TB-Profiler result

Run: ERR2510774
Summary

Run ID: ERR2510774

Sample name:

Date: 2025-05-10T09:06:07.468274

Number of reads: 2290445

Percentage reads mapped: 99.74

Median coverage: 76.0

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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 779229 c.-749A>G upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1258c 1407532 c.-192G>A upstream_gene_variant 1.0 isoniazid Uncertain significance
pyrazinamide Uncertain significance
streptomycin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
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
bacA 2064579 c.150G>A synonymous_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
katG 2154477 c.1635G>T synonymous_variant 1.0 isoniazid Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
eis 2715432 c.-100C>T upstream_gene_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
Rv2680 2995848 c.-257G>A upstream_gene_variant 1.0 capreomycin Uncertain significance
Rv3083 3448507 c.5_*1407del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
alr 3841568 c.-148G>A upstream_gene_variant 1.0 cycloserine Uncertain significance
alr 3841570 c.-151delA upstream_gene_variant 1.0 cycloserine Uncertain significance
alr 3841574 c.-154T>G upstream_gene_variant 1.0 cycloserine Uncertain significance
alr 3841578 c.-158G>T upstream_gene_variant 1.0 cycloserine Uncertain significance
alr 3841582 c.-162A>G upstream_gene_variant 1.0 cycloserine Uncertain significance
alr 3841584 c.-164C>A upstream_gene_variant 1.0 cycloserine Uncertain significance
alr 3841589 c.-170delG upstream_gene_variant 1.0 cycloserine Uncertain significance
alr 3841612 c.-193_-192insC upstream_gene_variant 1.0 cycloserine Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326106 c.1368C>G synonymous_variant 1.0 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
gid 4407945 c.258C>T synonymous_variant 1.0 streptomycin Not assoc w R - Interim