TB-Profiler result

Run: SRR13837752
Summary

Run ID: SRR13837752

Sample name:

Date: 2025-03-08T16:26:09.004301

Number of reads: 2936556

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