TB-Profiler result

Run: SRR13837718
Summary

Run ID: SRR13837718

Sample name:

Date: 2025-03-07T09:36:50.339201

Number of reads: 2936288

Percentage reads mapped: 100.0

Median coverage: 99.0

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
gyrB 5149 c.-91G>C upstream_gene_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 7090 p.Asp617Glu missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8436 p.Tyr379Asn missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
fgd1 491701 p.His307Asn missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
ccsA 619765 c.-126G>A upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
hadA 731718 c.-212T>C upstream_gene_variant 1.0 isoniazid Uncertain significance
mmpL5 775867 p.Arg872Gly missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 776710 p.Cys591Ser missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 777625 p.Gln286Lys missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpS5 778811 p.Phe32Ser missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
embR 1416901 c.447G>C synonymous_variant 1.0 ethambutol Uncertain significance
rrl 1474466 n.810delA non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475224 n.1567T>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476589 n.2932G>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
bacA 2063516 p.Val405Ile missense_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
PPE35 2170487 c.126T>A synonymous_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2221853 p.Phe438Ile missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
ribD 2987369 c.531G>A synonymous_variant 1.0 para-aminosalicylic_acid Uncertain significance
thyA 3073975 p.Arg166Pro missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
Rv3236c 3612013 c.1104A>T synonymous_variant 1.0 pyrazinamide Uncertain significance
Rv3236c 3612032 p.Met362Arg missense_variant 1.0 pyrazinamide Uncertain significance
Rv3236c 3613624 c.-508T>A upstream_gene_variant 1.0 pyrazinamide Uncertain significance
mtrB 3625654 c.959delT frameshift_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3627491 c.-878G>T upstream_gene_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
embC 4240425 p.Arg188Pro missense_variant 1.0 ethambutol Uncertain significance
embC 4240477 c.615C>A synonymous_variant 1.0 ethambutol Uncertain significance
embA 4244214 p.Ala328Ser missense_variant 1.0 ethambutol Uncertain significance
embA 4244849 c.1617C>G synonymous_variant 1.0 ethambutol Uncertain significance
embB 4247198 p.Thr229Pro missense_variant 1.0 ethambutol Uncertain significance
embB 4247381 p.Trp290Arg missense_variant 1.0 ethambutol Uncertain significance
aftB 4268115 p.Leu241Arg missense_variant 1.0 ethambutol Uncertain significance
aftB 4268696 c.141G>A synonymous_variant 0.99 ethambutol Uncertain significance
ethA 4326298 c.1176G>A synonymous_variant 1.0 ethionamide Uncertain significance
whiB6 4338567 c.-46C>A upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance