TB-Profiler result

Run: ERR13290102
Summary

Run ID: ERR13290102

Sample name:

Date: 2024-10-04T03:14:23.676119

Number of reads: 2600426

Percentage reads mapped: 99.77

Median coverage: 69.0

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
gyrA 9222 p.Asp641His missense_variant 1.0 levofloxacin
moxifloxacin
ccsA 620483 p.Val198Ala missense_variant 1.0 kanamycin
capreomycin
amikacin
rpoB 761843 c.2037C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 763867 c.498C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
atpE 1460825 c.-220C>T upstream_gene_variant 1.0 bedaquiline
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 2223344 c.-180A>G upstream_gene_variant 1.0 bedaquiline
clofazimine
pepQ 2859915 c.504C>T synonymous_variant 1.0 bedaquiline
clofazimine
whiB7 3569040 c.-361C>T upstream_gene_variant 1.0 kanamycin
amikacin
streptomycin
ddn 3987238 p.Ser132Ile missense_variant 1.0 pretomanid
delamanid
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R