TB-Profiler result

Run: ERR400538
Summary

Run ID: ERR400538

Sample name:

Date: 2024-04-15T21:16:51.204538

Number of reads: 1746642

Percentage reads mapped: 75.88

Median coverage: 37.0

Strain: lineage5.1.2

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage5.1.2 West-Africa 1 RD711 0.99
lineage5 West-Africa 1 RD711 0.98
lineage5.1 West-Africa 1 RD711 0.76
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Asp Assoc w R
isoniazid
ethambutol
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
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
rpoB 761139 p.His445Asp missense_variant 0.86 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.89 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
gyrB 6446 p.Ala403Ser missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
gyrA 7024 c.-278G>C upstream_gene_variant 0.17 levofloxacin
moxifloxacin
gyrA 7033 c.-269G>C upstream_gene_variant 0.2 levofloxacin
moxifloxacin
gyrB 7051 p.Glu604Asp missense_variant 0.18 levofloxacin
moxifloxacin
gyrB 7060 c.1821T>C synonymous_variant 0.18 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7066 c.-236G>C upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7571 c.270G>C synonymous_variant 0.21 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7574 c.273G>C synonymous_variant 0.21 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8324 c.1023T>C synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 8339 c.1038A>G synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 8340 p.Ala347Ser missense_variant 0.12 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8915 c.1614A>G synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8924 c.1623C>T synonymous_variant 0.2 levofloxacin
moxifloxacin
gyrA 8945 c.1644G>C synonymous_variant 0.19 levofloxacin
moxifloxacin
gyrA 8946 c.1645_1647delTTGinsCC frameshift_variant&missense_variant 0.18 levofloxacin
moxifloxacin
gyrA 8967 p.Ala556Lys missense_variant 0.22 levofloxacin
moxifloxacin
gyrA 9143 c.1842T>C synonymous_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
gyrA 9566 c.2265C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0010c 13460 c.99T>C synonymous_variant 0.92 isoniazid Not assoc w R
Rv0010c 13579 c.-21G>A upstream_gene_variant 1.0 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.97 ethionamide
hadA 731750 c.-180G>C upstream_gene_variant 0.87 isoniazid
nusG 734475 c.222T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
nusG 734497 c.244_246delGTGinsAC frameshift_variant&missense_variant 0.16 rifampicin
rpoB 760184 c.378A>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 760196 c.390C>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 760223 c.417T>C synonymous_variant 0.21 rifampicin
rpoB 760235 c.429T>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 760382 c.576G>C synonymous_variant 0.15 rifampicin
rpoB 760400 c.594G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760406 c.600G>C synonymous_variant 0.16 rifampicin
rpoB 760407 p.Ser201Gly missense_variant 0.16 rifampicin Uncertain significance
rpoB 760412 c.606C>T synonymous_variant 0.15 rifampicin
rpoB 760415 c.609C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760418 c.612G>A synonymous_variant 0.14 rifampicin
rpoB 760430 c.624T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760433 c.627C>T synonymous_variant 0.19 rifampicin
rpoB 760454 c.648C>G synonymous_variant 0.18 rifampicin
rpoB 760457 c.651C>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 760522 p.Ser239Asn missense_variant 0.16 rifampicin Uncertain significance
rpoB 760532 c.726T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 760541 c.735G>T synonymous_variant 0.14 rifampicin
rpoB 760561 c.757_758delCG frameshift_variant 0.15 rifampicin
rpoB 760567 c.761delCinsGGG frameshift_variant&missense_variant 0.15 rifampicin
rpoB 760571 c.765G>C synonymous_variant 0.16 rifampicin
rpoB 760588 p.Thr261Ile missense_variant 0.15 rifampicin
rpoB 760591 p.Val262Ala missense_variant 0.15 rifampicin
rpoB 760595 c.789C>T synonymous_variant 0.14 rifampicin
rpoB 760596 p.Thr264Pro missense_variant 0.14 rifampicin
rpoB 760607 c.801G>C synonymous_variant 0.18 rifampicin
rpoB 760611 c.805T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 760634 c.828T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 760646 c.840C>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 760655 c.849A>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 760661 c.855A>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 760668 p.Thr288Ala missense_variant 0.22 rifampicin Uncertain significance
rpoB 760674 c.868T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 760679 c.873A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 760683 c.877T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761147 c.1341C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761150 c.1344A>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761159 c.1353G>T synonymous_variant 0.16 rifampicin
