TB-Profiler result

Run: SRR21764243
Summary

Run ID: SRR21764243

Sample name:

Date: 2025-03-09T00:45:04.897551

Number of reads: 31458703

Percentage reads mapped: 99.96

Median coverage: 809.0

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.Glu340* Assoc w R High-level resistance
p.Ser315Ile Assoc w R - Interim High-level resistance
c.678delG Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G 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
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.97 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
katG 2155094 p.Glu340* stop_gained 0.42 isoniazid Assoc w R High-level resistance
katG 2155168 p.Ser315Ile missense_variant 0.29 isoniazid Assoc w R - Interim High-level resistance
katG 2155433 c.678delG frameshift_variant 0.12 isoniazid Assoc w R High-level resistance
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 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
PPE35 2170598 c.15G>A synonymous_variant 1.0 pyrazinamide Uncertain significance