TB-Profiler result

Run: SRR29231347
Summary

Run ID: SRR29231347

Sample name:

Date: 2025-02-11T11:11:27.389350

Number of reads: 355926

Percentage reads mapped: 99.65

Median coverage: 9.0

Strain: lineage4.3.2;lineage4.3.4.1

Spoligotype:

Drug-resistance: HR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 1.0
lineage4.3.2 Euro-American (LAM) None 0.19
lineage4.3.4.1 Euro-American (LAM) RD174 0.57
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 0.7
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
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
katG 2155168 p.Ser315Thr missense_variant 0.92 isoniazid Assoc w R High-level resistance
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 4988 c.-252C>G upstream_gene_variant 0.75 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
pepQ 2859830 p.Gly197Arg missense_variant 0.8 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv3236c 3612009 p.Ala370Thr missense_variant 0.67 pyrazinamide Not assoc w R
Rv3236c 3612768 p.Ala117Pro missense_variant 0.93 pyrazinamide Uncertain significance
Rv3236c 3613833 c.-717C>A upstream_gene_variant 0.47 pyrazinamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R