TB-Profiler

TB-Profiler result

Run: ERR8774149

This average coverage of the target regions is below the recommended 30x. Some mutations may not be detected due to low coverage.

Summary

Run ID: ERR8774149

Sample name:

Date: 2024-03-26T16:23:16.718647

Number of reads: 726710

Percentage reads mapped: 99.63

Median coverage: 20.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: RR-TB

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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
rifampicin	rpoB	p.His445Asp	Assoc w R
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
rpoB	761139	p.His445Asp	missense_variant	1.0	rifampicin	Assoc w R

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	6136	c.897G>A	synonymous_variant	1.0	levofloxacin	Not assoc w R - Interim
gyrB	6136	c.897G>A	synonymous_variant	1.0	moxifloxacin
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
nusG	734967	p.Ile238Met	missense_variant	1.0	rifampicin
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin	Not assoc w R
Rv2752c	3065058	c.1134C>T	synonymous_variant	1.0	ethambutol	Not assoc w R - Interim
					moxifloxacin	Not assoc w R - Interim
					levofloxacin	Not assoc w R - Interim
					rifampicin	Not assoc w R - Interim
					isoniazid	Not assoc w R - Interim
Rv2752c	3065528	c.664C>T	synonymous_variant	1.0	ethambutol
					moxifloxacin
					levofloxacin
					rifampicin
					isoniazid
whiB6	4338595	c.-75delG	upstream_gene_variant	1.0	capreomycin	Not assoc w R
					amikacin	Not assoc w R
					kanamycin	Not assoc w R
whiB6	4338849	c.-328T>G	upstream_gene_variant	1.0	capreomycin
					amikacin
					kanamycin