TB-Profiler result

Run: SRR13837932
Summary

Run ID: SRR13837932

Sample name:

Date: 2024-10-05T02:16:49.918321

Number of reads: 1472870

Percentage reads mapped: 96.25

Median coverage: 50.0

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 0.98 isoniazid
gyrB 5807 p.Val190Phe missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 6898 c.-404G>C upstream_gene_variant 1.0 levofloxacin
moxifloxacin
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 isoniazid
ethionamide
mshA 575414 p.Gly23Ser missense_variant 1.0 isoniazid
ethionamide
Rv0565c 656618 p.His285Asp missense_variant 1.0 ethionamide
mmaA3 738178 c.-29T>A upstream_gene_variant 1.0 isoniazid
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
rpsA 1834248 p.His236Leu missense_variant 0.98 pyrazinamide
bacA 2063871 p.Phe286Leu missense_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
katG 2154449 p.Ala555Ser missense_variant 1.0 isoniazid
PPE35 2170218 p.Ala132Glu missense_variant 1.0 pyrazinamide
eis 2715396 c.-65delT upstream_gene_variant 1.0 kanamycin
amikacin
ribD 2987136 p.Val100Ile missense_variant 1.0 para-aminosalicylic_acid
ribD 2987590 p.Leu251Arg missense_variant 1.0 para-aminosalicylic_acid
Rv2681 2996731 c.-8C>A upstream_gene_variant 1.0 capreomycin
Rv2752c 3064996 p.Thr399Asn missense_variant 0.98 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
alr 3841281 p.His47Arg missense_variant 1.0 cycloserine
clpC1 4039292 c.1413C>A synonymous_variant 1.0 pyrazinamide
clpC1 4039426 p.Lys427Gln missense_variant 1.0 pyrazinamide
embA 4243228 c.-5G>T upstream_gene_variant 1.0 ethambutol Uncertain significance
embA 4243540 p.Ala103Asp missense_variant 1.0 ethambutol
embA 4244146 p.Asp305Ala missense_variant 1.0 ethambutol
embB 4249506 c.2994delG frameshift_variant 1.0 ethambutol