TB-Profiler

TB-Profiler result

Run: SRR1172916

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: SRR1172916

Sample name:

Date: 2024-04-15T07:40:57.987166

Number of reads: 295192

Percentage reads mapped: 97.49

Median coverage: 6.0

Strain: lineage4.3.3;lineage4.9

Spoligotype:

Drug-resistance: RR-TB

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

Lineage	Family	RDs	Frequency
lineage4.3	Euro-American (LAM)	None	0.53
lineage4	Euro-American	None	1.0
lineage4.9	Euro-American (H37Rv-like)	None	0.65
lineage4.3.3	Euro-American (LAM)	RD115	0.98

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

Drug	Resistance	Supporting mutations	WHO confidence
rifampicin	rpoB	p.Ile491Phe	Assoc w R
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
rpoB	761277	p.Ile491Phe	missense_variant	1.0	rifampicin	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
rpoB	761283	p.Ser493Thr	missense_variant	1.0	rifampicin	Uncertain significance
rpoC	764995	c.1626C>G	synonymous_variant	1.0	rifampicin	Not assoc w R
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
rrl	1476056	n.2399G>A	non_coding_transcript_exon_variant	1.0	capreomycin	Not assoc w R
rrl	1476056	n.2399G>A	non_coding_transcript_exon_variant	1.0	linezolid	Uncertain significance
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