TB-Profiler result

Run: SRR13837989
Summary

Run ID: SRR13837989

Sample name:

Date: 2024-04-15T14:54:07.343354

Number of reads: 883308

Percentage reads mapped: 98.21

Median coverage: 30.0

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
moxifloxacin
gyrB 7090 p.Asp617Glu missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 8436 p.Tyr379Asn missense_variant 1.0 levofloxacin
moxifloxacin
fgd1 491701 p.His307Asn missense_variant 1.0 clofazimine
pretomanid
delamanid
ccsA 619765 c.-126G>A upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
hadA 731718 c.-212T>C upstream_gene_variant 1.0 isoniazid
mmpL5 775867 p.Arg872Gly missense_variant 1.0 clofazimine
bedaquiline
mmpL5 776710 p.Cys591Ser missense_variant 1.0 clofazimine
bedaquiline
mmpL5 777625 p.Gln286Lys missense_variant 1.0 clofazimine
bedaquiline
mmpS5 778811 p.Phe32Ser missense_variant 1.0 clofazimine
bedaquiline
embR 1416901 c.447G>C synonymous_variant 1.0 ethambutol
rrl 1474466 n.810delA non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1475224 n.1567T>C non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476589 n.2932G>A non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
bacA 2063516 p.Val405Ile missense_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
PPE35 2170487 c.126T>A synonymous_variant 1.0 pyrazinamide
Rv1979c 2221853 p.Phe438Ile missense_variant 0.97 clofazimine
bedaquiline
ribD 2987369 c.531G>A synonymous_variant 1.0 para-aminosalicylic_acid
thyA 3073975 p.Arg166Pro missense_variant 1.0 para-aminosalicylic_acid
Rv3236c 3612013 c.1104A>T synonymous_variant 1.0 pyrazinamide
Rv3236c 3612032 p.Met362Arg missense_variant 1.0 pyrazinamide
Rv3236c 3613624 c.-508T>A upstream_gene_variant 1.0 pyrazinamide
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
rifampicin
embC 4240425 p.Arg188Pro missense_variant 1.0 ethambutol
embC 4240477 c.615C>A synonymous_variant 1.0 ethambutol
embA 4244214 p.Ala328Ser missense_variant 1.0 ethambutol
embA 4244849 c.1617C>G synonymous_variant 1.0 ethambutol
embB 4247198 p.Thr229Pro missense_variant 1.0 ethambutol
embB 4247381 p.Trp290Arg missense_variant 1.0 ethambutol
aftB 4268115 p.Leu241Arg missense_variant 1.0 ethambutol
aftB 4268696 c.141G>A synonymous_variant 1.0 ethambutol
ethA 4326298 c.1176G>A synonymous_variant 1.0 ethionamide
whiB6 4338567 c.-46C>A upstream_gene_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance