TB-Profiler result

Run: SRR29539660
Summary

Run ID: SRR29539660

Sample name:

Date: 2025-02-11T19:12:31.962795

Number of reads: 3009551

Percentage reads mapped: 99.52

Median coverage: 76.0

Strain: lineage2.2.1;lineage4.3.4.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.82
lineage2 East-Asian RD105 0.19
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.16
lineage2.2 East-Asian (Beijing) RD105;RD207 0.2
lineage4.3.4.1 Euro-American (LAM) RD174 0.8
lineage4 Euro-American None 0.85
lineage4.3.4 Euro-American (LAM) RD174 0.89
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-12C>T Uncertain significance Mutation from literature
pyrazinamide
streptomycin rpsL p.Lys88Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-12C>T Assoc w R
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 761155 p.Ser450Leu missense_variant 0.27 rifampicin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.24 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.22 isoniazid Assoc w R High-level resistance
eis 2715344 c.-12C>T upstream_gene_variant 0.16 kanamycin Assoc w R
embA 4243221 c.-12C>T upstream_gene_variant 0.29 ethambutol Uncertain significance 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
Rv0010c 13638 c.-80A>G upstream_gene_variant 0.16 isoniazid Uncertain significance
mshA 575907 p.Ala187Val missense_variant 0.24 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.25 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.21 ethionamide Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.21 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.81 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_variant 0.22 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 776100 p.Thr794Ile missense_variant 0.16 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.14 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.18 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.21 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
sigE 1364434 p.Arg8Trp missense_variant 0.79 pyrazinamide Not assoc w R
sigE 1364706 c.294G>A synonymous_variant 0.2 pyrazinamide Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
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 0.19 isoniazid Not assoc w R
katG 2156618 c.-507C>G upstream_gene_variant 0.18 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.17 pyrazinamide Not assoc w R
Rv1979c 2223123 c.42G>A synonymous_variant 0.86 bedaquiline Not assoc w R - Interim
clofazimine 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 2518020 c.-95A>C upstream_gene_variant 0.75 isoniazid
thyA 3073868 p.Thr202Ala missense_variant 0.7 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.88 pyrazinamide Not assoc w R
Rv3236c 3612813 p.Thr102Ala missense_variant 0.16 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.95 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267097 c.1740C>G synonymous_variant 0.68 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.19 ethambutol Not assoc w R
ethR 4328030 p.Ala161Gly missense_variant 0.24 ethionamide
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 0.18 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.13 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.8 streptomycin Not assoc w R