TB-Profiler result

Run: SRR13837744
Summary

Run ID: SRR13837744

Sample name:

Date: 2025-03-09T03:25:42.404763

Number of reads: 2936428

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
gyrB 6561 p.Lys441Arg missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7705 p.Thr135Ser missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8409 p.Leu370Ile missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
Rv0010c 13327 p.Leu78Ile missense_variant 1.0 isoniazid Uncertain significance
ccsA 619637 c.-254T>G upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
ccsA 620157 c.267G>T synonymous_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
rplC 801215 c.408delC frameshift_variant 1.0 linezolid Uncertain significance
Rv1129c 1253639 p.Leu299* stop_gained 1.0 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
fbiC 1304409 c.1479C>G synonymous_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiC 1304501 p.Ala524Gly missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
sigE 1365081 c.669G>T synonymous_variant 1.0 pyrazinamide Uncertain significance
rrs 1472791 n.946G>C non_coding_transcript_exon_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
PPE35 2168564 c.2049T>A synonymous_variant 1.0 pyrazinamide Uncertain significance
kasA 2519179 c.1065G>C synonymous_variant 1.0 isoniazid Uncertain significance
folC 2746546 p.Asp351Glu missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
Rv2477c 2784407 c.-365A>G 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
Rv2680 2996063 c.-42G>C upstream_gene_variant 1.0 capreomycin Uncertain significance
thyX 3068038 c.-93C>A upstream_gene_variant 1.0 para-aminosalicylic_acid Uncertain significance
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 amikacin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
Rv3236c 3612721 c.396G>T synonymous_variant 1.0 pyrazinamide Uncertain significance
fbiA 3641221 p.Pro227Ala missense_variant 0.99 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
rpoA 3879230 c.-723C>G upstream_gene_variant 0.99 rifampicin Uncertain significance
clpC1 4039647 p.Glu353Ala missense_variant 1.0 pyrazinamide Uncertain significance
clpC1 4040955 c.-251A>C upstream_gene_variant 1.0 pyrazinamide Uncertain significance
embC 4239484 c.-379T>C upstream_gene_variant 0.99 ethambutol Uncertain significance
embC 4240006 c.144A>C synonymous_variant 1.0 ethambutol Uncertain significance
embA 4244074 p.Ala281Val missense_variant 1.0 ethambutol Uncertain significance
embA 4245739 p.Arg836His missense_variant 1.0 ethambutol Uncertain significance
ethA 4326731 p.Ala248Gly missense_variant 1.0 ethionamide Uncertain significance
ethR 4327623 c.75_76insC frameshift_variant 1.0 ethionamide Uncertain significance
gid 4408334 c.-132G>T upstream_gene_variant 1.0 streptomycin Uncertain significance