TB-Profiler result

Run: SRR6397536
Summary

Run ID: SRR6397536

Sample name:

Date: 2024-10-05T10:32:04.420101

Number of reads: 6013749

Percentage reads mapped: 99.61

Median coverage: 171.0

Strain: lineage4.7

Spoligotype:

Drug-resistance: Other

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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 0.99
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 gyrB p.Thr500Ile Uncertain significance Mutation from literature
ofloxacin
levofloxacin gyrB p.Thr500Ile Uncertain significance Mutation from literature
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
gyrB 6738 p.Thr500Ile missense_variant 0.92 levofloxacin Uncertain significance Mutation from literature
moxifloxacin Uncertain significance Mutation from literature
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 408 p.Ser136Arg missense_variant 1.0 isoniazid Uncertain significance
dnaA 1272 c.1272C>T synonymous_variant 0.99 isoniazid Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8353 p.Gly351Ala missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
mmaA3 738278 c.-129T>C upstream_gene_variant 1.0 isoniazid
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 775700 c.2781G>T synonymous_variant 0.99 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
fbiC 1303116 c.186C>T synonymous_variant 0.97 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv3236c 3613779 c.-663T>C upstream_gene_variant 0.93 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244732 c.1500G>C synonymous_variant 0.99 ethambutol Not assoc w R - Interim
embB 4249732 c.3219C>G synonymous_variant 1.0 ethambutol Not assoc w R
ethR 4327828 p.Pro94Ser missense_variant 0.99 ethionamide Uncertain significance
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 4407590 p.Ala205Thr missense_variant 0.99 streptomycin Uncertain significance