TB-Profiler result

Run: SRR7851312
Summary

Run ID: SRR7851312

Sample name:

Date: 2024-10-05T14:37:54.589723

Number of reads: 3252955

Percentage reads mapped: 87.49

Median coverage: 70.0

Strain: La1.2

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
La1.2 M.bovis None 1.0
La1 M.bovis None 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 pncA p.His57Asp Assoc w R
streptomycin rrs n.799C>T Uncertain significance Mutation from literature
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
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.34 streptomycin Uncertain significance Mutation from literature
pncA 2289073 p.His57Asp missense_variant 1.0 pyrazinamide Assoc w R
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
dnaA 467 p.His156Arg missense_variant 1.0 isoniazid Not assoc w R
dnaA 937 p.Thr313Ala missense_variant 1.0 isoniazid
gyrB 5752 c.513G>A synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6406 c.1167C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6446 p.Ala403Ser missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7475 c.174A>G synonymous_variant 1.0 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 7821 c.520C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8285 c.984C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8741 c.1440C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
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
Rv0010c 13197 p.Thr121Ser missense_variant 1.0 isoniazid Not assoc w R
Rv0010c 13228 c.330delG frameshift_variant 1.0 isoniazid Uncertain significance
Rv0010c 13460 c.99T>C synonymous_variant 1.0 isoniazid 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
mshA 575793 p.Asp149Gly missense_variant 1.0 isoniazid
ethionamide
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
rpoB 762197 c.2391C>G synonymous_variant 0.11 rifampicin
rpoB 762218 c.2412T>C synonymous_variant 0.12 rifampicin
rpoB 762233 c.2427G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762245 c.2439G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762254 c.2448T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762266 c.2460T>C synonymous_variant 0.16 rifampicin
rpoB 762284 c.2478G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 762989 c.-381G>C upstream_gene_variant 0.14 rifampicin
rpoB 762995 c.3189G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763022 c.-348C>G upstream_gene_variant 0.13 rifampicin
rpoB 763028 c.3222T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763052 c.-318G>T upstream_gene_variant 0.11 rifampicin
rpoB 763088 c.3282C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 763094 c.3288G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 763106 c.3300C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 763118 p.Glu1104Asp missense_variant 0.12 rifampicin
rpoB 763130 p.Glu1108Asp missense_variant 0.11 rifampicin
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 0.11 streptomycin
rpsL 781817 c.258G>C synonymous_variant 0.12 streptomycin
rpsL 781832 c.273T>G synonymous_variant 0.15 streptomycin
rpsL 781859 c.300T>C synonymous_variant 0.11 streptomycin Not assoc w R - Interim
rpsL 781860 p.Ser101Ala missense_variant 0.11 streptomycin Uncertain significance
rpsL 781871 c.312G>C synonymous_variant 0.1 streptomycin
rpsL 781880 c.321C>G synonymous_variant 0.11 streptomycin
rpsL 781884 p.Asn109Asp missense_variant 0.11 streptomycin
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254582 c.-48A>G upstream_gene_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
sigE 1364961 c.549A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471878 n.33C>T non_coding_transcript_exon_variant 0.12 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1471923 n.78_79delTCinsCCCAAGCTT non_coding_transcript_exon_variant 0.19 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471925 n.80T>G non_coding_transcript_exon_variant 0.19 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471929 n.84C>G non_coding_transcript_exon_variant 0.19 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471931 n.87_89delAGA non_coding_transcript_exon_variant 0.2 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472030 n.185delGinsTTCTT non_coding_transcript_exon_variant 0.17 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472053 n.211_212delGC non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472057 n.212C>T non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472062 n.217G>T non_coding_transcript_exon_variant 0.2 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.28 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.39 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.45 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.43 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.26 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.41 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.42 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.4 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.28 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.28 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472671 n.826G>A non_coding_transcript_exon_variant 0.22 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472674 n.829_838delTTCCTTCCTTinsCCCTTCCAC non_coding_transcript_exon_variant 0.24 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472687 n.842A>G non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.23 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.29 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.29 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472880 n.1035G>A non_coding_transcript_exon_variant 0.13 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.39 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.38 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.44 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.42 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.12 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.35 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473284 n.1439_1448delAACCCTCGGGinsGTCAA non_coding_transcript_exon_variant 0.28 kanamycin
capreomycin
streptomycin
amikacin
rrl 1473677 n.20C>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1473697 n.40C>G non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1473698 n.41G>C non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1473699 n.42A>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1473718 n.61G>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1473728 n.71A>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1473743 n.86C>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1473746 n.89T>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1473751 n.94C>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1473752 n.95G>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1473770 n.113T>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474130 n.473C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474182 n.525C>A non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1474183 n.526T>G non_coding_transcript_exon_variant 0.34 capreomycin
