TB-Profiler result

Run: SRR23650981
Summary

Run ID: SRR23650981

Sample name:

Date: 2024-03-26T15:23:40.683263

Number of reads: 11266431

Percentage reads mapped: 99.94

Median coverage: 250.0

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.Lys414Asn Mutation from literature
p.Asn138Ser 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 2154870 p.Lys414Asn missense_variant 0.38 isoniazid Mutation from literature
katG 2155699 p.Asn138Ser missense_variant 0.41 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1476561 n.2904C>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
katG 2155627 p.Ala162Glu missense_variant 0.18 isoniazid Uncertain significance
ahpC 2726121 c.-72C>T upstream_gene_variant 0.38 isoniazid Uncertain significance
ahpC 2726213 c.21C>A synonymous_variant 0.14 isoniazid Not assoc w R - Interim
rpoA 3878614 c.-107A>C upstream_gene_variant 0.15 rifampicin
embB 4247028 p.Leu172Arg missense_variant 0.21 ethambutol
embB 4247033 p.Ser174Arg missense_variant 0.17 ethambutol