TB-Profiler

TB-Profiler result

Run: ERR4818582

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: ERR4818582

Sample name:

Date: 2024-10-05T04:37:39.274825

Number of reads: 312742

Percentage reads mapped: 98.41

Median coverage: 9.0

Strain: lineage1.1.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs

Lineage	Family	RDs	Frequency
lineage1.1.2	Indo-Oceanic	RD239	1.0
lineage1.1	Indo-Oceanic	RD239	1.0
lineage1	Indo-Oceanic	RD239	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	7585	p.Ser95Thr	missense_variant	1.0	levofloxacin	Not assoc w R
gyrA	7585	p.Ser95Thr	missense_variant	1.0	moxifloxacin	Not assoc w R
gyrA	8452	p.Ala384Val	missense_variant	1.0	levofloxacin	Not assoc w R
gyrA	8452	p.Ala384Val	missense_variant	1.0	moxifloxacin	Not assoc w R
gyrA	9143	c.1842T>C	synonymous_variant	1.0	levofloxacin	Not assoc w R
gyrA	9143	c.1842T>C	synonymous_variant	1.0	moxifloxacin	Not assoc w R
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
Rv0010c	13298	p.Ile87Met	missense_variant	1.0	isoniazid	Not assoc w R
Rv0010c	13460	c.99T>C	synonymous_variant	1.0	isoniazid	Not assoc w R
fgd1	491742	c.960T>C	synonymous_variant	1.0	pretomanid
					delamanid	Not assoc w R - Interim
					clofazimine	Not assoc w R
mshA	576000	p.Asp218Ala	missense_variant	0.9	isoniazid	Not assoc w R - Interim
mshA	576000	p.Asp218Ala	missense_variant	0.9	ethionamide	Uncertain significance
Rv0565c	657578	c.-108T>C	upstream_gene_variant	1.0	ethionamide
rpoB	759546	c.-261A>G	upstream_gene_variant	1.0	rifampicin	Not assoc w R
rpoB	763031	c.3225T>C	synonymous_variant	1.0	rifampicin	Not assoc w R
rpoC	763884	p.Ala172Val	missense_variant	1.0	rifampicin	Not assoc w R
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	bedaquiline	Not assoc w R - Interim
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	clofazimine	Not assoc w R
ahpC	2726051	c.-142G>A	upstream_gene_variant	1.0	isoniazid
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
lpqB	3624486	p.Asp142Gly	missense_variant	1.0	rifampicin	Not assoc w R
lpqB	3624486	p.Asp142Gly	missense_variant	1.0	bedaquiline	Uncertain significance
clpC1	4040517	p.Val63Ala	missense_variant	1.0	pyrazinamide	Not assoc w R - Interim
panD	4044740	c.-459C>T	upstream_gene_variant	1.0	pyrazinamide
embA	4245969	p.Pro913Ser	missense_variant	1.0	ethambutol	Not assoc w R
whiB6	4338595	c.-75delG	upstream_gene_variant	1.0	kanamycin	Not assoc w R
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
whiB6	4338603	c.-82C>T	upstream_gene_variant	1.0	kanamycin	Not assoc w R
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
whiB6	4338732	c.-211C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					amikacin
gid	4407588	c.615A>G	synonymous_variant	1.0	streptomycin	Not assoc w R