TB-Profiler result

Run: SRR1062918
Summary

Run ID: SRR1062918

Sample name:

Date: 2024-04-15T00:25:19.798149

Number of reads: 1513049

Percentage reads mapped: 43.1

Median coverage: 28.0

Strain: lineage3

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.99
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 rrs n.799C>T Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1402C>A Uncertain significance Mutation from literature
n.1484G>T Assoc w R
capreomycin rrs n.1402C>A Uncertain significance Mutation from literature
n.1484G>T Assoc w R
kanamycin rrs n.1402C>A Uncertain significance Mutation from literature
n.1484G>T Assoc w R
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
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.51 streptomycin Uncertain significance Mutation from literature
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance Mutation from literature
amikacin Uncertain significance Mutation from literature
kanamycin Uncertain significance Mutation from literature
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.4 kanamycin Assoc w R
amikacin Assoc w R
capreomycin 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
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 0.94 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
rpoB 759746 c.-61C>T upstream_gene_variant 1.0 rifampicin Not assoc w R
rpoB 762026 c.2220G>C synonymous_variant 0.44 rifampicin
rpoB 762030 p.Thr742Ser missense_variant 0.42 rifampicin
rpoB 762053 c.2247T>C synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoB 762057 p.Ile751Val missense_variant 0.39 rifampicin Uncertain significance
rpoB 762062 c.2256T>C synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoB 762065 c.2259T>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoB 762194 c.2388G>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 762233 c.2427G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 762245 c.2439G>T synonymous_variant 0.3 rifampicin
rpoB 762251 c.2445G>C synonymous_variant 0.29 rifampicin
rpoB 762254 c.2448T>G synonymous_variant 0.29 rifampicin
rpoB 762257 c.2451C>G synonymous_variant 0.29 rifampicin
rpoB 762273 p.Ala823Ser missense_variant 0.27 rifampicin
rpoB 762278 c.2472C>T synonymous_variant 0.24 rifampicin
rpoB 762284 c.2478G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 762434 c.2628T>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 762866 c.-504C>A upstream_gene_variant 0.24 rifampicin
rpoB 762878 p.Ile1024Met missense_variant 0.28 rifampicin
rpoB 762879 c.3073_3075delATGinsCC frameshift_variant&missense_variant 0.28 rifampicin
rpoB 762887 c.3081G>C synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoC 762896 c.-474G>C upstream_gene_variant 0.43 rifampicin
rpoB 762899 c.3093G>C synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoB 762917 c.3111C>G synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>T synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoC 762980 c.-390T>C upstream_gene_variant 0.22 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 763094 c.3288G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763100 c.-270G>A upstream_gene_variant 0.19 rifampicin
rpoC 763103 c.-267G>C upstream_gene_variant 0.21 rifampicin
rpoB 763122 c.3316_3318delATCinsCG frameshift_variant&missense_variant 0.2 rifampicin
rpoB 763127 c.3321G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 763130 p.Glu1108Asp missense_variant 0.22 rifampicin
rpoC 763136 c.-234C>A upstream_gene_variant 0.21 rifampicin
rpoC 763157 c.-213G>C upstream_gene_variant 0.2 rifampicin
rpoC 763483 c.114G>C synonymous_variant 0.28 rifampicin
rpoC 763486 c.117T>G synonymous_variant 0.32 rifampicin
rpoC 763504 c.135C>A synonymous_variant 0.41 rifampicin
rpoC 763507 c.138G>C synonymous_variant 0.37 rifampicin
rpoC 763528 c.159G>C synonymous_variant 0.41 rifampicin
rpoC 763531 c.162G>C synonymous_variant 0.43 rifampicin Not assoc w R
rpoC 763534 c.165T>C synonymous_variant 0.41 rifampicin
rpoC 763537 c.168C>T synonymous_variant 0.42 rifampicin
rpoC 763546 c.177A>G synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoC 763550 p.Tyr61Ala missense_variant 0.42 rifampicin
rpoC 763570 c.201G>C synonymous_variant 0.48 rifampicin Not assoc w R - Interim
rpoC 763585 c.216C>G synonymous_variant 0.52 rifampicin
rpoC 763621 c.252C>T synonymous_variant 0.57 rifampicin
rpoC 763633 c.264T>C synonymous_variant 0.56 rifampicin Not assoc w R - Interim
rpoC 763642 c.273G>C synonymous_variant 0.58 rifampicin Not assoc w R - Interim
rpoC 763660 c.291T>C synonymous_variant 0.53 rifampicin Not assoc w R - Interim
rpoC 763666 c.297G>T synonymous_variant 0.58 rifampicin
rpoC 763696 c.327T>C synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoC 763699 c.330G>T synonymous_variant 0.44 rifampicin
rpoC 763708 c.339G>C synonymous_variant 0.3 rifampicin
rpoC 763709 c.340C>T synonymous_variant 0.29 rifampicin
rpoC 763714 c.345G>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 763723 c.354G>C synonymous_variant 0.32 rifampicin
rpoC 763726 c.357C>T synonymous_variant 0.39 rifampicin
rpoC 763729 c.360G>C synonymous_variant 0.32 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.32 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.31 rifampicin
rpoC 763751 p.Ile128Val missense_variant 0.32 rifampicin
rpoC 764521 c.1152T>C synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoC 764524 c.1155C>T synonymous_variant 0.41 rifampicin
rpoC 764527 c.1158C>T synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoC 764533 c.1164C>T synonymous_variant 0.42 rifampicin
rpoC 764536 c.1167G>T synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoC 764542 c.1173C>G synonymous_variant 0.48 rifampicin
rpoC 764548 c.1179G>A synonymous_variant 0.49 rifampicin
rpoC 764560 c.1191T>C synonymous_variant 0.59 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.53 rifampicin Not assoc w R - Interim
rpoC 764578 c.1209C>G synonymous_variant 0.53 rifampicin
rpoC 764581 c.1212T>C synonymous_variant 0.52 rifampicin
rpoC 764582 p.Leu405Met missense_variant 0.52 rifampicin
rpoC 764611 c.1242G>C synonymous_variant 0.52 rifampicin
