 1.0 pyrazinamide Not assoc w R
rpsA 1834298 p.Gln253Thr missense_variant 0.27 pyrazinamide
rpsA 1834303 c.762T>G synonymous_variant 0.29 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.29 pyrazinamide
rpsA 1834327 c.786G>C synonymous_variant 0.29 pyrazinamide
rpsA 1834340 p.Met267Leu missense_variant 0.26 pyrazinamide Uncertain significance
rpsA 1834348 c.807T>C synonymous_variant 0.3 pyrazinamide Not assoc w R - Interim
rpsA 1834354 c.813G>C synonymous_variant 0.31 pyrazinamide Not assoc w R - Interim
rpsA 1834357 c.816T>C synonymous_variant 0.31 pyrazinamide
rpsA 1834361 c.820T>C synonymous_variant 0.31 pyrazinamide
rpsA 1834366 c.825A>G synonymous_variant 0.3 pyrazinamide Not assoc w R - Interim
rpsA 1834378 c.837T>C synonymous_variant 0.33 pyrazinamide Not assoc w R - Interim
rpsA 1834384 c.843A>G synonymous_variant 0.34 pyrazinamide
rpsA 1834387 c.846C>T synonymous_variant 0.31 pyrazinamide
rpsA 1834396 c.855G>C synonymous_variant 0.33 pyrazinamide
rpsA 1834399 p.His286Gln missense_variant 0.3 pyrazinamide
rpsA 1834408 c.867C>G synonymous_variant 0.37 pyrazinamide
rpsA 1834411 c.870T>C synonymous_variant 0.37 pyrazinamide
rpsA 1834417 c.876G>C synonymous_variant 0.39 pyrazinamide
rpsA 1834423 c.882G>C synonymous_variant 0.39 pyrazinamide
rpsA 1834435 c.894G>C synonymous_variant 0.39 pyrazinamide
rpsA 1834451 c.910_912delTTGinsCTC synonymous_variant 0.39 pyrazinamide
rpsA 1834456 c.915T>C synonymous_variant 0.42 pyrazinamide
rpsA 1834465 c.924T>C synonymous_variant 0.44 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.44 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.41 pyrazinamide
rpsA 1834501 c.960G>C synonymous_variant 0.4 pyrazinamide
rpsA 1834504 c.963G>C synonymous_variant 0.4 pyrazinamide
rpsA 1834690 c.1149T>C synonymous_variant 0.27 pyrazinamide
rpsA 1834700 p.Gln387Asn missense_variant 0.28 pyrazinamide
rpsA 1834706 p.Asn389Glu missense_variant 0.29 pyrazinamide
rpsA 1834733 p.Ala398Pro missense_variant 0.3 pyrazinamide
rpsA 1834738 c.1197A>G synonymous_variant 0.3 pyrazinamide
rpsA 1834747 c.1206A>G synonymous_variant 0.26 pyrazinamide
rpsA 1834751 p.Leu404Ile missense_variant 0.24 pyrazinamide
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
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 2222732 c.432delT frameshift_variant 0.92 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 1.0 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 1.0 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3877704 c.804G>T synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoA 3877728 c.780C>G synonymous_variant 0.28 rifampicin
rpoA 3877731 c.777G>C synonymous_variant 0.28 rifampicin
rpoA 3877743 c.765T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoA 3877746 c.762G>C synonymous_variant 0.32 rifampicin
rpoA 3877752 p.Asp252Glu missense_variant 0.33 rifampicin
rpoA 3877764 p.Ala248Ser missense_variant 0.3 rifampicin
rpoA 3877770 p.Ser246Ala missense_variant 0.3 rifampicin
rpoA 3877776 c.732T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoA 3877782 c.726T>C synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoA 3877803 c.705G>C synonymous_variant 0.36 rifampicin
rpoA 3877818 c.690A>G synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoA 3877836 c.672A>G synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoA 3877842 c.666A>C synonymous_variant 0.31 rifampicin
rpoA 3877845 c.663G>C synonymous_variant 0.31 rifampicin
rpoA 3877848 c.660C>G synonymous_variant 0.32 rifampicin
rpoA 3877856 c.652T>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoA 3877866 c.642G>C synonymous_variant 0.36 rifampicin
rpoA 3877875 c.633T>G synonymous_variant 0.37 rifampicin
rpoA 3877893 c.615C>T synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoA 3877898 p.Pro204Ala missense_variant 0.32 rifampicin
rpoA 3877900 p.Ser203Thr missense_variant 0.32 rifampicin
rpoA 3877902 p.Ile202Met missense_variant 0.32 rifampicin
rpoA 3877905 c.603A>G synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoA 3877908 c.600T>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoA 3877920 c.588G>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoA 3877935 p.Lys191Arg missense_variant 0.31 rifampicin
rpoA 3877938 c.570C>T synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoA 3877971 p.Asp179Glu missense_variant 0.25 rifampicin Uncertain significance
rpoA 3877974 c.534G>C synonymous_variant 0.26 rifampicin
clpC1 4038740 c.1965G>C synonymous_variant 0.36 pyrazinamide
clpC1 4038755 c.1950G>C synonymous_variant 0.37 pyrazinamide
clpC1 4038761 c.1944C>G synonymous_variant 0.37 pyrazinamide
clpC1 4038764 c.1941C>G synonymous_variant 0.37 pyrazinamide
clpC1 4038767 c.1938G>C synonymous_variant 0.37 pyrazinamide
clpC1 4038773 c.1932T>C synonymous_variant 0.39 pyrazinamide
clpC1 4038794 p.Ser637Thr missense_variant 0.39 pyrazinamide
clpC1 4038808 c.1896_1897insC frameshift_variant 0.44 pyrazinamide
clpC1 4038811 c.1893delT frameshift_variant 0.44 pyrazinamide
clpC1 4038836 c.1869G>C synonymous_variant 0.43 pyrazinamide
clpC1 4038845 c.1860G>C synonymous_variant 0.4 pyrazinamide
clpC1 4038860 c.1845G>C synonymous_variant 0.43 pyrazinamide Not assoc w R - Interim
clpC1 4038878 c.1827A>G synonymous_variant 0.41 pyrazinamide Not assoc w R - Interim
clpC1 4038899 c.1806C>G synonymous_variant 0.41 pyrazinamide
clpC1 4038905 c.1800A>G synonymous_variant 0.4 pyrazinamide
clpC1 4038911 c.1794G>T synonymous_variant 0.38 pyrazinamide
clpC1 4038914 c.1791G>C synonymous_variant 0.32 pyrazinamide
clpC1 4038917 c.1788C>T synonymous_variant 0.33 pyrazinamide
clpC1 4038923 c.1782A>G synonymous_variant 0.33 pyrazinamide
clpC1 4038926 c.1779G>C synonymous_variant 0.32 pyrazinamide
clpC1 4038932 c.1773G>C synonymous_variant 0.34 pyrazinamide
clpC1 4038941 c.1764G>C synonymous_variant 0.35 pyrazinamide
clpC1 4038953 c.1752A>G synonymous_variant 0.42 pyrazinamide
clpC1 4038965 c.1740T>C synonymous_variant 0.45 pyrazinamide
clpC1 4038971 c.1734T>C synonymous_variant 0.44 pyrazinamide
clpC1 4038974 c.1731T>C synonymous_variant 0.4 pyrazinamide Not assoc w R - Interim
clpC1 4038986 p.Asp573Glu missense_variant 0.44 pyrazinamide
clpC1 4038989 c.1716T>C synonymous_variant 0.44 pyrazinamide
clpC1 4038997 c.1708T>C synonymous_variant 0.46 pyrazinamide Not assoc w R - Interim
clpC1 4039004 c.1701C>G synonymous_variant 0.47 pyrazinamide
clpC1 4039007 c.1698G>C synonymous_variant 0.46 pyrazinamide
clpC1 4039016 c.1689C>G synonymous_variant 0.4 pyrazinamide
clpC1 4039022 c.1683A>G synonymous_variant 0.39 pyrazinamide
clpC1 4039025 c.1680C>G synonymous_variant 0.39 pyrazinamide
clpC1 4039034 c.1671C>G synonymous_variant 0.42 pyrazinamide
clpC1 4039037 c.1668T>C synonymous_variant 0.43 pyrazinamide
clpC1 4039079 c.1626C>G synonymous_variant 0.4 pyrazinamide Not assoc w R - Interim
clpC1 4039085 c.1620A>G synonymous_variant 0.39 pyrazinamide
clpC1 4039091 c.1614G>C synonymous_variant 0.4 pyrazinamide
clpC1 4039094 c.1611C>G synonymous_variant 0.38 pyrazinamide
clpC1 4039097 c.1608G>T synonymous_variant 0.38 pyrazinamide
clpC1 4039100 c.1605C>G synonymous_variant 0.37 pyrazinamide
clpC1 4039106 c.1599G>T synonymous_variant 0.34 pyrazinamide
clpC1 4039112 c.1593C>G synonymous_variant 0.34 pyrazinamide
clpC1 4039118 c.1587C>G synonymous_variant 0.31 pyrazinamide
clpC1 4039121 c.1584T>C synonymous_variant 0.31 pyrazinamide
clpC1 4039124 c.1581C>G synonymous_variant 0.32 pyrazinamide
clpC1 4039142 c.1563A>G synonymous_variant 0.31 pyrazinamide
clpC1 4039145 c.1560G>C synonymous_variant 0.3 pyrazinamide
clpC1 4039169 p.Glu512Asp missense_variant 0.31 pyrazinamide
clpC1 4039172 c.1533A>G synonymous_variant 0.31 pyrazinamide
