TB-Profiler result

Run: ERR3470585
Summary

Run ID: ERR3470585

Sample name:

Date: 2024-04-16T09:41:45.226424

Number of reads: 6314675

Percentage reads mapped: 99.76

Median coverage: 186.0

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
gyrA 7362 p.Glu21Gln missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 576108 p.Ala254Gly missense_variant 0.25 ethionamide
isoniazid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2169044 c.1569G>C synonymous_variant 0.46 pyrazinamide Not assoc w R - Interim
PPE35 2169047 c.1564_1566delATCinsGT frameshift_variant&missense_variant 0.33 pyrazinamide Uncertain significance
PPE35 2169053 c.1560T>C synonymous_variant 1.0 pyrazinamide Not assoc w R
PPE35 2169056 c.1557A>G synonymous_variant 0.33 pyrazinamide Not assoc w R - Interim
PPE35 2169063 p.Met517Thr missense_variant 1.0 pyrazinamide
PPE35 2169071 c.1542A>G synonymous_variant 0.25 pyrazinamide Not assoc w R - Interim
embA 4244697 p.Val489Ile missense_variant 1.0 ethambutol Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R