TB-Profiler result

Run: ERR5979538
Summary

Run ID: ERR5979538

Sample name:

Date: 2024-10-03T18:15:30.057993

Number of reads: 5753114

Percentage reads mapped: 99.64

Median coverage: 169.0

Strain: lineage4.1.2.1;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
lineage4.1 Euro-American None 0.08
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.1
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.91
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
fgd1 491591 p.Lys270Met missense_variant 0.11 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575891 p.Ala182Thr missense_variant 0.94 isoniazid Uncertain significance
ethionamide Uncertain significance
mshA 576108 p.Ala254Gly missense_variant 0.26 isoniazid
ethionamide
Rv0565c 656761 p.Thr237Ile missense_variant 0.91 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.1 ethionamide Uncertain significance
mmaA3 737880 c.270G>A synonymous_variant 0.94 isoniazid
rpoB 760115 c.309C>T synonymous_variant 0.13 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.87 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 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.11 cycloserine
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 0.95 ethionamide Uncertain significance
mtrB 3626251 c.363T>G synonymous_variant 0.92 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
mtrA 3627756 c.-407A>T upstream_gene_variant 0.12 rifampicin
bedaquiline
rpoA 3878928 c.-421G>A upstream_gene_variant 0.89 rifampicin
clpC1 4040941 c.-237G>T upstream_gene_variant 0.91 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242928 c.3066A>G synonymous_variant 0.94 ethambutol Not assoc w R - Interim
embB 4247595 p.Cys361Ser missense_variant 0.9 ethambutol Uncertain significance
aftB 4268040 p.Leu266Pro missense_variant 0.91 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 0.13 kanamycin
capreomycin
amikacin