TB-Profiler result

Run: SRR28045811
Summary

Run ID: SRR28045811

Sample name:

Date: 2024-05-22T18:44:46.737172

Number of reads: 6300054

Percentage reads mapped: 99.77

Median coverage: 179.0

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
dnaA 796 p.Asp266His missense_variant 1.0 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mmpL5 776407 c.2073delG frameshift_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 778071 p.Thr137Asn missense_variant 1.0 clofazimine
bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471795 n.-51C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tlyA 1917972 c.33A>G synonymous_variant 0.99 capreomycin Not assoc w R
Rv1979c 2222914 p.Ala84Val missense_variant 0.98 clofazimine
bedaquiline
pepQ 2859639 c.780T>G synonymous_variant 1.0 clofazimine
bedaquiline
clpC1 4039094 c.1611C>A synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
whiB6 4338298 p.Leu75Pro missense_variant 1.0 capreomycin
amikacin
kanamycin
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R