TB-Profiler

TB-Profiler result

Run: 011b9474-be91-4763-b182-6159c4442c85

This result has been migrated from an older version of TB-Profiler. Some information may be missing, and it has not been profiled using the latest mutation database. It is advised to re-run the analysis.

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: 011b9474-be91-4763-b182-6159c4442c85

Sample name:

Date: 24-01-2023 10:21:54

Number of reads: 27702

Percentage reads mapped: 91.33

Median coverage: 0

Strain: lineage2.2

Spoligotype:

Drug-resistance: HR-TB

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

Lineage	Family	RDs	Frequency
lineage2.2	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
rifampicin
isoniazid	fabG1	c.-15C>T	Assoc w R
isoniazid	katG	p.Ser315Thr	Assoc w R
ethambutol
pyrazinamide
moxifloxacin	gyrA	p.Asp94Gly	Assoc w R
levofloxacin	gyrA	p.Asp94Gly	Assoc w R
bedaquiline
delamanid
pretomanid
linezolid
streptomycin
amikacin	eis	c.-14C>T	Assoc w R
kanamycin	eis	c.-14C>T	Assoc w R
capreomycin
clofazimine
ethionamide	fabG1	c.-15C>T	Assoc w R
para-aminosalicylic_acid
cycloserine

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
gyrA	7582	p.Asp94Gly	missense_variant	0.99	ofloxacin	Uncertain significance
					moxifloxacin	Assoc w R
					levofloxacin	Assoc w R
					fluoroquinolones	Uncertain significance
					ciprofloxacin	Uncertain significance
fabG1	1673425	c.-15C>T	upstream_gene_variant	0.97	isoniazid	Assoc w R
fabG1	1673425	c.-15C>T	upstream_gene_variant	0.97	ethionamide	Assoc w R
katG	2155168	p.Ser315Thr	missense_variant	0.98	isoniazid	Assoc w R
eis	2715346	c.-14C>T	upstream_gene_variant	0.88	kanamycin	Assoc w R
eis	2715346	c.-14C>T	upstream_gene_variant	0.88	amikacin	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
gyrA	7362	p.Glu21Gln	missense_variant	0.99	fluoroquinolones
					moxifloxacin	Uncertain significance
					levofloxacin	Uncertain significance
					ciprofloxacin
					ofloxacin
gyrA	7585	p.Ser95Thr	missense_variant	0.99	fluoroquinolones
					moxifloxacin	Uncertain significance
					levofloxacin	Uncertain significance
					ciprofloxacin
					ofloxacin
gyrA	9304	p.Gly668Asp	missense_variant	0.94	fluoroquinolones
					moxifloxacin	Uncertain significance
					levofloxacin	Uncertain significance
					ciprofloxacin
					ofloxacin
rrs	1471659	n.-187C>T	upstream_gene_variant	0.93	linezolid
					kanamycin
					capreomycin
					amikacin
					aminoglycosides
					streptomycin
rpsA	1834177	c.636A>C	synonymous_variant	0.76	pyrazinamide
tlyA	1917972	c.33A>G	synonymous_variant	0.98	capreomycin
katG	2154724	p.Arg463Leu	missense_variant	0.88	isoniazid	Uncertain significance
ribD	2987091	p.Val85Met	missense_variant	0.94	para-aminosalicylic_acid
ald	3087246	p.Gln143*	stop_gained	0.89	cycloserine
ethA	4326676	p.Ser266Arg	missense_variant	0.88	ethionamide	Uncertain significance
ethA	4326974	p.Trp167Ser	missense_variant	1.0	ethionamide	Uncertain significance
ethR	4327941	p.Ser131Arg	missense_variant	0.99	ethionamide	Uncertain significance
gid	4407588	c.615A>G	synonymous_variant	0.99	streptomycin
gid	4407927	p.Glu92Asp	missense_variant	0.97	streptomycin	Uncertain significance