rpoB 761165 c.1359G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761171 c.1365C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761234 c.1428G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 761579 c.1773G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 761612 c.1806G>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761615 c.1809A>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761636 c.1830G>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761645 c.1839C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762008 c.2202C>T synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 762014 c.2208C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 762038 c.2232C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762047 c.2241G>A synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 762053 c.2247T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 762056 c.2250G>A synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 762065 c.2259T>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 762083 c.2277T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 762086 c.2280G>T synonymous_variant 0.19 rifampicin
rpoB 762101 c.2295C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762221 c.2415G>A synonymous_variant 0.22 rifampicin
rpoB 762233 c.2427G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 762236 c.2430G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 762245 c.2439G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 762959 c.3153G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.77 rifampicin Not assoc w R
rpoB 763031 c.3225T>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 763034 c.-336C>A upstream_gene_variant 0.23 rifampicin
rpoB 763040 c.3234C>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 763082 c.3276C>T synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoB 763085 c.3279C>T synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 763088 c.3282C>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 763094 c.3288G>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 763528 c.159G>A synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763531 c.162G>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoC 763618 c.249C>T synonymous_variant 0.3 rifampicin
rpoC 763633 c.264T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763660 c.291T>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 763669 c.300C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763675 c.306C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764497 c.1128A>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764506 c.1137C>T synonymous_variant 0.22 rifampicin
rpoC 764566 c.1197C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764713 c.1344G>T synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 764746 c.1377G>T synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 764752 c.1383G>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764758 c.1389C>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764803 c.1434C>T synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 764810 c.1441_1443delCCCinsGT frameshift_variant&missense_variant 0.28 rifampicin
rpoC 764815 c.1446A>G synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 764827 c.1458G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764858 c.1489T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764869 c.1500C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764875 c.1506C>A synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764878 c.1509C>G synonymous_variant 0.18 rifampicin
rpoC 764887 c.1518G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764888 c.1519T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764911 c.1542A>G synonymous_variant 0.22 rifampicin
rpoC 764912 p.Met515Gln missense_variant 0.22 rifampicin Uncertain significance
rpoC 765394 c.2025G>A synonymous_variant 0.15 rifampicin
rpoC 765403 c.2034G>C synonymous_variant 0.18 rifampicin
rpoC 765405 p.Leu679His missense_variant 0.17 rifampicin Uncertain significance
rpoC 765409 c.2040T>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765412 c.2043T>C synonymous_variant 0.17 rifampicin
rpoC 765421 c.2052C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
Rv1258c 1407273 p.Asp23Val missense_variant 1.0 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.22 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472380 n.535G>C non_coding_transcript_exon_variant 0.26 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.31 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.33 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.28 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.25 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.22 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473082 n.1237G>A non_coding_transcript_exon_variant 0.25 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473099 n.1254T>A non_coding_transcript_exon_variant 0.2 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.21 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473288 n.1443C>T non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473291 n.1446G>T non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1473770 n.113T>G non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473839 n.182G>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473887 n.230T>C non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473888 n.231T>C