TB-Profiler result

Run: 7d642402-4dba-4603-904d-ac690689400a
Summary

Run ID: 7d642402-4dba-4603-904d-ac690689400a

Sample name:

Date: 27-11-2023 14:59:04

Number of reads: 4271155

Percentage reads mapped: 98.48

Median coverage: 117

Strain: lineage4.8

Spoligotype:

Drug-resistance: Sensitive

Download CSV Download TXT Download JSON
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
moxifloxacin
levofloxacin
bedaquiline
delamanid
pretomanid
linezolid
streptomycin
amikacin
kanamycin
capreomycin
clofazimine
ethionamide
para-aminosalicylic_acid
cycloserine
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 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
mshA 576108 p.Ala254Gly missense_variant 0.25 ethionamide Uncertain significance
isoniazid
mshA 576113 p.Arg256Gly missense_variant 0.32 ethionamide
isoniazid
mshA 576456 p.Val370Gly missense_variant 0.23 ethionamide
isoniazid
rpoB 759844 p.Pro13Leu missense_variant 1.0 rifampicin
rpoC 765369 p.Thr667Met missense_variant 1.0 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
fbiD 3339734 p.Ala206Gly missense_variant 0.28 delamanid
rpoA 3878641 c.-134C>G upstream_gene_variant 0.32 rifampicin
embC 4240409 p.Pro183Ala missense_variant 0.22 ethambutol
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
aftB 4268619 p.Val73Gly missense_variant 0.26 capreomycin
amikacin
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338630 c.-109C>A upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide