TB-Profiler result

Run: ERR5917732
Summary

Run ID: ERR5917732

Sample name:

Date: 2025-07-16T15:00:03.081056

Number of reads: 2437770

Percentage reads mapped: 99.58

Median coverage: 79.0

Strain: lineage4.1.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 100.0
lineage4.1 Euro-American None 95.51
lineage4.1.2 Euro-American None 93.74
lineage4.1.2.1 Euro-American (Haarlem) RD182 93.63
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Tyr Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gln497Arg Assoc w R
pyrazinamide
streptomycin gid c.487_507dupAAAGGCGAGCGGGCTCACGAC Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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 761109 p.Asp435Tyr missense_variant 0.97 rifampicin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.93 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 0.92 isoniazid Assoc w R High-level resistance
embB 4248003 p.Gln497Arg missense_variant 0.86 ethambutol Assoc w R
gid 4407695 c.487_507dupAAAGGCGAGCGGGCTCACGAC conservative_inframe_insertion 0.76 streptomycin Mutation from literature
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.95 clofazimine Not assoc w R
delamanid Uncertain significance
pretomanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.94 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657142 p.Arg110His missense_variant 0.11 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.94 ethionamide Uncertain significance
rpoB 760106 c.300G>A synonymous_variant 0.92 rifampicin Not assoc w R
rpoB 760115 c.309C>T synonymous_variant 0.93 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.92 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781276 c.-284A>C upstream_gene_variant 0.97 streptomycin Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254583 c.-49A>C upstream_gene_variant 0.94 isoniazid Not assoc w R
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin 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
katG 2154724 p.Arg463Leu missense_variant 0.13 isoniazid Not assoc w R
PPE35 2169221 c.1392T>C synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 0.99 isoniazid Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.17 capreomycin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.99 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.9 ethambutol Not assoc w R
embB 4248397 c.1884C>T synonymous_variant 0.93 ethambutol Not assoc w R - Interim
ethA 4326864 p.Met204Val missense_variant 0.94 ethionamide Uncertain significance
whiB6 4338513 c.9C>T synonymous_variant 0.95 amikacin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
gid 4407927 p.Glu92Asp missense_variant 0.1 streptomycin Not assoc w R