TB-Profiler result

Run: dfac438a-2e74-4490-b6fe-7fac09d58af5
Summary

Run ID: dfac438a-2e74-4490-b6fe-7fac09d58af5

Sample name:

Date: 27-11-2023 08:54:58

Number of reads: 1051284

Percentage reads mapped: 99.23

Median coverage: 34

Strain: lineage4.8

Spoligotype:

Drug-resistance: HR-TB

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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 katG p.Thr275Ser Uncertain significance
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
katG 2155289 p.Thr275Ser missense_variant 0.1 isoniazid Uncertain significance
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
gyrB 7119 p.Asp627Ala missense_variant 1.0 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
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
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
rrs 1472893 n.1048G>A non_coding_transcript_exon_variant 0.11 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
PPE35 2167854 p.Phe920Ser missense_variant 0.11 pyrazinamide
PPE35 2168149 p.Pro822Ser missense_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embB 4246552 p.Asn13Lys missense_variant 0.2 ethambutol
whiB6 4338595 c.-75delG 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