TB-Profiler result

Run: SRR13837621
Summary

Run ID: SRR13837621

Sample name:

Date: 2024-03-26T19:22:08.444069

Number of reads: 293850

Percentage reads mapped: 98.01

Median coverage: 10.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: HR-TB

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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 katG p.Gly234Glu Uncertain significance Mutation from literature
ethambutol
pyrazinamide
streptomycin
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
katG 2155411 p.Gly234Glu missense_variant 1.0 isoniazid 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
mshA 576259 c.912C>T synonymous_variant 1.0 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rpoC 764895 p.Ile509Thr missense_variant 1.0 rifampicin
mmpL5 778982 c.-502A>C upstream_gene_variant 1.0 clofazimine
bedaquiline
rplC 801169 p.Lys121* stop_gained 1.0 linezolid
rrl 1474052 n.395G>T non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476479 n.2822T>G non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
ndh 2101769 p.Arg425His missense_variant 1.0 ethionamide
delamanid
isoniazid Uncertain significance
pncA 2289474 c.-233C>G upstream_gene_variant 1.0 pyrazinamide
Rv2752c 3065109 c.1083A>G synonymous_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
whiB7 3568816 c.-137C>T upstream_gene_variant 1.0 streptomycin
amikacin
kanamycin
mtrB 3625247 p.Arg456Pro missense_variant 1.0 bedaquiline
rifampicin
embC 4240125 p.Cys88Tyr missense_variant 1.0 ethambutol
ethR 4327643 p.Thr32Ile missense_variant 1.0 ethionamide