TB-Profiler

TB-Profiler result

Run: SRR6797440

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: SRR6797440

Sample name:

Date: 2024-10-05T14:34:44.016944

Number of reads: 530315

Percentage reads mapped: 99.09

Median coverage: 9.0

Strain: lineage3

Spoligotype:

Drug-resistance: Sensitive

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

Lineage	Family	RDs	Frequency
lineage3	East-African-Indian	RD750	0.48

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
Rv0565c	657081	c.390G>A	synonymous_variant	1.0	ethionamide	Not assoc w R - Interim
nusG	734129	c.-125G>T	upstream_gene_variant	1.0	rifampicin	Uncertain significance
rpoB	759746	c.-61C>T	upstream_gene_variant	1.0	rifampicin	Not assoc w R
Rv1129c	1254562	c.-28T>C	upstream_gene_variant	1.0	levofloxacin	Not assoc w R
					moxifloxacin	Not assoc w R
					isoniazid	Not assoc w R
					rifampicin	Not assoc w R
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
PPE35	2167926	p.Leu896Ser	missense_variant	1.0	pyrazinamide	Not assoc w R
pncA	2289365	c.-125delC	upstream_gene_variant	1.0	pyrazinamide
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
alr	3841473	c.-53G>A	upstream_gene_variant	1.0	cycloserine
whiB6	4338595	c.-75delG	upstream_gene_variant	1.0	kanamycin	Not assoc w R
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
whiB6	4338732	c.-211C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					amikacin
gid	4407588	c.615A>G	synonymous_variant	1.0	streptomycin	Not assoc w R