linezolid
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474185 n.529delA non_coding_transcript_exon_variant 0.34 capreomycin
linezolid
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid
rrl 1474253 n.596A>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474467 n.810A>G non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1474487 n.830G>T non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1474495 n.838G>A non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1474496 n.839C>G non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474508 n.851C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474517 n.860C>G non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474736 n.1079C>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474751 n.1094G>A non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474784 n.1127C>T non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474798 n.1141C>G non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474825 n.1168G>A non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474837 n.1180A>G non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.29 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474901 n.1244A>G non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474904 n.1247G>T non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474921 n.1264C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475525 n.1868G>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475531 n.1874C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475538 n.1881T>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475539 n.1882A>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475542 n.1885A>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475544 n.1887A>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475550 n.1893A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid
rrl 1475758 n.2101_2107delACCCGCAinsG non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1475769 n.2112_2113insC non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1475879 n.2222T>C non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.23 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475989 n.2332T>C non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1475990 n.2333G>A non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475997 n.2340A>G non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.31 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.31 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.31 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558_2559insTA non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid
rrl 1476255 n.2598A>T non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.34 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476298 n.2641C>A non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476307 n.2650A>T non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1476309 n.2652G>T non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.56 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.46 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476524 n.2867_2868delCAinsT non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1476535 n.2878G>A non_coding_transcript_exon_variant 0.37 capreomycin
linezolid
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid
rrl 1476580 n.2923G>A non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.2 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.16 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1833422 c.-120G>T upstream_gene_variant 1.0 pyrazinamide
rpsA 1834501 c.960G>C synonymous_variant 0.11 pyrazinamide
rpsA 1834859 p.Ala440Thr missense_variant 1.0 pyrazinamide 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 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
ndh 2102106 p.Gly313Arg missense_variant 0.99 isoniazid Not assoc w R - Interim
delamanid Uncertain significance
ethionamide Uncertain significance
ndh 2103173 c.-132delG upstream_gene_variant 1.0 isoniazid
delamanid
ethionamide
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155503 c.609C>T synonymous_variant 1.0 isoniazid Not assoc w R
katG 2156025 c.87C>A synonymous_variant 1.0 isoniazid Not assoc w R
katG 2156465 c.-354C>T upstream_gene_variant 1.0 isoniazid Not assoc w R - Interim
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2168011 p.Ser868Arg missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2168814 c.1798dupA frameshift_variant 1.0 pyrazinamide Uncertain significance
PPE35 2170048 p.Leu189Val missense_variant 0.42 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.41 pyrazinamide
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
kasA 2518654 c.540C>T synonymous_variant 1.0 isoniazid
Rv2477c 2782927 c.1116A>G synonymous_variant 1.0 kanamycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R - Interim
Rv2681 2997325 p.Ala196Val missense_variant 1.0 capreomycin Uncertain significance
thyX 3067786 p.Thr54Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086728 c.-92C>T upstream_gene_variant 1.0 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087084 c.266delA frameshift_variant 1.0 cycloserine
Rv3083 3448745 p.Ile81Ser missense_variant 1.0 ethionamide Uncertain significance
Rv3083 3448783 p.Val94Ile missense_variant 1.0 ethionamide Uncertain significance
lpqB 3623730 p.Ser394Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
lpqB 3624350 c.561G>T synonymous_variant 1.0 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
lpqB 3624593 c.318G>A synonymous_variant 1.0 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
lpqB 3624710 c.201G>A synonymous_variant 1.0 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038403 c.2302T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
glpK 4139183 c.572dupG frameshift_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
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
embC 4242970 c.3108C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246551 p.Asn13Ser missense_variant 1.0 ethambutol Not assoc w R
embB 4246864 c.351C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247173 c.660G>A synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
aftB 4267858 p.Ile327Val missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269351 c.483C>T synonymous_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
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