TB-Profiler result

Run: ERR6198317
Summary

Run ID: ERR6198317

Sample name:

Date: 2024-04-16T07:36:27.169915

Number of reads: 1385489

Percentage reads mapped: 84.96

Median coverage: 35.0

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 0.99
La1 M.bovis None 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 pncA p.His57Asp Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid fgd1 c.412_414delCTAinsTG Assoc w R - Interim Confers DLM-PMD cross-resistance
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
fgd1 491194 c.412_414delCTAinsTG frameshift_variant&stop_gained 0.2 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
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
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 7585 p.Ser95Thr missense_variant 0.98 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7821 c.520C>T synonymous_variant 0.95 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 8603 c.1302A>G synonymous_variant 0.24 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8619 c.1318T>C synonymous_variant 0.28 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8624 c.1323G>C synonymous_variant 0.27 levofloxacin
moxifloxacin
gyrA 8636 c.1335A>C synonymous_variant 0.32 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8642 c.1341A>G synonymous_variant 0.3 levofloxacin
moxifloxacin
gyrA 8672 c.1371A>G synonymous_variant 0.3 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8693 c.1392T>C synonymous_variant 0.32 levofloxacin
moxifloxacin
gyrA 8741 c.1440C>T synonymous_variant 0.95 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.Gly668Glu missense_variant 1.0 levofloxacin
moxifloxacin
Rv0010c 13197 p.Thr121Ser missense_variant 1.0 isoniazid Not assoc w R
Rv0010c 13228 c.330delG frameshift_variant 1.0 isoniazid Uncertain significance
fgd1 491133 c.351A>C synonymous_variant 0.27 clofazimine
pretomanid
delamanid
fgd1 491144 p.Ala121Asp missense_variant 0.29 clofazimine
pretomanid
delamanid
fgd1 491166 c.384G>C synonymous_variant 0.26 clofazimine
pretomanid
delamanid
fgd1 491178 c.396G>A synonymous_variant 0.22 clofazimine
pretomanid
delamanid
fgd1 491181 c.399T>C synonymous_variant 0.22 clofazimine
pretomanid
delamanid
fgd1 491191 p.Gly137Arg missense_variant 0.21 clofazimine
pretomanid
delamanid
fgd1 491203 p.Gln141Glu missense_variant 0.19 clofazimine
pretomanid
delamanid
fgd1 491206 c.424C>T synonymous_variant 0.19 clofazimine
pretomanid
delamanid
fgd1 491212 p.Ser144Arg missense_variant 0.18 clofazimine
pretomanid
delamanid
fgd1 491232 c.450T>C synonymous_variant 0.26 clofazimine
pretomanid
delamanid
fgd1 491241 p.Asp153Glu missense_variant 0.26 clofazimine
pretomanid
delamanid
fgd1 491244 c.462T>C synonymous_variant 0.26 clofazimine
pretomanid
delamanid
fgd1 491250 c.468G>C synonymous_variant 0.26 clofazimine
pretomanid
delamanid
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 656297 p.Asn392Asp missense_variant 0.85 ethionamide
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
nusG 734451 c.198G>C synonymous_variant 0.17 rifampicin
nusG 734454 c.201A>G synonymous_variant 0.17 rifampicin
nusG 734460 c.207G>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760913 c.1107C>T synonymous_variant 0.25 rifampicin
rpoB 760917 c.1111_1113delCGCinsAG frameshift_variant&missense_variant 0.27 rifampicin
rpoB 760928 c.1122G>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 760938 c.1132C>T synonymous_variant 0.29 rifampicin
rpoB 762284 c.2478G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 762803 c.-567C>T upstream_gene_variant 0.92 rifampicin
rpoC 762863 c.-507T>G upstream_gene_variant 0.3 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763945 c.576T>C synonymous_variant 0.29 rifampicin
rpoC 763948 c.579G>C synonymous_variant 0.3 rifampicin
rpoC 763951 c.582G>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 763960 c.591T>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 763969 c.600C>T synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 763978 c.609C>G synonymous_variant 0.28 rifampicin
rpoC 763991 p.Ile208Leu missense_variant 0.24 rifampicin
rpoC 764002 c.633C>G synonymous_variant 0.31 rifampicin
rpoC 764005 c.636G>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 764024 c.655T>C synonymous_variant 0.3 rifampicin
rpoC 764044 c.675T>C synonymous_variant 0.26 rifampicin
rpoC 764059 c.690G>C synonymous_variant 0.24 rifampicin
rpoC 764932 c.1563C>G synonymous_variant 0.2 rifampicin
rpoC 764948 c.1579T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764968 c.1599T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.19 rifampicin Not assoc w R
rpoC 765421 c.2052C>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 765451 c.2082C>T synonymous_variant 0.29 rifampicin
