TB-Profiler result

Run: SRR13861398
Summary

Run ID: SRR13861398

Sample name:

Date: 2024-04-15T05:25:17.620406

Number of reads: 263630

Percentage reads mapped: 8.8

Median coverage: 9.0

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 6027 p.His263Arg missense_variant 1.0 levofloxacin
moxifloxacin
rpoB 760178 c.372G>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
mmpL5 777280 p.Ala401Ser missense_variant 1.0 clofazimine
bedaquiline
rpsL 781277 c.-283G>C upstream_gene_variant 1.0 streptomycin
rplC 800213 c.-596G>T upstream_gene_variant 1.0 linezolid
katG 2155675 p.Arg146Leu missense_variant 1.0 isoniazid Uncertain significance
Rv1979c 2222433 c.732A>G synonymous_variant 1.0 clofazimine
bedaquiline
Rv2680 2996147 p.Glu15Gln missense_variant 1.0 capreomycin
Rv2681 2996821 p.Gly28Val missense_variant 1.0 capreomycin
alr 3840284 p.Trp379* stop_gained 1.0 cycloserine
embB 4245806 c.-708G>A upstream_gene_variant 1.0 ethambutol
embB 4249763 p.Thr1084Pro missense_variant 1.0 ethambutol Uncertain significance
ethA 4326860 p.Leu205Pro missense_variant 1.0 ethionamide Uncertain significance