TB-Profiler result

Run: ERR2202618
Summary

Run ID: ERR2202618

Sample name:

Date: 2024-10-04T20:17:59.867255

Number of reads: 2390826

Percentage reads mapped: 99.72

Median coverage: 80.0

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 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
dnaA 371 p.Pro124Leu missense_variant 1.0 isoniazid Not assoc w R
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 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168963 c.1650A>G synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
PPE35 2168975 c.1638C>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
PPE35 2168981 c.1632A>G synonymous_variant 0.96 pyrazinamide Not assoc w R - Interim
PPE35 2168985 p.Thr543Met missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2168987 p.Thr542Ala missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2168990 c.1623T>G synonymous_variant 1.0 pyrazinamide
PPE35 2170048 p.Leu189Val missense_variant 0.25 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0 ethionamide Uncertain significance
alr 3840764 c.657G>C synonymous_variant 0.99 cycloserine
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326166 c.1308A>G synonymous_variant 1.0 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R