non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473899 n.242A>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474130 n.473C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524_525insT non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474184 n.527C>A non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474185 n.529delA non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474263 n.606G>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1474282 n.625G>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1474496 n.839C>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474507 n.850G>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1474709 n.1052_1057delGTGGTGinsAATAAGT non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474717 n.1060A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1474722 n.1065T>C non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1474743 n.1086T>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475061 n.1406delA non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1475076 n.1419C>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475090 n.1433A>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475114 n.1457C>T non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475120 n.1463G>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid
rrl 1475129 n.1472G>A non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid
rrl 1475760 n.2105_2106delGC non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1475765 n.2108A>T non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1475954 n.2297A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.35 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.27 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.23 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.15 capreomycin Not assoc w R
linezolid Uncertain significance
fabG1 1673338 c.-102G>A upstream_gene_variant 1.0 ethionamide
isoniazid
rpsA 1833583 c.42C>T synonymous_variant 0.16 pyrazinamide
rpsA 1833589 c.48A>C synonymous_variant 0.14 pyrazinamide
rpsA 1833595 c.54T>G synonymous_variant 0.14 pyrazinamide
rpsA 1833596 p.Ser19Ala missense_variant 0.14 pyrazinamide
rpsA 1833604 c.63C>T synonymous_variant 0.16 pyrazinamide
rpsA 1833829 c.288A>G synonymous_variant 0.19 pyrazinamide
rpsA 1833832 c.291G>A synonymous_variant 0.19 pyrazinamide
rpsA 1833838 c.297G>T synonymous_variant 0.15 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.15 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.17 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.15 pyrazinamide
rpsA 1833862 c.321G>T synonymous_variant 0.16 pyrazinamide
rpsA 1833886 c.345C>G synonymous_variant 0.14 pyrazinamide
rpsA 1833892 c.351G>A synonymous_variant 0.13 pyrazinamide
rpsA 1833894 p.Ala118Glu missense_variant 0.13 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.14 pyrazinamide
rpsA 1833949 c.408T>C synonymous_variant 0.16 pyrazinamide
rpsA 1833970 c.429G>C synonymous_variant 0.23 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.2 pyrazinamide
rpsA 1833991 c.450C>G synonymous_variant 0.21 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.21 pyrazinamide
rpsA 1834069 c.528G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834073 p.Lys178Arg missense_variant 0.12 pyrazinamide
rpsA 1834264 c.723G>C synonymous_variant 0.21 pyrazinamide
rpsA 1834297 c.756C>T synonymous_variant 0.31 pyrazinamide
rpsA 1834303 c.762T>G synonymous_variant 0.27 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.27 pyrazinamide
rpsA 1834339 c.798C>T synonymous_variant 0.21 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.2 pyrazinamide Not assoc w R - Interim
rpsA 1834366 c.825A>G synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
rpsA 1834375 c.834G>A synonymous_variant 0.12 pyrazinamide
rpsA 1834483 c.942G>A synonymous_variant 0.13 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.17 pyrazinamide
rpsA 1834498 c.957C>T synonymous_variant 0.19 pyrazinamide
rpsA 1834520 p.Ala327Ser missense_variant 0.18 pyrazinamide
rpsA 1834528 c.987T>C synonymous_variant 0.19 pyrazinamide
rpsA 1834543 c.1002C>G synonymous_variant 0.13 pyrazinamide
rpsA 1834633 c.1092A>G synonymous_variant 0.2 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.21 pyrazinamide
rpsA 1834666 c.1125G>C synonymous_variant 0.17 pyrazinamide
rpsA 1834667 p.Ala376Ser missense_variant 0.17 pyrazinamide
tsnR 1853565 c.-41G>A upstream_gene_variant 1.0 linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 1.0 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
ndh 2101921 c.1122G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
delamanid Not assoc w R - Interim
isoniazid Not assoc w R - Interim
ndh 2103112 c.-70G>T upstream_gene_variant 1.0 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R - Interim
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
PPE35 2170265 c.347delG frameshift_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2290062 c.-821G>A upstream_gene_variant 0.97 pyrazinamide
kasA 2517917 c.-198G>C upstream_gene_variant 0.17 isoniazid
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
ahpC 2726261 c.69G>T synonymous_variant 1.0 isoniazid Not assoc w R - Interim
