TB-Profiler result

Run: ERR11465214
Summary

Run ID: ERR11465214

Sample name:

Date: 2024-04-16T06:36:33.331183

Number of reads: 8931861

Percentage reads mapped: 99.69

Median coverage: 254.0

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
dnaA 1428 c.1428C>T synonymous_variant 0.35 isoniazid Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13331 c.228G>A synonymous_variant 0.65 isoniazid
Rv0010c 13368 p.Thr64Ser missense_variant 0.36 isoniazid Uncertain significance
mshA 576108 p.Ala254Gly missense_variant 0.19 ethionamide
isoniazid
ccsA 620069 p.Thr60Ile missense_variant 0.51 capreomycin
amikacin Uncertain significance
kanamycin Uncertain significance
rpoC 762836 c.-534C>A upstream_gene_variant 0.34 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
atpE 1460992 c.-53A>C upstream_gene_variant 0.37 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2681 2996911 p.Ala58Gly missense_variant 0.64 capreomycin
Rv2752c 3066401 c.-210A>G upstream_gene_variant 0.61 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
mtrA 3627221 c.129C>T synonymous_variant 0.64 bedaquiline
rifampicin Not assoc w R - Interim
alr 3840764 c.657G>C synonymous_variant 1.0 cycloserine
rpoA 3878637 c.-130G>C upstream_gene_variant 0.23 rifampicin
ddn 3986651 c.-193G>C upstream_gene_variant 0.31 delamanid
pretomanid
embC 4242004 p.Leu714Phe missense_variant 0.55 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245553 p.Pro774His missense_variant 0.64 ethambutol Uncertain significance
ethA 4328073 c.-600G>C upstream_gene_variant 0.6 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R