TB-Profiler

TB-Profiler result

Run: SRR11972171

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: SRR11972171

Sample name:

Date: 2024-04-15T17:10:51.078515

Number of reads: 509505

Percentage reads mapped: 97.29

Median coverage: 11.0

Strain: lineage2.2.2

Spoligotype:

Drug-resistance: RR-TB

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

Lineage	Family	RDs	Frequency
lineage2	East-Asian	RD105	0.79
lineage2.2.2	East-Asian (Beijing)	RD105;RD207	1.0
lineage2.2	East-Asian (Beijing)	RD105;RD207	1.0

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

Drug	Resistance	Supporting mutations	WHO confidence	Comment
rifampicin	rpoB	p.Pro454Ser	Uncertain significance	Mutation from literature
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	761166	p.Pro454Ser	missense_variant	1.0	rifampicin	Uncertain significance	Mutation from literature

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	6490	c.-812T>A	upstream_gene_variant	1.0	levofloxacin
gyrA	6490	c.-812T>A	upstream_gene_variant	1.0	moxifloxacin
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
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
fgd1	491742	c.960T>C	synonymous_variant	1.0	clofazimine	Not assoc w R
					pretomanid
					delamanid	Not assoc w R - Interim
Rv0565c	657081	c.390G>A	synonymous_variant	1.0	ethionamide	Not assoc w R - Interim
rpoB	763031	c.3225T>C	synonymous_variant	1.0	rifampicin	Not assoc w R
mmpS5	779615	c.-710C>G	upstream_gene_variant	1.0	clofazimine
mmpS5	779615	c.-710C>G	upstream_gene_variant	1.0	bedaquiline
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
rrs	1472214	n.369C>G	non_coding_transcript_exon_variant	0.12	streptomycin	Uncertain significance
					kanamycin
					capreomycin
					amikacin
rrs	1472225	n.380C>A	non_coding_transcript_exon_variant	0.13	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					amikacin	Uncertain significance
rrs	1472235	n.390G>C	non_coding_transcript_exon_variant	0.13	streptomycin	Uncertain significance
					kanamycin
					capreomycin
					amikacin
rrs	1472240	n.395G>C	non_coding_transcript_exon_variant	0.14	streptomycin	Uncertain significance
					kanamycin
					capreomycin
					amikacin
fabG1	1673380	c.-60C>G	upstream_gene_variant	0.42	ethionamide
fabG1	1673380	c.-60C>G	upstream_gene_variant	0.42	isoniazid
rpsA	1834177	c.636A>C	synonymous_variant	1.0	pyrazinamide	Not assoc w R - Interim
katG	2154724	p.Arg463Leu	missense_variant	1.0	isoniazid	Not assoc w R
PPE35	2167868	c.2745A>C	synonymous_variant	0.21	pyrazinamide
PPE35	2167926	p.Leu896Ser	missense_variant	1.0	pyrazinamide	Not assoc w R
PPE35	2170048	p.Leu189Val	missense_variant	0.32	pyrazinamide
PPE35	2170839	c.-227C>T	upstream_gene_variant	0.99	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
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
clpC1	4040976	c.-272T>G	upstream_gene_variant	1.0	pyrazinamide
whiB6	4338595	c.-75delG	upstream_gene_variant	1.0	capreomycin	Not assoc w R
					amikacin	Not assoc w R
					kanamycin	Not assoc w R
whiB6	4338732	c.-211C>T	upstream_gene_variant	1.0	capreomycin
					amikacin
					kanamycin
whiB6	4338794	c.-273A>G	upstream_gene_variant	1.0	capreomycin
					amikacin
					kanamycin
gid	4407588	c.615A>G	synonymous_variant	1.0	streptomycin	Not assoc w R
gid	4407927	p.Glu92Asp	missense_variant	1.0	streptomycin	Not assoc w R