TB-Profiler

TB-Profiler result

Run: SRR22048424

Summary

Run ID: SRR22048424

Sample name:

Date: 2024-10-05T13:09:38.457968

Number of reads: 4903777

Percentage reads mapped: 99.69

Median coverage: 138.0

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
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
mmpL5	775639	p.Ile948Val	missense_variant	1.0	bedaquiline	Not assoc w R - Interim
mmpL5	775639	p.Ile948Val	missense_variant	1.0	clofazimine	Not assoc w R
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
Rv1129c	1253934	p.Arg201Trp	missense_variant	1.0	levofloxacin
					moxifloxacin
					isoniazid	Uncertain significance
					rifampicin	Uncertain significance
fbiC	1304193	c.1263G>T	synonymous_variant	1.0	pretomanid
					delamanid
					clofazimine
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
rrl	1474001	n.344C>T	non_coding_transcript_exon_variant	1.0	capreomycin	Not assoc w R
rrl	1474001	n.344C>T	non_coding_transcript_exon_variant	1.0	linezolid	Not assoc w R
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin	Not assoc w R
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	bedaquiline	Not assoc w R - Interim
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	clofazimine	Not assoc w R
ald	3086767	c.-53A>C	upstream_gene_variant	0.99	cycloserine
fbiD	3338935	c.-183T>C	upstream_gene_variant	1.0	pretomanid
					delamanid
					clofazimine
Rv3083	3448507	c.5_*1408del	frameshift_variant&stop_lost&splice_region_variant	1.0	ethionamide	Uncertain significance
Rv3236c	3612118	c.999G>A	synonymous_variant	1.0	pyrazinamide	Not assoc w R - Interim
fbiB	3640668	c.-867C>T	upstream_gene_variant	1.0	pretomanid
					delamanid
					clofazimine
panD	4043878	c.403delC	frameshift_variant	1.0	pyrazinamide	Uncertain significance
glpK	4139030	c.726C>T	synonymous_variant	1.0	levofloxacin	Not assoc w R - Interim
					moxifloxacin
					isoniazid	Not assoc w R - Interim
					streptomycin	Not assoc w R - Interim
					rifampicin	Not assoc w R - Interim
					ethambutol	Not assoc w R - Interim
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
embA	4244000	c.768G>A	synonymous_variant	1.0	ethambutol	Not assoc w R - Interim
whiB6	4338250	p.Ala91Val	missense_variant	1.0	kanamycin	Uncertain significance
					capreomycin
					amikacin	Uncertain significance
whiB6	4338595	c.-75delG	upstream_gene_variant	1.0	kanamycin	Not assoc w R
					capreomycin	Not assoc w R
					amikacin	Not assoc w R