TB-Profiler result

Run: SRR13837963
Summary

Run ID: SRR13837963

Sample name:

Date: 2025-03-05T19:27:05.070112

Number of reads: 2936204

Percentage reads mapped: 100.0

Median coverage: 100.0

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
rpoB 761402 c.1596C>T synonymous_variant 1.0 rifampicin Uncertain significance
rpoC 762473 c.-897C>A upstream_gene_variant 1.0 rifampicin Uncertain significance
mmpS5 778694 p.Tyr71Ser missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpR5 779478 p.Glu163Asp missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rplC 800969 p.Tyr54Ser missense_variant 1.0 linezolid Uncertain significance
embR 1417498 c.-151G>T upstream_gene_variant 1.0 ethambutol Uncertain significance
embR 1417937 c.-591_-590insA upstream_gene_variant 1.0 ethambutol Uncertain significance
rrs 1473125 n.1280A>T non_coding_transcript_exon_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1475195 n.1538G>T non_coding_transcript_exon_variant 0.99 capreomycin Uncertain significance
linezolid Uncertain significance
katG 2155952 p.Val54Ile missense_variant 1.0 isoniazid Uncertain significance
Rv1979c 2223817 c.-653C>A upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
kasA 2518986 p.Met291Arg missense_variant 1.0 isoniazid Uncertain significance
Rv2752c 3065218 p.Ser325Ile missense_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv3083 3448654 p.Pro51Ala missense_variant 1.0 ethionamide Uncertain significance
whiB7 3568465 p.Asp72Val missense_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
mtrB 3627381 c.-768G>A upstream_gene_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
fbiA 3640597 p.Val19Leu missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
alr 3840493 p.Leu310Val missense_variant 1.0 cycloserine Uncertain significance
panD 4044931 c.-650C>G upstream_gene_variant 1.0 pyrazinamide Uncertain significance
embC 4239802 c.-61T>A upstream_gene_variant 1.0 ethambutol Uncertain significance
embC 4241184 p.Thr441Lys missense_variant 1.0 ethambutol Uncertain significance
embA 4243518 p.Gly96Cys missense_variant 1.0 ethambutol Uncertain significance
embA 4244162 c.931dupC frameshift_variant 1.0 ethambutol Uncertain significance
embB 4247920 c.1407T>C synonymous_variant 1.0 ethambutol Uncertain significance
ethA 4327042 p.Asp144Glu missense_variant 1.0 ethionamide Uncertain significance
ethR 4327865 p.Gly106Ala missense_variant 1.0 ethionamide Uncertain significance