TB-Profiler result

Run: SRR13837535

Summary

Run ID: SRR13837535

Sample name:

Date: 2024-04-15T05:24:51.750107

Number of reads: 588938

Percentage reads mapped: 98.22

Median coverage: 19.0

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 1168 p.Ile390Leu missense_variant 1.0 isoniazid
gyrB 5210 c.-30C>G upstream_gene_variant 1.0 levofloxacin
moxifloxacin
fgd1 490574 c.-209G>C upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
ccsA 620747 p.Gly286Val missense_variant 1.0 capreomycin
amikacin
kanamycin
mmpS5 778670 p.Gln79Pro missense_variant 1.0 clofazimine
bedaquiline
rpsL 781927 p.Lys123Met missense_variant 0.95 streptomycin
Rv1129c 1253316 p.Gly407Ser missense_variant 1.0 moxifloxacin
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
fbiC 1304806 p.Pro626Thr missense_variant 0.95 clofazimine
pretomanid
delamanid
embR 1417610 c.-264_-263insA upstream_gene_variant 1.0 ethambutol
rpsA 1834614 p.Ile358Ser missense_variant 1.0 pyrazinamide
tsnR 1853786 c.181T>C synonymous_variant 1.0 linezolid
PPE35 2169834 p.Gly260Val missense_variant 1.0 pyrazinamide
kasA 2518887 p.Gly258Val missense_variant 1.0 isoniazid
eis 2715520 c.-188C>T upstream_gene_variant 1.0 amikacin
kanamycin
ahpC 2725916 c.-277_-276insA upstream_gene_variant 1.0 isoniazid
Rv2477c 2782523 p.Thr507Met missense_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2782875 p.Asp390His missense_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2784377 c.-335T>C upstream_gene_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
pepQ 2859750 c.669C>T synonymous_variant 1.0 clofazimine
bedaquiline
lpqB 3623317 p.Gln532Glu missense_variant 1.0 bedaquiline
rifampicin
panD 4044912 c.-631T>A upstream_gene_variant 1.0 pyrazinamide
glpK 4139251 p.Gly169Cys missense_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embA 4245437 p.Met735Ile missense_variant 1.0 ethambutol Uncertain significance
embB 4246876 c.363G>A synonymous_variant 1.0 ethambutol
embB 4248914 p.Ala801Thr missense_variant 1.0 ethambutol Uncertain significance
ubiA 4269329 p.Lys169Glu missense_variant 1.0 ethambutol
ethA 4326973 p.Trp167Cys missense_variant 1.0 ethionamide Uncertain significance
ethA 4327382 p.Ser31Ile missense_variant 1.0 ethionamide