TB-Profiler result

Run: ERR13265833

Summary

Run ID: ERR13265833

Sample name:

Date: 2025-02-11T12:52:22.222453

Number of reads: 52498

Percentage reads mapped: 27.53

Median coverage: 0.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other


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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) 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
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid fgd1 c.355delG Assoc w R - Interim Confers DLM-PMD cross-resistance
c.361_363delGCCinsAG 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 491136 c.355delG frameshift_variant 1.0 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fgd1 491143 c.361_363delGCCinsAG frameshift_variant&missense_variant 1.0 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
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 1220 p.Asn407Thr missense_variant 1.0 isoniazid
dnaA 1230 c.1230A>G synonymous_variant 1.0 isoniazid
dnaA 1236 c.1236C>T synonymous_variant 1.0 isoniazid
dnaA 1237 p.Ala413Thr missense_variant 1.0 isoniazid Uncertain significance
dnaA 1243 p.Thr415Ala missense_variant 1.0 isoniazid Uncertain significance
dnaA 1254 c.1254T>G synonymous_variant 1.0 isoniazid
dnaA 1266 c.1266A>G synonymous_variant 1.0 isoniazid
dnaA 1275 p.Asp425Glu missense_variant 1.0 isoniazid
dnaA 1278 c.1278T>C synonymous_variant 1.0 isoniazid
dnaA 1281 c.1281C>G synonymous_variant 1.0 isoniazid
dnaA 1287 c.1287A>G synonymous_variant 1.0 isoniazid
dnaA 1293 c.1293T>G synonymous_variant 1.0 isoniazid
dnaA 1314 c.1314A>T synonymous_variant 1.0 isoniazid
dnaA 1317 c.1317A>G synonymous_variant 1.0 isoniazid
dnaA 1329 c.1329A>C synonymous_variant 1.0 isoniazid
dnaA 1332 c.1332A>T synonymous_variant 1.0 isoniazid
dnaA 1338 c.1338T>C synonymous_variant 1.0 isoniazid
dnaA 1341 c.1341G>C synonymous_variant 1.0 isoniazid
dnaA 1347 c.1347C>T synonymous_variant 1.0 isoniazid
dnaA 1353 c.1353T>C synonymous_variant 1.0 isoniazid
gyrA 7108 c.-194G>A upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrA 7123 c.-179C>G upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrA 7126 c.-176G>A upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrA 7129 c.-173T>G upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrA 7132 c.-170T>G upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrA 7153 c.-149G>T upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrB 7156 c.1917C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 7159 c.1920C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 7162 c.1923C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7165 c.-137C>T upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrA 7168 c.-134C>G upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrA 7178 c.-124T>C upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrB 7210 p.Asp657Glu missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 7213 c.-89G>A upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrA 7225 c.-77T>C upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrB 7234 c.1995C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7243 c.-59G>A upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrB 7246 c.2007T>C synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrA 7391 c.90C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7394 c.93T>C synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrA 7397 c.96G>C synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7406 c.105G>C synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7412 c.111C>G synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7418 c.117C>T synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7433 c.132G>A synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7442 c.141G>C synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7457 c.156T>C synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7463 c.162G>C synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7472 c.171T>C synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrA 7475 c.174A>G synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7480 p.Phe60Tyr missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 7484 c.183T>C synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7499 c.198G>C synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7526 c.225G>C synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7532 c.231T>G synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7541 c.240C>G synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7547 c.246C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7601 c.300C>T synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7607 c.306C>G synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7613 c.312G>A synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7622 c.321C>T synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7631 c.330G>C synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7637 c.336C>T synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7652 c.351C>T synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7694 c.393A>G synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7697 c.396C>G synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7706 c.405C>T synonymous_variant 0.91 levofloxacin
moxifloxacin
gyrA 7709 c.408G>C synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7710 c.409T>C synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7728 c.427_429delAGGinsCGC synonymous_variant 1.0 levofloxacin
moxifloxacin
fgd1 491091 c.309T>C synonymous_variant 1.0 pretomanid
delamanid
clofazimine
fgd1 491115 c.333G>C synonymous_variant 1.0 pretomanid
delamanid
clofazimine
fgd1 491121 c.339A>G synonymous_variant 1.0 pretomanid
delamanid
clofazimine
fgd1 491166 c.384G>C synonymous_variant 1.0 pretomanid
delamanid
clofazimine
fgd1 491508 c.726A>C synonymous_variant 1.0 pretomanid
delamanid
clofazimine
fgd1 491512 p.Asn244Glu missense_variant 1.0 pretomanid
delamanid
clofazimine
fgd1 491523 c.741G>C synonymous_variant 1.0 pretomanid
delamanid
clofazimine
fgd1 491526 c.744T>C synonymous_variant 1.0 pretomanid
delamanid
clofazimine
fgd1 491542 c.760T>C synonymous_variant 1.0 pretomanid
delamanid
clofazimine
fgd1 491563 c.781_783delAGCinsTCG synonymous_variant 1.0 pretomanid
delamanid
clofazimine
fgd1 491595 c.813C>T synonymous_variant 1.0 pretomanid
delamanid
clofazimine
fgd1 491610 c.828A>G synonymous_variant 1.0 pretomanid
delamanid
clofazimine
fgd1 491616 c.834A>G synonymous_variant 1.0 pretomanid
delamanid
clofazimine
fgd1 491620 p.Ile280Val missense_variant 1.0 pretomanid
delamanid
clofazimine
fgd1 491649 c.867C>T synonymous_variant 1.0 pretomanid
delamanid
clofazimine
fgd1 491652 c.870C>T synonymous_variant 0.82 pretomanid
delamanid
clofazimine Not assoc w R - Interim
fgd1 491655 c.873C>T synonymous_variant 1.0 pretomanid
delamanid
clofazimine
fgd1 491658 c.876A>G synonymous_variant 1.0 pretomanid
delamanid
clofazimine
fgd1 491661 c.879C>G synonymous_variant 1.0 pretomanid
delamanid
clofazimine
fgd1 491667 c.885A>G synonymous_variant 1.0 pretomanid
delamanid
clofazimine
mshA 575837 c.490C>T synonymous_variant 1.0 isoniazid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
mshA 575842 c.495G>C synonymous_variant 1.0 isoniazid
ethionamide
mshA 575864 c.517T>C synonymous_variant 1.0 isoniazid
ethionamide
mshA 575881 c.534C>T synonymous_variant 1.0 isoniazid
ethionamide
mshA 575884 c.537G>C synonymous_variant 1.0 isoniazid
ethionamide
mshA 575893 c.546C>A synonymous_variant 1.0 isoniazid
ethionamide
rpoC 764932 c.1563C>A synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 764935 c.1566T>C synonymous_variant 1.0 rifampicin
rpoC 764948 c.1579T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 764968 c.1599T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 765007 c.1638T>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 765008 c.1639T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 765011 c.1642_1644delAGCinsTCG synonymous_variant 1.0 rifampicin
rpoC 765016 c.1647C>A synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 765022 c.1653G>T synonymous_variant 1.0 rifampicin
rpoC 765034 c.1665T>C synonymous_variant 1.0 rifampicin
rpoC 765040 c.1671T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 765041 c.1672T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 765047 c.1678T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 765055 c.1686C>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
sigE 1364931 c.519C>T synonymous_variant 1.0 pyrazinamide
sigE 1364950 p.Ala180Ser missense_variant 1.0 pyrazinamide
sigE 1364956 c.544C>T synonymous_variant 1.0 pyrazinamide
sigE 1364962 p.Pro184Ala missense_variant 1.0 pyrazinamide
sigE 1364976 c.564T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
sigE 1364979 c.567C>G synonymous_variant 1.0 pyrazinamide
sigE 1364980 c.568T>C synonymous_variant 1.0 pyrazinamide
sigE 1364984 p.Ala191Asp missense_variant 1.0 pyrazinamide
sigE 1364989 c.577C>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
sigE 1364992 p.Pro194Ala missense_variant 1.0 pyrazinamide
sigE 1365000 c.588G>A synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
sigE 1365003 c.591T>C synonymous_variant 1.0 pyrazinamide
sigE 1365006 c.594T>C synonymous_variant 1.0 pyrazinamide
sigE 1365018 c.606G>C synonymous_variant 1.0 pyrazinamide
sigE 1365042 c.630G>C synonymous_variant 1.0 pyrazinamide
sigE 1365048 c.636G>A synonymous_variant 1.0 pyrazinamide
sigE 1365051 c.639G>A synonymous_variant 1.0 pyrazinamide
sigE 1365063 c.651A>G synonymous_variant 1.0 pyrazinamide
sigE 1365069 c.657C>T synonymous_variant 1.0 pyrazinamide
katG 2155691 c.421T>C synonymous_variant 1.0 isoniazid
katG 2155696 p.Ala139Val missense_variant 1.0 isoniazid
katG 2155716 c.396T>G synonymous_variant 1.0 isoniazid
katG 2155722 c.390G>C synonymous_variant 1.0 isoniazid
katG 2155728 c.384G>C synonymous_variant 1.0 isoniazid
katG 2155742 p.Gly124Arg missense_variant 1.0 isoniazid
katG 2155747 p.Ala122Gly missense_variant 1.0 isoniazid
katG 2155764 p.His116Glu missense_variant 1.0 isoniazid
katG 2155769 p.Ile115Val missense_variant 1.0 isoniazid
katG 2155770 c.342C>G synonymous_variant 1.0 isoniazid
katG 2155782 c.330C>A synonymous_variant 1.0 isoniazid
katG 2155785 c.327T>C synonymous_variant 1.0 isoniazid
katG 2155794 p.Ala106Ser missense_variant 1.0 isoniazid
katG 2155800 c.312G>C synonymous_variant 1.0 isoniazid
katG 2155805 p.Ile103Val missense_variant 1.0 isoniazid Uncertain significance
katG 2155806 c.306T>C synonymous_variant 1.0 isoniazid
clpC1 4038383 c.2322G>C synonymous_variant 1.0 pyrazinamide
clpC1 4038388 c.2317T>C synonymous_variant 1.0 pyrazinamide
clpC1 4038398 c.2307G>T synonymous_variant 1.0 pyrazinamide
clpC1 4038401 c.2302_2304delTTGinsCTC synonymous_variant 1.0 pyrazinamide
clpC1 4038410 c.2295C>T synonymous_variant 1.0 pyrazinamide
clpC1 4038419 c.2286T>C synonymous_variant 1.0 pyrazinamide
clpC1 4038433 c.2272C>T synonymous_variant 1.0 pyrazinamide
clpC1 4038434 c.2271G>C synonymous_variant 1.0 pyrazinamide
clpC1 4038444 p.Ala754Lys missense_variant 1.0 pyrazinamide
clpC1 4038446 c.2259T>C synonymous_variant 1.0 pyrazinamide
clpC1 4038456 p.Val750Gln missense_variant 1.0 pyrazinamide
clpC1 4038460 p.Leu749Met missense_variant 1.0 pyrazinamide
clpC1 4038462 p.Ala748Glu missense_variant 1.0 pyrazinamide
clpC1 4038474 p.Ser744Ala missense_variant 1.0 pyrazinamide
clpC1 4038479 c.2226C>G synonymous_variant 1.0 pyrazinamide
clpC1 4038486 p.Gly740Asn missense_variant 1.0 pyrazinamide
clpC1 4038489 p.Ala739Gly missense_variant 1.0 pyrazinamide
clpC1 4038499 p.Ser736Gly missense_variant 1.0 pyrazinamide
clpC1 4038519 p.Arg729Gln missense_variant 1.0 pyrazinamide
embB 4247491 c.978G>C synonymous_variant 1.0 ethambutol
embB 4247497 c.984T>C synonymous_variant 1.0 ethambutol
embB 4247511 p.Tyr333Phe missense_variant 1.0 ethambutol
embB 4247527 c.1014G>C synonymous_variant 1.0 ethambutol
embB 4247536 c.1023C>G synonymous_variant 1.0 ethambutol
embB 4247554 c.1041T>C synonymous_variant 1.0 ethambutol
embB 4247555 p.Leu348Ile missense_variant 1.0 ethambutol
embB 4247566 c.1053C>A synonymous_variant 1.0 ethambutol
embB 4247572 c.1059A>C synonymous_variant 1.0 ethambutol
embB 4247578 c.1065_1066insATCTGT conservative_inframe_insertion 1.0 ethambutol
embB 4247581 c.1069_1074delGCCGGG conservative_inframe_deletion 1.0 ethambutol
embB 4247590 c.1077A>G synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embB 4248112 c.1599C>G synonymous_variant 1.0 ethambutol