TB-Profiler result

Run: ERR11464996
Summary

Run ID: ERR11464996

Sample name:

Date: 2024-10-04T13:57:40.309594

Number of reads: 5961137

Percentage reads mapped: 99.73

Median coverage: 130.0

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 5611 c.372C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mmaA3 737358 c.792A>C synonymous_variant 0.15 isoniazid
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777122 c.1359C>T synonymous_variant 0.14 bedaquiline
clofazimine
mmpL5 777128 c.1353A>G synonymous_variant 0.15 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
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
ndh 2101834 c.1209C>T synonymous_variant 1.0 isoniazid
delamanid Not assoc w R - Interim
ethionamide
PPE35 2169402 p.Thr404Met missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2169902 p.Leu237Phe missense_variant 0.15 pyrazinamide
PPE35 2169910 p.Asn235Tyr missense_variant 0.17 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223724 c.-560C>G upstream_gene_variant 1.0 bedaquiline
clofazimine
kasA 2519140 c.1026G>C synonymous_variant 0.15 isoniazid
kasA 2519143 c.1029G>C synonymous_variant 0.14 isoniazid
embB 4246548 p.Pro12Gln missense_variant 0.25 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.35 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.38 ethambutol 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