TB-Profiler result

Run: SRR12619585
Summary

Run ID: SRR12619585

Sample name:

Date: 2024-10-04T11:42:02.944804

Number of reads: 55013654

Percentage reads mapped: 98.92

Median coverage: 1555.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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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 gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
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
gyrA 7582 p.Asp94Gly missense_variant 1.0 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
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 6524 p.Arg429Ser missense_variant 0.15 levofloxacin
moxifloxacin
Rv0010c 13619 c.-61C>T upstream_gene_variant 0.11 isoniazid
Rv0010c 13627 c.-69A>G upstream_gene_variant 0.21 isoniazid Uncertain significance
hadA 732359 c.435_439delTGCCG frameshift_variant 1.0 isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472767 n.925dupC non_coding_transcript_exon_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
kasA 2518527 p.Ser138Tyr missense_variant 1.0 isoniazid
glpK 4139604 p.Pro51Leu missense_variant 1.0 levofloxacin
moxifloxacin
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance