TB-Profiler result

Run: SRR7070496
Summary

Run ID: SRR7070496

Sample name:

Date: 2024-10-05T06:33:34.038799

Number of reads: 1983170

Percentage reads mapped: 96.33

Median coverage: 55.0

Strain: lineage4.7

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.7 Euro-American (mainly T) None 0.98
lineage4 Euro-American 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
dnaA 1126 c.1126C>T synonymous_variant 0.95 isoniazid Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
ccsA 619898 p.Thr3Met missense_variant 0.95 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rpoB 760715 c.909C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 775878 p.Thr868Ile missense_variant 1.0 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1258c 1407604 c.-264C>T upstream_gene_variant 1.0 streptomycin
pyrazinamide
isoniazid
embR 1416814 c.534G>A synonymous_variant 0.98 ethambutol Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1833312 c.-230A>G upstream_gene_variant 1.0 pyrazinamide
rpsA 1833961 c.420C>G synonymous_variant 0.13 pyrazinamide
rpsA 1833970 c.429G>T synonymous_variant 0.12 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.13 pyrazinamide
rpsA 1833991 c.450C>G synonymous_variant 0.12 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.12 pyrazinamide
rpsA 1834009 c.468C>T synonymous_variant 0.11 pyrazinamide
rpsA 1834012 c.471G>C synonymous_variant 0.11 pyrazinamide
rpsA 1834015 c.474G>C synonymous_variant 0.11 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.11 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.11 pyrazinamide
rpsA 1834033 c.492C>T synonymous_variant 0.11 pyrazinamide
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2167963 p.Gly884Trp missense_variant 0.93 pyrazinamide Uncertain significance
PPE35 2170675 c.-63G>C upstream_gene_variant 0.97 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpoA 3878816 c.-309T>G upstream_gene_variant 0.96 rifampicin Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249732 c.3219C>G synonymous_variant 0.98 ethambutol Not assoc w R
ubiA 4270004 c.-171G>A upstream_gene_variant 0.98 ethambutol
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R