TB-Profiler

TB-Profiler result

Run: SRR6153027

Summary

Run ID: SRR6153027

Sample name:

Date: 2024-04-15T10:34:55.292533

Number of reads: 6171425

Percentage reads mapped: 99.77

Median coverage: 161.0

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
mmpL5	776328	p.Phe718Ser	missense_variant	1.0	clofazimine
mmpL5	776328	p.Phe718Ser	missense_variant	1.0	bedaquiline
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
Rv2477c	2784230	c.-189dupC	upstream_gene_variant	0.56	ethambutol
					moxifloxacin
					streptomycin
					levofloxacin
					kanamycin
					rifampicin
					amikacin
glpK	4139272	p.Val162Leu	missense_variant	0.99	ethambutol	Uncertain significance
					moxifloxacin
					streptomycin	Uncertain significance
					levofloxacin
					rifampicin	Uncertain significance
					isoniazid	Uncertain significance
embC	4240108	c.246G>A	synonymous_variant	0.99	ethambutol	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