TB-Profiler result

Run: ERR10112415
Summary

Run ID: ERR10112415

Sample name:

Date: 2024-10-05T09:20:22.058387

Number of reads: 381950

Percentage reads mapped: 99.31

Median coverage: 6.0

Strain: lineage2.2.1.1;lineage4

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.2
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.5
lineage2.2 East-Asian (Beijing) RD105;RD207 0.31
lineage4 Euro-American None 0.96
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.18
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 pepQ p.Trp245* Assoc w R - Interim
para-aminosalicylic_acid
delamanid
bedaquiline pepQ p.Trp245* Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
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
pepQ 2859684 p.Trp245* stop_gained 0.4 bedaquiline Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
clofazimine Assoc w R - Interim
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
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 1.0 ethionamide Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 bedaquiline
clofazimine
rpsL 781301 c.-259C>T upstream_gene_variant 1.0 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
eis 2714846 p.Val163Ile missense_variant 1.0 kanamycin Not assoc w R
amikacin Not assoc w R
folC 2747575 c.24G>A synonymous_variant 0.43 para-aminosalicylic_acid
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin