TB-Profiler

TB-Profiler result

Run: SRR1002697

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: SRR1002697

Sample name:

Date: 2024-04-15T12:14:42.740976

Number of reads: 510918

Percentage reads mapped: 98.08

Median coverage: 11.0

Strain: lineage4.2.1.1

Spoligotype:

Drug-resistance: Sensitive

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

Lineage	Family	RDs	Frequency
lineage4.2	Euro-American	None	0.99
lineage4	Euro-American	None	1.0
lineage4.2.1.1	Euro-American (TUR)	None	1.0
lineage4.2.1	Euro-American (TUR)	None	0.99

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
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
mmpL5	777451	p.Val344Leu	missense_variant	1.0	clofazimine	Uncertain significance
mmpL5	777451	p.Val344Leu	missense_variant	1.0	bedaquiline	Uncertain significance
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
rplC	800204	c.-605T>C	upstream_gene_variant	1.0	linezolid
Rv1129c	1254582	c.-48A>C	upstream_gene_variant	1.0	moxifloxacin	Not assoc w R
					levofloxacin	Not assoc w R
					rifampicin	Not assoc w R
					isoniazid	Not assoc w R
rrs	1471647	n.-199G>A	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
rrl	1475919	n.2262C>A	non_coding_transcript_exon_variant	1.0	capreomycin	Uncertain significance
rrl	1475919	n.2262C>A	non_coding_transcript_exon_variant	1.0	linezolid
fabG1	1673380	c.-60C>G	upstream_gene_variant	0.38	ethionamide
fabG1	1673380	c.-60C>G	upstream_gene_variant	0.38	isoniazid
bacA	2063685	c.1044G>A	synonymous_variant	1.0	streptomycin	Not assoc w R - Interim
					kanamycin	Not assoc w R - Interim
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
bacA	2063911	p.Ile273Thr	missense_variant	1.0	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
ndh	2102875	c.168C>T	synonymous_variant	0.33	ethionamide	Not assoc w R - Interim
					delamanid
					isoniazid	Not assoc w R - Interim
PPE35	2169879	p.Phe245Cys	missense_variant	1.0	pyrazinamide	Uncertain significance
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
ald	3086742	c.-78A>C	upstream_gene_variant	1.0	cycloserine
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
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