Rv2681 2997508 p.Thr257Ile missense_variant 1.0 capreomycin
ald 3087084 c.266delA frameshift_variant 1.0 cycloserine
ald 3087184 c.368_373delCCGACG disruptive_inframe_deletion 1.0 cycloserine
Rv3083 3449644 p.Ala381Thr missense_variant 1.0 ethionamide Uncertain significance
Rv3083 3449792 p.Ala430Gly missense_variant 1.0 ethionamide
lpqB 3624350 c.561G>T synonymous_variant 1.0 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626750 c.-137T>G upstream_gene_variant 0.2 bedaquiline
rifampicin
mtrA 3626804 c.546A>G synonymous_variant 0.16 bedaquiline
rifampicin Not assoc w R - Interim
fbiB 3641490 c.-45G>A upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
alr 3840932 c.489C>T synonymous_variant 1.0 cycloserine
rpoA 3877587 c.921A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877596 c.912G>C synonymous_variant 0.19 rifampicin
rpoA 3877602 c.906C>T synonymous_variant 0.18 rifampicin
rpoA 3877656 c.852T>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877662 c.846C>T synonymous_variant 0.16 rifampicin
rpoA 3877665 c.843C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877668 c.840A>G synonymous_variant 0.17 rifampicin
rpoA 3877737 c.771G>C synonymous_variant 0.21 rifampicin
rpoA 3877818 c.690A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3877887 c.621G>C synonymous_variant 0.15 rifampicin
rpoA 3878493 c.15G>A synonymous_variant 1.0 rifampicin Not assoc w R - Interim
ddn 3986987 c.144G>T synonymous_variant 1.0 delamanid Not assoc w R - Interim
pretomanid
ddn 3987180 p.Asp113Asn missense_variant 1.0 delamanid Uncertain significance
pretomanid
clpC1 4039208 c.1497C>G synonymous_variant 0.18 pyrazinamide
clpC1 4039220 c.1485G>C synonymous_variant 0.21 pyrazinamide
clpC1 4039238 c.1467C>T synonymous_variant 0.22 pyrazinamide
clpC1 4039277 c.1428C>G synonymous_variant 0.17 pyrazinamide
clpC1 4039292 c.1413C>T synonymous_variant 0.19 pyrazinamide
clpC1 4039360 p.Ser449Arg missense_variant 0.15 pyrazinamide
clpC1 4039361 c.1344C>G synonymous_variant 0.15 pyrazinamide
clpC1 4039412 c.1293T>G synonymous_variant 0.21 pyrazinamide
clpC1 4039415 p.Glu430Asp missense_variant 0.24 pyrazinamide Uncertain significance
clpC1 4039430 c.1275T>C synonymous_variant 0.31 pyrazinamide
clpC1 4039442 c.1263A>G synonymous_variant 0.32 pyrazinamide
clpC1 4039451 c.1254G>A synonymous_variant 0.28 pyrazinamide
clpC1 4039454 c.1251A>T synonymous_variant 0.3 pyrazinamide
clpC1 4039457 c.1248C>T synonymous_variant 0.27 pyrazinamide
clpC1 4039586 c.1119G>C synonymous_variant 0.18 pyrazinamide
clpC1 4039589 c.1116G>C synonymous_variant 0.22 pyrazinamide
clpC1 4039610 c.1095G>T synonymous_variant 0.22 pyrazinamide
clpC1 4039616 c.1089G>C synonymous_variant 0.26 pyrazinamide
clpC1 4039622 c.1083C>T synonymous_variant 0.24 pyrazinamide
clpC1 4039649 c.1056G>C synonymous_variant 0.22 pyrazinamide
clpC1 4039652 c.1053G>C synonymous_variant 0.23 pyrazinamide
clpC1 4039682 c.1023C>G synonymous_variant 0.27 pyrazinamide
clpC1 4039694 c.1011G>C synonymous_variant 0.29 pyrazinamide
clpC1 4039724 c.981A>G synonymous_variant 0.26 pyrazinamide
clpC1 4039733 c.972G>C synonymous_variant 0.24 pyrazinamide
clpC1 4039739 c.966C>G synonymous_variant 0.24 pyrazinamide
clpC1 4039751 c.954A>G synonymous_variant 0.2 pyrazinamide
clpC1 4039757 c.948A>G synonymous_variant 0.18 pyrazinamide
clpC1 4039769 c.936C>T synonymous_variant 0.24 pyrazinamide
clpC1 4039775 c.930G>C synonymous_variant 0.23 pyrazinamide
clpC1 4039778 c.927A>G synonymous_variant 0.24 pyrazinamide
clpC1 4039793 c.912C>G synonymous_variant 0.21 pyrazinamide
clpC1 4039805 c.900C>T synonymous_variant 0.19 pyrazinamide Not assoc w R - Interim
clpC1 4039814 c.891C>G synonymous_variant 0.18 pyrazinamide
clpC1 4039817 c.888A>C synonymous_variant 0.18 pyrazinamide Not assoc w R - Interim
clpC1 4039820 c.885T>G synonymous_variant 0.18 pyrazinamide
clpC1 4039831 c.874T>C synonymous_variant 0.16 pyrazinamide
clpC1 4039958 c.747G>C synonymous_variant 0.22 pyrazinamide
clpC1 4039964 c.741C>G synonymous_variant 0.24 pyrazinamide
clpC1 4039975 p.Asp244Asn missense_variant 0.21 pyrazinamide Uncertain significance
clpC1 4039979 c.726C>G synonymous_variant 0.19 pyrazinamide
clpC1 4040021 c.684A>C synonymous_variant 0.22 pyrazinamide Not assoc w R - Interim
clpC1 4040024 c.681A>G synonymous_variant 0.23 pyrazinamide
clpC1 4040033 c.672G>C synonymous_variant 0.29 pyrazinamide
clpC1 4040042 c.663C>T synonymous_variant 0.22 pyrazinamide Not assoc w R - Interim
clpC1 4040824 c.-120C>T upstream_gene_variant 1.0 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
glpK 4139131 p.Glu209Lys missense_variant 1.0 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Uncertain significance
embC 4239843 c.-20A>C upstream_gene_variant 1.0 ethambutol Not assoc w R - Interim
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244635 p.Val468Ala missense_variant 1.0 ethambutol Not assoc w R - Interim
embA 4245147 p.Pro639Ser missense_variant 1.0 ethambutol Not assoc w R - Interim
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326928 c.546C>T synonymous_variant 1.0 ethionamide Not assoc w R - Interim
ethA 4327103 p.Gly124Asp missense_variant 1.0 ethionamide 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