TB-Profiler result

Run: ERR2229744
Summary

Run ID: ERR2229744

Sample name:

Date: 2024-04-15T11:19:26.499483

Number of reads: 1193536

Percentage reads mapped: 99.2

Median coverage: 29.0

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 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
fbiC 1303747 p.Thr273Ala missense_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
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
fabG1 1673346 c.-94C>G upstream_gene_variant 0.28 ethionamide
isoniazid
fabG1 1673349 c.-91G>C upstream_gene_variant 0.28 ethionamide
isoniazid
fabG1 1673357 c.-83G>A upstream_gene_variant 0.26 ethionamide
isoniazid
fabG1 1673359 c.-81T>C upstream_gene_variant 0.26 ethionamide
isoniazid
fabG1 1673361 c.-79C>G upstream_gene_variant 0.26 ethionamide
isoniazid
fabG1 1673380 c.-60C>G upstream_gene_variant 0.41 ethionamide
isoniazid
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168728 p.Gly629Arg missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2170048 p.Leu189Val missense_variant 0.33 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.35 pyrazinamide
PPE35 2170147 p.Ser156Ala missense_variant 0.21 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246544 p.Thr11Pro missense_variant 0.44 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.53 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.4 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.4 ethambutol Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R