TB-Profiler

TB-Profiler result

Run: SRR6797481

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: SRR6797481

Sample name:

Date: 2024-04-15T11:08:15.530580

Number of reads: 345723

Percentage reads mapped: 99.42

Median coverage: 6.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: HR-TB

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

Lineage	Family	RDs	Frequency
lineage2	East-Asian	RD105	1.0
lineage2.2.1	East-Asian (Beijing)	RD105;RD207;RD181	0.25
lineage2.2	East-Asian (Beijing)	RD105;RD207	0.43

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

Drug	Resistance	Supporting mutations	WHO confidence	Comment
rifampicin
isoniazid	katG	p.Ser315Thr	Assoc w R	High-level resistance
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
katG	2155168	p.Ser315Thr	missense_variant	1.0	isoniazid	Assoc w R	High-level resistance

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
rpoC	763501	p.Asp44Glu	missense_variant	1.0	rifampicin	Uncertain significance
mmpL5	776182	p.Asp767Asn	missense_variant	1.0	clofazimine	Not assoc w R
mmpL5	776182	p.Asp767Asn	missense_variant	1.0	bedaquiline	Not assoc w R
Rv1129c	1254562	c.-28T>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	1471659	n.-187C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
whiB6	4338732	c.-211C>T	upstream_gene_variant	1.0	capreomycin
					amikacin
					kanamycin