TB-Profiler result

Run: ERR4815116
Summary

Run ID: ERR4815116

Sample name:

Date: 2024-10-05T07:16:47.281026

Number of reads: 2980347

Percentage reads mapped: 99.39

Median coverage: 65.5

Strain: lineage4

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
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 13473 p.Thr29Ile missense_variant 1.0 isoniazid Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
fbiC 1302626 c.-305G>A upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
embR 1417270 c.78C>T synonymous_variant 1.0 ethambutol 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
Rv2477c 2782818 p.Gly409Ser missense_variant 1.0 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
amikacin Uncertain significance
Rv2681 2996837 c.99G>A synonymous_variant 1.0 capreomycin Not assoc w R - Interim
Rv2752c 3065805 c.387C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethR 4327854 p.Met102Ile missense_variant 1.0 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