TB-Profiler result

Run: SRR13837693
Summary

Run ID: SRR13837693

Sample name:

Date: 2024-10-05T14:21:12.349489

Number of reads: 293853

Percentage reads mapped: 98.01

Median coverage: 9.0

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) None 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
fgd1 490676 c.-107G>C upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
rpoB 760454 c.650delG frameshift_variant 1.0 rifampicin
rpsL 781409 c.-151T>A upstream_gene_variant 1.0 streptomycin
Rv1129c 1254013 p.Met174Ile missense_variant 1.0 levofloxacin
moxifloxacin
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254452 p.Glu28Ala missense_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
rrs 1471874 n.29A>C non_coding_transcript_exon_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
bacA 2064843 c.-115C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
katG 2154654 p.Ser486Arg missense_variant 1.0 isoniazid
katG 2155857 c.255C>A synonymous_variant 1.0 isoniazid
PPE35 2170198 p.Ala139Ser missense_variant 1.0 pyrazinamide
thyA 3074067 c.405C>G synonymous_variant 1.0 para-aminosalicylic_acid
lpqB 3624738 p.Ala58Val missense_variant 1.0 rifampicin
bedaquiline
alr 3840711 p.Ser237Leu missense_variant 1.0 cycloserine
embA 4245071 c.1839G>A synonymous_variant 1.0 ethambutol
ethA 4327364 p.Lys37Arg missense_variant 1.0 ethionamide