TB-Profiler result

Run: SRR13837526
Summary

Run ID: SRR13837526

Sample name:

Date: 2024-04-14T10:51:23.864459

Number of reads: 590292

Percentage reads mapped: 96.43

Median coverage: 20.0

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 6561 p.Lys441Arg missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 7705 p.Thr135Ser missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 8409 p.Leu370Ile missense_variant 1.0 levofloxacin
moxifloxacin
Rv0010c 13327 p.Leu78Ile missense_variant 1.0 isoniazid
ccsA 619637 c.-254T>G upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
ccsA 620157 c.267G>T synonymous_variant 1.0 capreomycin
amikacin
kanamycin
Rv1129c 1253639 p.Leu299* stop_gained 1.0 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
fbiC 1304409 c.1479C>G synonymous_variant 1.0 clofazimine
pretomanid
delamanid
fbiC 1304501 p.Ala524Gly missense_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
sigE 1365081 c.669G>T synonymous_variant 1.0 pyrazinamide
rrs 1472791 n.946G>C non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin Uncertain significance
capreomycin
amikacin Uncertain significance
PPE35 2168564 c.2049T>A synonymous_variant 1.0 pyrazinamide
kasA 2519179 c.1065G>C synonymous_variant 1.0 isoniazid
folC 2746546 p.Asp351Glu missense_variant 1.0 para-aminosalicylic_acid
Rv2477c 2784407 c.-365A>G upstream_gene_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2680 2996063 c.-42G>C upstream_gene_variant 1.0 capreomycin
thyX 3068038 c.-93C>A upstream_gene_variant 1.0 para-aminosalicylic_acid
Rv3083 3448608 c.105G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
whiB7 3569032 c.-353C>A upstream_gene_variant 1.0 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
Rv3236c 3612721 c.396G>T synonymous_variant 1.0 pyrazinamide
fbiA 3641221 p.Pro227Ala missense_variant 1.0 clofazimine
pretomanid
delamanid
rpoA 3879230 c.-723C>G upstream_gene_variant 1.0 rifampicin
clpC1 4039647 p.Glu353Ala missense_variant 0.95 pyrazinamide
clpC1 4040955 c.-251A>C upstream_gene_variant 1.0 pyrazinamide
embC 4239484 c.-379T>C upstream_gene_variant 1.0 ethambutol
embC 4240006 c.144A>C synonymous_variant 1.0 ethambutol
embA 4244074 p.Ala281Val missense_variant 1.0 ethambutol
embA 4245739 p.Arg836His missense_variant 1.0 ethambutol
ethA 4326731 p.Ala248Gly missense_variant 1.0 ethionamide
ethR 4327623 c.75_76insC frameshift_variant 1.0 ethionamide Uncertain significance