TB-Profiler result

Run: SRR13837699
Summary

Run ID: SRR13837699

Sample name:

Date: 2024-04-15T05:24:58.995108

Number of reads: 295602

Percentage reads mapped: 95.58

Median coverage: 10.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

Download CSV Download TXT Download JSON
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
mshA 576327 p.Phe327Tyr missense_variant 1.0 ethionamide
isoniazid
rpoB 759707 c.-100C>T upstream_gene_variant 1.0 rifampicin
rpoB 760178 c.372G>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 762284 c.2478G>A synonymous_variant 1.0 rifampicin
rpoC 764262 p.Val298Ala missense_variant 1.0 rifampicin
mmpL5 777280 p.Ala401Ser missense_variant 1.0 clofazimine
bedaquiline
mmpS5 778853 p.Val18Ala missense_variant 1.0 clofazimine
bedaquiline
rrl 1476288 n.2631T>C non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
Rv2681 2996821 p.Gly28Val missense_variant 1.0 capreomycin
ald 3086631 c.-189A>G upstream_gene_variant 1.0 cycloserine
Rv3236c 3613619 c.-503T>G upstream_gene_variant 1.0 pyrazinamide
alr 3840284 p.Trp379* stop_gained 1.0 cycloserine
glpK 4139736 p.Gly7Val missense_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4239589 c.-273delA upstream_gene_variant 1.0 ethambutol
embB 4245806 c.-708G>A upstream_gene_variant 0.93 ethambutol