TB-Profiler

TB-Profiler result

Run: SRR27450226

Summary

Run ID: SRR27450226

Sample name:

Date: 2024-04-15T18:12:30.071434

Number of reads: 5947270

Percentage reads mapped: 99.25

Median coverage: 190.0

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
gyrA	7362	p.Glu21Gln	missense_variant	1.0	levofloxacin	Not assoc w R
gyrA	7362	p.Glu21Gln	missense_variant	1.0	moxifloxacin	Not assoc w R
Rv0565c	656195	p.Gly426Cys	missense_variant	1.0	ethionamide
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin	Not assoc w R
kasA	2518031	c.-84G>A	upstream_gene_variant	1.0	isoniazid
rpoA	3878049	c.459G>A	synonymous_variant	0.99	rifampicin	Not assoc w R - Interim
glpK	4138415	c.1341G>T	synonymous_variant	1.0	ethambutol	Not assoc w R - Interim
					moxifloxacin	Not assoc w R - Interim
					streptomycin	Not assoc w R - Interim
					levofloxacin	Not assoc w R - Interim
					rifampicin	Not assoc w R - Interim
					isoniazid	Not assoc w R - Interim
whiB6	4338595	c.-75delG	upstream_gene_variant	1.0	capreomycin	Not assoc w R
					amikacin	Not assoc w R
					kanamycin	Not assoc w R