TB-Profiler result

Run: ERR11465367
Summary

Run ID: ERR11465367

Sample name:

Date: 2024-04-15T23:19:56.234232

Number of reads: 3349699

Percentage reads mapped: 99.73

Median coverage: 63.0

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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13852 c.-294A>G upstream_gene_variant 1.0 isoniazid
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
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 streptomycin
kanamycin
capreomycin
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 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
clpC1 4038408 p.Pro766Gln missense_variant 1.0 pyrazinamide
embA 4244832 p.Val534Met missense_variant 1.0 ethambutol Uncertain significance
embB 4246544 p.Thr11Pro missense_variant 0.65 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.43 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.42 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.42 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.36 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.34 ethambutol Not assoc w R - Interim
embB 4248409 p.Leu632Phe 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