TB-Profiler result

Run: SRR1202499
Summary

Run ID: SRR1202499

Sample name:

Date: 2024-03-25T21:31:32.628542

Number of reads: 1042164

Percentage reads mapped: 68.45

Median coverage: 4.0

Strain: lineage4.1.2.1;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
lineage4.1 Euro-American None 0.29
lineage4.1.2 Euro-American None 0.38
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.26
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) None 0.6
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
rpoB 760106 c.300G>A synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 760115 c.309C>T synonymous_variant 0.97 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 1.0 isoniazid