rpoC 764632 c.1263T>C synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoC 764662 c.1293G>C synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoC 764668 c.1299C>T synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 764679 p.Lys437Ser missense_variant 0.33 rifampicin
rpoC 764683 c.1314G>C synonymous_variant 0.34 rifampicin
rpoC 764690 p.Cys441Ala missense_variant 0.4 rifampicin
rpoC 764701 c.1332C>G synonymous_variant 0.45 rifampicin Not assoc w R - Interim
rpoC 764705 p.Leu446Thr missense_variant 0.42 rifampicin
rpoC 764716 c.1347G>C synonymous_variant 0.51 rifampicin Not assoc w R - Interim
rpoC 764737 c.1368G>C synonymous_variant 0.4 rifampicin
rpoC 764746 c.1377G>C synonymous_variant 0.35 rifampicin
rpoC 764752 c.1383G>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 764755 c.1386C>T synonymous_variant 0.3 rifampicin
rpoC 764764 c.1395T>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 764780 c.1411_1413delAGCinsTCG synonymous_variant 0.28 rifampicin
rpoC 764797 c.1428G>C synonymous_variant 0.38 rifampicin
rpoC 764948 c.1579_1581delTTGinsCC frameshift_variant&missense_variant 0.23 rifampicin
rpoC 764956 c.1587T>C synonymous_variant 0.23 rifampicin
rpoC 764957 p.Glu530Ser missense_variant 0.23 rifampicin
rpoC 764968 c.1599T>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 764998 c.1629G>C synonymous_variant 0.32 rifampicin
rpoC 765007 c.1638T>G synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 765008 c.1639T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 765014 p.Ala549Pro missense_variant 0.35 rifampicin
rpoC 765019 c.1650A>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 765923 p.Asn852Ala missense_variant 0.41 rifampicin
rpoC 765926 p.Thr853Ser missense_variant 0.44 rifampicin Uncertain significance
rpoC 765937 c.2568T>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 765940 c.2571A>C synonymous_variant 0.39 rifampicin
rpoC 765947 c.2578_2580delTTGinsCC frameshift_variant&missense_variant 0.37 rifampicin
rpoC 765958 c.2589C>G synonymous_variant 0.37 rifampicin
rpoC 765962 c.2593T>C synonymous_variant 0.32 rifampicin
rpoC 765967 c.2598C>T synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 765973 c.2604C>T synonymous_variant 0.3 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.96 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.31 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.33 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 0.43 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 0.56 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.54 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Uncertain significance
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472245 n.400C>A non_coding_transcript_exon_variant 0.5 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.47 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 0.42 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472496 n.651T>A non_coding_transcript_exon_variant 0.44 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.47 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472506 n.661A>T non_coding_transcript_exon_variant 0.54 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.65 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472572 n.727T>A non_coding_transcript_exon_variant 0.74 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.69 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 0.71 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.61 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.43 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472790 n.945T>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 0.39 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.54 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.53 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.53 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.53 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.58 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.51 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.51 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.49 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G 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 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 0.35 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.29 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.29 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.37 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 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.67 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.66 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473157 n.1312C>T non_coding_transcript_exon_variant 0.68 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.7 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.7 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.7 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 0.61 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473288 n.1443delCinsAGTTT non_coding_transcript_exon_variant 0.4 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473291 n.1446G>T non_coding_transcript_exon_variant 0.39 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473298 n.1453A>G non_coding_transcript_exon_variant 0.41 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.41 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473305 n.1460G>T non_coding_transcript_exon_variant 0.4 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.4 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.4 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.41 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474202 n.545T>C non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1474263 n.606G>A non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474287 n.630T>A non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1474292 n.635_651delTTCCTCTCCGGAGGAGGinsGGTT non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1474348 n.691C>T non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474351 n.694G>C non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid
rrl 1474353 n.696A>G non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474354 n.697C>T non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1474355 n.698A>G non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid
