TB-Profiler result

Run: ERR13290892
Summary

Run ID: ERR13290892

Sample name:

Date: 2024-10-04T01:28:05.216791

Number of reads: 331459

Percentage reads mapped: 99.69

Median coverage: 9.0

Strain: lineage2.1;lineage4.3

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.78
lineage2.1 East-Asian (non-Beijing) None 0.08
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 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.9 rifampicin Not assoc w R
rplC 800179 c.-630G>C upstream_gene_variant 0.93 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.29 pyrazinamide Not assoc w R - Interim
rpsA 1834836 p.Met432Thr missense_variant 0.9 pyrazinamide Not assoc w R - Interim
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.55 isoniazid 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 2783320 c.723C>T synonymous_variant 0.77 kanamycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
amikacin Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
glpK 4139365 p.Arg131Ser missense_variant 0.82 levofloxacin
moxifloxacin
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol 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
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407720 c.483C>G synonymous_variant 0.85 streptomycin Not assoc w R - Interim