clpC1 4039178 c.1527G>C synonymous_variant 0.28 pyrazinamide
clpC1 4039181 c.1522_1524delTTGinsCTC synonymous_variant 0.29 pyrazinamide
clpC1 4039187 c.1518G>T synonymous_variant 0.27 pyrazinamide
clpC1 4039199 p.Ala502Glu missense_variant 0.22 pyrazinamide
clpC1 4039217 c.1488G>C synonymous_variant 0.19 pyrazinamide
clpC1 4039220 c.1485G>C synonymous_variant 0.17 pyrazinamide
clpC1 4039226 c.1479T>C synonymous_variant 0.18 pyrazinamide Not assoc w R - Interim
clpC1 4039616 c.1089G>C synonymous_variant 0.23 pyrazinamide
clpC1 4039622 c.1083C>T synonymous_variant 0.28 pyrazinamide
clpC1 4039642 p.Thr355Ala missense_variant 0.19 pyrazinamide
clpC1 4039649 c.1056G>C synonymous_variant 0.18 pyrazinamide
clpC1 4039652 p.Thr351Ser missense_variant 0.19 pyrazinamide
clpC1 4039661 c.1044T>C synonymous_variant 0.21 pyrazinamide
clpC1 4039670 c.1035G>C synonymous_variant 0.21 pyrazinamide
clpC1 4039673 c.1032G>C synonymous_variant 0.23 pyrazinamide
clpC1 4039724 c.981A>G synonymous_variant 0.26 pyrazinamide
clpC1 4039733 c.972G>C synonymous_variant 0.27 pyrazinamide
clpC1 4039739 c.966C>G synonymous_variant 0.26 pyrazinamide
clpC1 4039748 c.957G>C synonymous_variant 0.23 pyrazinamide
clpC1 4039751 c.954A>G synonymous_variant 0.23 pyrazinamide
clpC1 4039757 c.948A>G synonymous_variant 0.22 pyrazinamide
clpC1 4039760 c.945T>C synonymous_variant 0.23 pyrazinamide
clpC1 4039766 c.939T>C synonymous_variant 0.23 pyrazinamide
clpC1 4039769 c.936C>G synonymous_variant 0.24 pyrazinamide
clpC1 4039790 c.915C>G synonymous_variant 0.21 pyrazinamide
clpC1 4039817 c.888A>T synonymous_variant 0.18 pyrazinamide
clpC1 4039820 c.885T>G synonymous_variant 0.18 pyrazinamide
clpC1 4039829 c.874_876delTTGinsCTC synonymous_variant 0.21 pyrazinamide
clpC1 4039832 c.873C>G synonymous_variant 0.22 pyrazinamide
clpC1 4039850 c.855T>C synonymous_variant 0.24 pyrazinamide
clpC1 4039865 c.840T>C synonymous_variant 0.2 pyrazinamide
clpC1 4039876 p.Asn277Asp missense_variant 0.21 pyrazinamide
clpC1 4039889 c.816G>C synonymous_variant 0.34 pyrazinamide
clpC1 4039896 p.Lys270Arg missense_variant 0.28 pyrazinamide Uncertain significance
clpC1 4039898 c.807C>G synonymous_variant 0.28 pyrazinamide
clpC1 4039904 c.801A>G synonymous_variant 0.28 pyrazinamide
clpC1 4039928 c.775_777delAGCinsTCG synonymous_variant 0.24 pyrazinamide
clpC1 4039931 c.774T>C synonymous_variant 0.25 pyrazinamide
clpC1 4039934 c.771G>C synonymous_variant 0.26 pyrazinamide
clpC1 4039943 c.762G>C synonymous_variant 0.24 pyrazinamide
clpC1 4039946 c.759A>G synonymous_variant 0.23 pyrazinamide
clpC1 4039949 c.756G>C synonymous_variant 0.22 pyrazinamide
clpC1 4039952 c.753T>C synonymous_variant 0.26 pyrazinamide
clpC1 4039958 c.747G>C synonymous_variant 0.26 pyrazinamide
clpC1 4039994 p.Glu237Asn missense_variant 0.29 pyrazinamide
clpC1 4040002 p.His235Asn missense_variant 0.28 pyrazinamide
clpC1 4040003 c.702G>C synonymous_variant 0.28 pyrazinamide
clpC1 4040009 c.696C>G synonymous_variant 0.31 pyrazinamide
clpC1 4040018 c.687G>C synonymous_variant 0.31 pyrazinamide
clpC1 4040021 c.684A>C synonymous_variant 0.3 pyrazinamide Not assoc w R - Interim
clpC1 4040024 c.681A>G synonymous_variant 0.31 pyrazinamide
clpC1 4040033 c.672G>C synonymous_variant 0.32 pyrazinamide
clpC1 4040036 c.669C>G synonymous_variant 0.3 pyrazinamide
clpC1 4040090 c.615T>G synonymous_variant 0.3 pyrazinamide
clpC1 4040107 p.Val200Ile missense_variant 0.23 pyrazinamide
clpC1 4040108 c.597G>C synonymous_variant 0.23 pyrazinamide
clpC1 4040117 c.588A>G synonymous_variant 0.23 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 1.0 pyrazinamide
embC 4242075 p.Arg738Gln missense_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249195 c.2682C>A synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4408175 p.Ala10Pro missense_variant 1.0 streptomycin Uncertain significance