rrl 1474359 n.702C>G non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474387 n.730C>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474402 n.745T>C non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474406 n.749T>C non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1474558 n.901G>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474584 n.927C>T non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474692 n.1035G>A non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474694 n.1037C>T non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474806 n.1149A>G non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1474822 n.1165G>T non_coding_transcript_exon_variant 0.57 capreomycin
linezolid
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.61 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474905 n.1248T>A non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1475696 n.2039T>A non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid
rrl 1475697 n.2040C>T non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475703 n.2046A>T non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.68 capreomycin Uncertain significance
linezolid
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475765 n.2108A>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.83 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.83 capreomycin Uncertain significance
linezolid
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.83 capreomycin Uncertain significance
linezolid
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.81 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475963 n.2306G>A non_coding_transcript_exon_variant 0.66 capreomycin
linezolid
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475978 n.2321C>T non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476130 n.2473G>A non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.63 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.53 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.54 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.49 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.69 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.78 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.73 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.75 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.72 capreomycin Uncertain significance
linezolid
rrl 1476519 n.2862C>T non_coding_transcript_exon_variant 0.72 capreomycin
linezolid Uncertain significance
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.68 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.68 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476534 n.2877A>T non_coding_transcript_exon_variant 0.68 capreomycin
linezolid
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.66 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.66 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.34 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476594 n.2937C>A non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
inhA 1673816 c.-386G>A upstream_gene_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
rpsA 1833668 p.Ile43Val missense_variant 0.25 pyrazinamide
rpsA 1833676 c.135A>G synonymous_variant 0.26 pyrazinamide
rpsA 1833679 c.138G>C synonymous_variant 0.28 pyrazinamide
rpsA 1833682 c.141C>T synonymous_variant 0.29 pyrazinamide
rpsA 1833685 c.144G>C synonymous_variant 0.27 pyrazinamide
rpsA 1833694 c.153G>C synonymous_variant 0.26 pyrazinamide
rpsA 1833698 p.Leu53Val missense_variant 0.25 pyrazinamide
rpsA 1833709 c.168C>A synonymous_variant 0.27 pyrazinamide
rpsA 1833718 c.177C>G synonymous_variant 0.29 pyrazinamide
rpsA 1834327 c.786G>T synonymous_variant 0.32 pyrazinamide
rpsA 1834348 c.807T>G synonymous_variant 0.33 pyrazinamide
rpsA 1834354 c.813G>C synonymous_variant 0.33 pyrazinamide Not assoc w R - Interim
rpsA 1834357 c.816T>C synonymous_variant 0.37 pyrazinamide
rpsA 1834361 c.820_822delTTGinsCC frameshift_variant&missense_variant 0.33 pyrazinamide Uncertain significance
rpsA 1834366 c.825A>G synonymous_variant 0.33 pyrazinamide Not assoc w R - Interim
rpsA 1834378 c.837T>G synonymous_variant 0.43 pyrazinamide
rpsA 1834387 c.846C>T synonymous_variant 0.52 pyrazinamide
rpsA 1834395 p.Arg285Gln missense_variant 0.46 pyrazinamide
rpsA 1834408 c.867C>G synonymous_variant 0.35 pyrazinamide
rpsA 1834411 c.870T>C synonymous_variant 0.32 pyrazinamide
rpsA 1834416 p.Ala292Val missense_variant 0.32 pyrazinamide
rpsA 1834423 c.882G>C synonymous_variant 0.36 pyrazinamide
rpsA 1834451 c.910_912delTTGinsCC frameshift_variant&missense_variant 0.35 pyrazinamide Uncertain significance
rpsA 1834468 c.927A>G synonymous_variant 0.3 pyrazinamide
rpsA 1834474 c.933C>G synonymous_variant 0.28 pyrazinamide
rpsA 1834486 p.Glu315Asp 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 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289047 c.195C>T synonymous_variant 0.95 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 1.0 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.97 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
thyX 3067987 c.-42C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4039976 p.Lys243Thr missense_variant 0.25 pyrazinamide
clpC1 4039982 p.Thr241Ile missense_variant 0.21 pyrazinamide
clpC1 4039991 c.714G>T synonymous_variant 0.35 pyrazinamide
clpC1 4040002 p.His235Asn missense_variant 0.38 pyrazinamide
clpC1 4040003 c.702G>C synonymous_variant 0.39 pyrazinamide
clpC1 4040009 c.696C>G synonymous_variant 0.42 pyrazinamide
clpC1 4040021 c.684A>T synonymous_variant 0.47 pyrazinamide
clpC1 4040024 c.681A>G synonymous_variant 0.49 pyrazinamide
clpC1 4040030 c.675C>G synonymous_variant 0.54 pyrazinamide
clpC1 4040033 c.672G>C synonymous_variant 0.54 pyrazinamide
clpC1 4040063 c.642G>C synonymous_variant 0.53 pyrazinamide Not assoc w R - Interim
clpC1 4040066 c.639G>T synonymous_variant 0.52 pyrazinamide
clpC1 4040081 c.624C>G synonymous_variant 0.54 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 4247358 p.Val282Ala missense_variant 0.64 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
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R