TB-Profiler

TB-Profiler result

Run: SRR5818433

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: SRR5818433

Sample name:

Date: 2024-04-16T08:38:01.848530

Number of reads: 606454

Percentage reads mapped: 99.5

Median coverage: 0.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

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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	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	7502	c.201C>T	synonymous_variant	0.16	levofloxacin
gyrA	7502	c.201C>T	synonymous_variant	0.16	moxifloxacin
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
mmpR5	779434	p.Val149Ile	missense_variant	1.0	clofazimine
mmpR5	779434	p.Val149Ile	missense_variant	1.0	bedaquiline
mmpL5	779478	c.-998C>T	upstream_gene_variant	0.18	clofazimine
mmpL5	779478	c.-998C>T	upstream_gene_variant	0.18	bedaquiline
rrs	1472118	n.273A>G	non_coding_transcript_exon_variant	0.22	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1473047	n.1204delT	non_coding_transcript_exon_variant	0.28	streptomycin
					kanamycin
					capreomycin
					amikacin
rrl	1476010	n.2353G>A	non_coding_transcript_exon_variant	0.27	capreomycin
rrl	1476010	n.2353G>A	non_coding_transcript_exon_variant	0.27	linezolid
rrl	1476538	n.2881A>G	non_coding_transcript_exon_variant	0.23	capreomycin	Uncertain significance
rrl	1476538	n.2881A>G	non_coding_transcript_exon_variant	0.23	linezolid	Uncertain significance
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin	Not assoc w R
ahpC	2726446	p.Val85Ala	missense_variant	0.16	isoniazid
ahpC	2726471	c.279T>C	synonymous_variant	0.17	isoniazid
embB	4247615	p.Glu368*	stop_gained	0.15	ethambutol
embB	4247646	p.Glu378Ala	missense_variant	1.0	ethambutol	Not assoc w R
ethA	4326764	p.Ala237Val	missense_variant	0.29	ethionamide