TB-Profiler

TB-Profiler result

Run: ERR2229630

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: ERR2229630

Sample name:

Date: 2024-04-16T04:33:28.174548

Number of reads: 586958

Percentage reads mapped: 99.06

Median coverage: 10.0

Strain: lineage4.8

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
lineage4.8	Euro-American (mainly T)	RD219	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
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
PPE35	2168728	p.Gly629Arg	missense_variant	1.0	pyrazinamide	Uncertain significance
PPE35	2170048	p.Leu189Val	missense_variant	0.64	pyrazinamide
PPE35	2170053	p.Thr187Ser	missense_variant	0.66	pyrazinamide
PPE35	2170147	p.Ser156Ala	missense_variant	0.23	pyrazinamide
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
Rv3083	3448507	c.5_*1408del	frameshift_variant&stop_lost&splice_region_variant	1.0	ethionamide	Uncertain significance
alr	3841612	c.-193_-192insC	upstream_gene_variant	0.26	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