TB-Profiler

TB-Profiler result

Run: SRR17856688

Summary

Run ID: SRR17856688

Sample name:

Date: 2024-10-04T23:37:19.376462

Number of reads: 1465867

Percentage reads mapped: 99.54

Median coverage: 40.0

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
rpoB	762856	p.Val1017Ala	missense_variant	1.0	rifampicin
mmpL5	776328	p.Phe718Ser	missense_variant	1.0	bedaquiline
mmpL5	776328	p.Phe718Ser	missense_variant	1.0	clofazimine
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin	Not assoc w R
glpK	4139272	p.Val162Leu	missense_variant	1.0	levofloxacin
					moxifloxacin
					isoniazid	Uncertain significance
					streptomycin	Uncertain significance
					rifampicin	Uncertain significance
					ethambutol	Uncertain significance
embC	4240108	c.246G>A	synonymous_variant	1.0	ethambutol	Not assoc w R - Interim
whiB6	4338595	c.-75delG	upstream_gene_variant	1.0	kanamycin	Not assoc w R
					capreomycin	Not assoc w R
					amikacin	Not assoc w R