TB-Profiler result

Run: SRR13837954

Summary

Run ID: SRR13837954

Sample name:

Date: 2024-03-26T17:00:49.839461

Number of reads: 1469114

Percentage reads mapped: 97.0

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
gyrB 5624 p.Asn129Asp missense_variant 1.0 levofloxacin
moxifloxacin
mshA 575194 c.-154G>T upstream_gene_variant 1.0 ethionamide
isoniazid
hadA 731960 p.His11Asp missense_variant 1.0 isoniazid
hadA 732111 p.Cys61Tyr missense_variant 1.0 isoniazid
rpoB 760907 c.1101_1102insT frameshift_variant 1.0 rifampicin
rplC 801226 p.Gly140Arg missense_variant 1.0 linezolid
Rv1129c 1253913 p.Ile208Phe missense_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv1129c 1254602 c.-68C>T upstream_gene_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv1129c 1254678 c.-144A>G upstream_gene_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
sigE 1364750 p.Thr113Ser missense_variant 1.0 pyrazinamide
embR 1417503 c.-156A>C upstream_gene_variant 1.0 ethambutol
embR 1417613 c.-266C>G upstream_gene_variant 1.0 ethambutol
rrl 1476753 n.3099delG non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
fabG1 1673233 c.-207T>G upstream_gene_variant 1.0 ethionamide
isoniazid
rpsA 1833593 c.53delC frameshift_variant 1.0 pyrazinamide Uncertain significance
rpsA 1834884 p.Gln448Leu missense_variant 1.0 pyrazinamide
bacA 2064646 p.Thr28Arg missense_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
PPE35 2169282 p.Arg444His missense_variant 1.0 pyrazinamide
ahpC 2725932 c.-261G>A upstream_gene_variant 1.0 isoniazid
Rv2477c 2783645 p.Asp133Gly missense_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
pepQ 2859739 p.Ala227Gly missense_variant 1.0 clofazimine
bedaquiline
pepQ 2860197 c.222T>C synonymous_variant 1.0 clofazimine
bedaquiline
Rv2681 2997172 p.Asp145Gly missense_variant 1.0 capreomycin
Rv3083 3448909 p.Leu136Ile missense_variant 1.0 ethionamide
mtrA 3627160 p.Gly64Ser missense_variant 1.0 bedaquiline
rifampicin
fbiA 3640691 p.Asp50Val missense_variant 1.0 clofazimine
pretomanid
delamanid
fbiA 3641204 p.Gly221Asp missense_variant 1.0 clofazimine
pretomanid
delamanid
rpoA 3878967 c.-460G>T upstream_gene_variant 1.0 rifampicin
clpC1 4039961 p.Tyr248* stop_gained 1.0 pyrazinamide
glpK 4138333 p.Ser475Pro missense_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4240818 p.Thr319Arg missense_variant 1.0 ethambutol
embB 4248081 c.1569dupG frameshift_variant 1.0 ethambutol
ethA 4327644 c.-171G>A upstream_gene_variant 1.0 ethionamide