rpoC 765469 c.2100G>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 765478 c.2109T>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 765499 c.2130C>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 765508 c.2139C>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 765517 c.2148C>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 765529 c.2160C>T synonymous_variant 0.24 rifampicin
rpoC 765553 c.2184C>T synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 765556 c.2187G>C synonymous_variant 0.24 rifampicin
rpoC 765562 c.2193G>C synonymous_variant 0.24 rifampicin
rpoC 765578 c.2209C>T synonymous_variant 0.24 rifampicin
rpoC 765589 c.2220G>C synonymous_variant 0.23 rifampicin
rpoC 765613 p.His748Gln missense_variant 0.18 rifampicin
rpoC 765625 c.2256C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 765628 c.2259G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765631 p.Asp754Glu missense_variant 0.19 rifampicin
rpoC 766843 c.3474T>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 766861 c.3492G>T synonymous_variant 0.37 rifampicin
rpoC 766864 c.3495G>C synonymous_variant 0.33 rifampicin
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
rpsL 781808 c.249C>T synonymous_variant 0.16 streptomycin
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
Rv1129c 1254582 c.-48A>G upstream_gene_variant 1.0 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
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
fbiC 1303846 p.Phe306Val missense_variant 0.27 clofazimine
pretomanid
delamanid
fbiC 1303854 c.924T>C synonymous_variant 0.28 clofazimine
pretomanid
delamanid
fbiC 1303857 c.927C>G synonymous_variant 0.28 clofazimine
pretomanid
delamanid
fbiC 1303860 c.930A>G synonymous_variant 0.27 clofazimine
pretomanid
delamanid
fbiC 1303866 p.Glu312Asp missense_variant 0.26 clofazimine
pretomanid
delamanid
fbiC 1303869 c.939T>C synonymous_variant 0.26 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fbiC 1303875 c.945G>C synonymous_variant 0.25 clofazimine
pretomanid
delamanid
fbiC 1303878 c.948G>A synonymous_variant 0.25 clofazimine
pretomanid
delamanid
fbiC 1303884 c.954T>G synonymous_variant 0.25 clofazimine
pretomanid
delamanid
fbiC 1303890 c.960G>C synonymous_variant 0.25 clofazimine
pretomanid
delamanid
fbiC 1303893 c.963G>C synonymous_variant 0.27 clofazimine
pretomanid
delamanid
fbiC 1303905 c.975G>C synonymous_variant 0.26 clofazimine
pretomanid
delamanid
fbiC 1303911 c.981G>C synonymous_variant 0.27 clofazimine
pretomanid
delamanid
fbiC 1303961 p.Arg344Leu missense_variant 0.25 clofazimine
pretomanid
delamanid
sigE 1364961 c.549A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
Rv1258c 1406663 c.678C>T synonymous_variant 1.0 streptomycin
isoniazid
pyrazinamide
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 1471925 n.80T>C non_coding_transcript_exon_variant 0.17 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471932 n.87A>G non_coding_transcript_exon_variant 0.17 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471934 n.89A>G non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471969 n.124T>C non_coding_transcript_exon_variant 0.24 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471970 n.125G>A non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.23 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1473752 n.95G>T non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1473756 n.99G>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473899 n.242A>C non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474717 n.1060A>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1474991 n.1334T>C non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1474995 n.1338T>G non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1475005 n.1348C>T non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1475013 n.1356G>A non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1475027 n.1370G>T non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1475028 n.1371G>T non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1475369 n.1712G>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475436 n.1779C>T non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.2 capreomycin
linezolid Uncertain significance
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1475619 n.1962C>T non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476689 n.3032A>T non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1476690 n.3033C>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid
rrl 1476693 n.3036G>A non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1476695 n.3038T>A non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1476716 n.3059A>C non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid
rrl 1476723 n.3066T>A non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1476726 n.3069A>G non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
inhA 1674624 c.423A>T synonymous_variant 0.25 ethionamide
isoniazid
rpsA 1833422 c.-120G>T upstream_gene_variant 1.0 pyrazinamide
rpsA 1833661 c.120A>G synonymous_variant 0.21 pyrazinamide
rpsA 1833721 c.180A>G synonymous_variant 0.17 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.17 pyrazinamide
rpsA 1833742 c.201A>G synonymous_variant 0.24 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.22 pyrazinamide
rpsA 1833760 c.219C>T synonymous_variant 0.2 pyrazinamide Not assoc w R - Interim
rpsA 1833771 p.Asn77Ser missense_variant 0.18 pyrazinamide
rpsA 1833793 c.252C>T synonymous_variant 0.18 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.2 pyrazinamide
rpsA 1834859 p.Ala440Thr missense_variant 1.0 pyrazinamide Uncertain significance
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 2102106 p.Gly313Arg missense_variant 1.0 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R - Interim
ndh 2103173 c.-132delG upstream_gene_variant 1.0 ethionamide
delamanid
isoniazid
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
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
Rv2477c 2782927 c.1116A>G synonymous_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R
amikacin Not assoc w R - Interim
Rv2681 2997325 p.Ala196Val missense_variant 1.0 capreomycin Uncertain significance
thyX 3067781 c.165C>G synonymous_variant 0.2 para-aminosalicylic_acid
thyX 3067786 p.Thr54Ala missense_variant 0.79 para-aminosalicylic_acid
thyX 3067799 c.147G>A synonymous_variant 0.2 para-aminosalicylic_acid
thyX 3067802 c.144C>G synonymous_variant 0.19 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
fbiD 3339154 p.Ile13Leu missense_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
Rv3083 3448745 p.Ile81Ser missense_variant 1.0 ethionamide Uncertain significance
Rv3083 3448783 p.Val94Ile missense_variant 1.0 ethionamide Uncertain significance
lpqB 3623442 p.Ser490Asn missense_variant 0.19 bedaquiline
rifampicin
lpqB 3623480 c.1431C>G synonymous_variant 0.19 bedaquiline
rifampicin
lpqB 3623730 p.Ser394Leu missense_variant 0.96 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3624350 c.561G>T synonymous_variant 0.96 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
lpqB 3624593 c.318G>A synonymous_variant 0.94 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
lpqB 3624710 c.201G>A synonymous_variant 0.92 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3625621 c.-711G>C upstream_gene_variant 0.22 bedaquiline
rifampicin
mtrB 3627263 c.-650C>T upstream_gene_variant 0.22 bedaquiline
rifampicin
mtrB 3627266 c.-653A>G upstream_gene_variant 0.21 bedaquiline
rifampicin
mtrB 3627272 c.-659G>T upstream_gene_variant 0.19 bedaquiline
rifampicin
mtrA 3627277 c.73C>T synonymous_variant 0.18 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627296 c.-683T>C upstream_gene_variant 0.2 bedaquiline
rifampicin
mtrB 3627301 c.-688T>C upstream_gene_variant 0.21 bedaquiline
rifampicin
mtrB 3627314 c.-701C>T upstream_gene_variant 0.22 bedaquiline
rifampicin
mtrB 3627317 c.-704T>C upstream_gene_variant 0.2 bedaquiline
rifampicin
mtrB 3627323 c.-710G>A upstream_gene_variant 0.2 bedaquiline
rifampicin
rpoA 3877587 c.921A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3877613 p.Ile299Val missense_variant 0.21 rifampicin
rpoA 3878169 c.339G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
clpC1 4038403 c.2302T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4038749 c.1956C>A synonymous_variant 0.17 pyrazinamide
clpC1 4038755 c.1950G>C synonymous_variant 0.17 pyrazinamide
clpC1 4038764 c.1941C>G synonymous_variant 0.18 pyrazinamide
clpC1 4038773 c.1932T>C synonymous_variant 0.16 pyrazinamide
clpC1 4038782 c.1923G>C synonymous_variant 0.14 pyrazinamide
clpC1 4038790 c.1915C>T synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
clpC1 4039280 c.1425G>A synonymous_variant 0.16 pyrazinamide
clpC1 4039286 c.1419T>C synonymous_variant 0.21 pyrazinamide
clpC1 4039292 c.1413C>T synonymous_variant 0.21 pyrazinamide
clpC1 4039298 c.1407T>C synonymous_variant 0.21 pyrazinamide
clpC1 4039319 c.1386T>C synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
clpC1 4039322 c.1383T>A synonymous_variant 0.19 pyrazinamide
clpC1 4039454 c.1251A>G synonymous_variant 0.22 pyrazinamide Not assoc w R - Interim
clpC1 4039466 c.1239T>C synonymous_variant 0.21 pyrazinamide
clpC1 4039469 c.1236T>C synonymous_variant 0.22 pyrazinamide
clpC1 4039481 c.1224T>C synonymous_variant 0.22 pyrazinamide
clpC1 4039484 c.1221T>C synonymous_variant 0.21 pyrazinamide
clpC1 4039487 c.1218G>C synonymous_variant 0.21 pyrazinamide
clpC1 4039517 c.1188C>G synonymous_variant 0.15 pyrazinamide
clpC1 4039610 c.1095G>C synonymous_variant 0.2 pyrazinamide
clpC1 4039616 c.1089G>C synonymous_variant 0.21 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
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 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 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