TB-Profiler

TB-Profiler result

Run: SRR6797630

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: SRR6797630

Sample name:

Date: 2024-04-15T08:49:11.062711

Number of reads: 896616

Percentage reads mapped: 99.23

Median coverage: 13.0

Strain: lineage4.1.1.1

Spoligotype:

Drug-resistance: Other

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

Lineage	Family	RDs	Frequency
lineage4.1	Euro-American	None	0.6
lineage4.1.1.1	Euro-American (X-type)	RD183	0.42
lineage4	Euro-American	None	1.0
lineage4.1.1	Euro-American (X-type)	None	0.57

Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes

Drug	Resistance	Supporting mutations	WHO confidence
rifampicin
isoniazid
ethambutol
pyrazinamide	pncA	p.Gly105Asp	Assoc w R
streptomycin	rpsL	p.Lys88Arg	Assoc w R
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
rpsL	781822	p.Lys88Arg	missense_variant	1.0	streptomycin	Assoc w R
pncA	2288928	p.Gly105Asp	missense_variant	1.0	pyrazinamide	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
hadA	732110	p.Cys61Gly	missense_variant	1.0	isoniazid	Uncertain significance
rpoC	765150	p.Gly594Glu	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	streptomycin
					kanamycin
					capreomycin
					amikacin
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
thyA	3074220	c.252A>T	synonymous_variant	1.0	para-aminosalicylic_acid
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
embC	4240897	c.1035C>G	synonymous_variant	1.0	ethambutol	Not assoc w R
ethA	4327303	c.171C>T	synonymous_variant	1.0	ethionamide	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
whiB6	4338732	c.-211C>T	upstream_gene_variant	1.0	capreomycin
					amikacin
					kanamycin