TB-Profiler result

Run: ERR2229756
Summary

Run ID: ERR2229756

Sample name:

Date: 2024-04-15T18:31:34.833914

Number of reads: 719738

Percentage reads mapped: 99.28

Median coverage: 18.0

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) RD219 0.68
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
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
fbiC 1303747 p.Thr273Ala missense_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
PPE35 2168728 p.Gly629Arg missense_variant 1.0 pyrazinamide Uncertain significance
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
alr 3841612 c.-193_-192insC upstream_gene_variant 0.26 cycloserine
embB 4246544 p.Thr11Pro missense_variant 0.4 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.37 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.44 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.44 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.43 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.4 ethambutol Not assoc w R - Interim