TB-Profiler

TB-Profiler result

Run: SRR19320505

Summary

Run ID: SRR19320505

Sample name:

Date: 2024-10-04T09:48:44.978793

Number of reads: 1781562

Percentage reads mapped: 99.75

Median coverage: 75.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: Other

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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	Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid	thyX	c.-16C>T	Mutation from literature
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
thyX	3067961	c.-16C>T	upstream_gene_variant	1.0	para-aminosalicylic_acid		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
dnaA	358	p.Ala120Pro	missense_variant	1.0	isoniazid	Uncertain significance
dnaA	371	p.Pro124Leu	missense_variant	0.99	isoniazid	Not assoc w R
gyrB	6815	p.Lys526Gln	missense_variant	1.0	levofloxacin	Uncertain significance
gyrB	6815	p.Lys526Gln	missense_variant	1.0	moxifloxacin	Uncertain significance
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	1253353	c.1182G>A	synonymous_variant	1.0	levofloxacin
					moxifloxacin
					isoniazid	Not assoc w R - Interim
					rifampicin	Not assoc w R - Interim
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
Rv3083	3448507	c.5_*1408del	frameshift_variant&stop_lost&splice_region_variant	1.0	ethionamide	Uncertain significance
alr	3840488	c.933G>A	synonymous_variant	0.58	cycloserine
alr	3840764	c.657G>C	synonymous_variant	1.0	cycloserine
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
whiB6	4338595	c.-75delG	upstream_gene_variant	1.0	kanamycin	Not assoc w R
					capreomycin	Not assoc w R
					amikacin	Not assoc w R