TB-Profiler

TB-Profiler result

Run: ERR2679265

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: ERR2679265

Sample name:

Date: 2024-04-15T04:19:18.295782

Number of reads: 165245

Percentage reads mapped: 99.51

Median coverage: 8.0

Strain: lineage4.1

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	1.0
lineage4	Euro-American	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
gyrB	6507	p.Ala423Val	missense_variant	1.0	levofloxacin	Uncertain significance
gyrB	6507	p.Ala423Val	missense_variant	1.0	moxifloxacin	Uncertain significance
gyrA	9304	p.Gly668Asp	missense_variant	1.0	levofloxacin	Not assoc w R
gyrA	9304	p.Gly668Asp	missense_variant	1.0	moxifloxacin	Not assoc w R
gyrA	9656	c.2355C>G	synonymous_variant	1.0	levofloxacin	Not assoc w R - Interim
gyrA	9656	c.2355C>G	synonymous_variant	1.0	moxifloxacin	Not assoc w R - Interim
rpoC	765150	p.Gly594Glu	missense_variant	1.0	rifampicin	Not assoc w R
rpoC	765187	c.1818C>T	synonymous_variant	1.0	rifampicin	Not assoc w R - Interim
rpoC	766012	c.2643C>G	synonymous_variant	1.0	rifampicin	Not assoc w R - Interim
mmpL5	776750	c.1731C>T	synonymous_variant	0.93	clofazimine
mmpL5	776750	c.1731C>T	synonymous_variant	0.93	bedaquiline
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
rpsL	781421	c.-139C>A	upstream_gene_variant	1.0	streptomycin	Uncertain significance
rrs	1471627	n.-219C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
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
katG	2156007	c.105C>T	synonymous_variant	1.0	isoniazid	Not assoc w R - Interim
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	clofazimine	Not assoc w R
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	bedaquiline	Not assoc w R - Interim
mtrA	3627293	c.57G>A	synonymous_variant	1.0	bedaquiline	Not assoc w R - Interim
mtrA	3627293	c.57G>A	synonymous_variant	1.0	rifampicin	Not assoc w R - Interim
alr	3840288	p.Asp378Gly	missense_variant	1.0	cycloserine
panD	4044479	c.-198C>T	upstream_gene_variant	1.0	pyrazinamide
embC	4242803	p.Val981Leu	missense_variant	1.0	ethambutol	Not assoc w R
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	4338732	c.-211C>T	upstream_gene_variant	1.0	capreomycin
					amikacin
					kanamycin