TB-Profiler result

Run: SRR13837517

Summary

Run ID: SRR13837517

Sample name:

Date: 2024-04-14T10:51:18.650414

Number of reads: 587618

Percentage reads mapped: 97.0

Median coverage: 20.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive


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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
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
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
Rv1129c 1254656 c.-123dupG upstream_gene_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rpsA 1833449 c.-93G>T upstream_gene_variant 1.0 pyrazinamide
PPE35 2168966 c.1647G>C synonymous_variant 1.0 pyrazinamide
PPE35 2170688 c.-76G>A upstream_gene_variant 1.0 pyrazinamide
Rv1979c 2222009 p.Phe386Ile missense_variant 1.0 clofazimine
bedaquiline
kasA 2519254 c.1140_1141insA frameshift_variant 1.0 isoniazid
ahpC 2726279 p.Lys29Asn missense_variant 1.0 isoniazid Uncertain significance
Rv2477c 2783642 p.Ala134Glu missense_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783761 c.282G>T synonymous_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2680 2996057 c.-48A>C upstream_gene_variant 1.0 capreomycin
Rv2681 2996557 c.-182G>A upstream_gene_variant 1.0 capreomycin
Rv2681 2997120 c.383dupG frameshift_variant 1.0 capreomycin Uncertain significance
Rv2681 2997593 c.855C>A synonymous_variant 1.0 capreomycin
thyA 3074493 c.-22C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
whiB7 3568433 p.Arg83Cys missense_variant 1.0 streptomycin
amikacin
kanamycin
lpqB 3624666 c.244dupG frameshift_variant 1.0 bedaquiline
rifampicin Uncertain significance
clpC1 4038485 c.2220C>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
embC 4239250 c.-613G>T upstream_gene_variant 1.0 ethambutol
embB 4248644 p.Ala711Pro missense_variant 1.0 ethambutol
aftB 4267225 p.Ile538Phe missense_variant 1.0 ethambutol
ubiA 4269050 p.Tyr262Asp missense_variant 1.0 ethambutol
ethR 4327699 p.Ala51Ser missense_variant 1.0 ethionamide
ethA 4328373 c.-900A>G upstream_gene_variant 1.0 ethionamide
whiB6 4338847 c.-326C>A upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin