TB-Profiler result

Run: SRR13837423
Summary

Run ID: SRR13837423

Sample name:

Date: 2025-03-05T08:00:09.375894

Number of reads: 2936357

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
dnaA 819 c.819C>A synonymous_variant 1.0 isoniazid Uncertain significance
gyrB 5807 p.Val190Phe missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 6898 c.-404G>C upstream_gene_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8039 c.738T>C synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
mshA 575293 c.-55T>A upstream_gene_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
mshA 575414 p.Gly23Ser missense_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
Rv0565c 656618 p.His285Asp missense_variant 1.0 ethionamide Uncertain significance
mmaA3 738178 c.-29T>A upstream_gene_variant 0.98 isoniazid Uncertain significance
rpoC 765124 c.1755G>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
embR 1417578 c.-231T>C upstream_gene_variant 1.0 ethambutol Uncertain significance
rpsA 1834248 p.His236Leu missense_variant 1.0 pyrazinamide Uncertain significance
bacA 2063871 p.Phe286Leu missense_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
katG 2154449 p.Ala555Ser missense_variant 1.0 isoniazid Uncertain significance
PPE35 2170218 p.Ala132Glu missense_variant 1.0 pyrazinamide Uncertain significance
eis 2715396 c.-65delT upstream_gene_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
ribD 2987136 p.Val100Ile missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
ribD 2987590 p.Leu251Arg missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
Rv2681 2996731 c.-8C>A upstream_gene_variant 1.0 capreomycin Uncertain significance
Rv2752c 3064996 p.Thr399Asn missense_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
alr 3841281 p.His47Arg missense_variant 1.0 cycloserine Uncertain significance
clpC1 4039292 c.1413C>A synonymous_variant 1.0 pyrazinamide Uncertain significance
clpC1 4039426 p.Lys427Gln missense_variant 0.99 pyrazinamide Uncertain significance
embA 4243228 c.-5G>T upstream_gene_variant 1.0 ethambutol Uncertain significance
embA 4243540 p.Ala103Asp missense_variant 1.0 ethambutol Uncertain significance
embA 4244146 p.Asp305Ala missense_variant 1.0 ethambutol Uncertain significance
embB 4249506 c.2994delG frameshift_variant 1.0 ethambutol Uncertain significance