TB-Profiler result

Run: ERR13261674
Summary

Run ID: ERR13261674

Sample name:

Date: 2025-02-11T19:48:42.463463

Number of reads: 5937870

Percentage reads mapped: 99.58

Median coverage: 186.0

Strain: lineage2.2.1;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
lineage2 East-Asian RD105 0.14
lineage4.1 Euro-American None 0.88
lineage4.1.2 Euro-American None 0.88
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.87
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.13
lineage2.2 East-Asian (Beijing) RD105;RD207 0.13
lineage4 Euro-American None 0.88
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Val Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin gid c.39dupA 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 761110 p.Asp435Val missense_variant 0.89 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
gid 4408163 c.39dupA frameshift_variant 0.77 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
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 0.87 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.18 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.87 isoniazid Not assoc w R
ethionamide Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.11 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.14 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.12 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.14 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.85 ethionamide Uncertain significance
rpoB 760106 c.300G>A synonymous_variant 0.89 rifampicin Not assoc w R
rpoB 760115 c.309C>T synonymous_variant 0.89 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.15 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.84 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 775817 c.2664T>C synonymous_variant 0.14 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.16 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.16 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.15 bedaquiline
clofazimine
rpsL 781276 c.-284A>C upstream_gene_variant 0.91 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254583 c.-49A>C upstream_gene_variant 0.9 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.15 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471647 n.-199G>C upstream_gene_variant 0.12 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
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
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 0.9 isoniazid
Rv2680 2996136 p.Ser11Asn missense_variant 0.18 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.11 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3641454 c.912G>A synonymous_variant 0.88 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
embC 4239298 c.-565C>T upstream_gene_variant 0.88 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 0.84 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.24 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.17 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 4407927 p.Glu92Asp missense_variant 0.15 streptomycin Not assoc w R