TB-Profiler

TB-Profiler result

Run: SRR6982476

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: SRR6982476

Sample name:

Date: 2024-10-04T13:46:25.018183

Number of reads: 424140

Percentage reads mapped: 99.21

Median coverage: 16.0

Strain: lineage4.3.2.1

Spoligotype:

Drug-resistance: Sensitive

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

Lineage	Family	RDs	Frequency
lineage4.3	Euro-American (LAM)	None	1.0
lineage4.3.2	Euro-American (LAM)	None	1.0
lineage4.3.2.1	Euro-American (LAM)	RD761	1.0
lineage4	Euro-American	None	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
gyrB	5520	p.Pro94Leu	missense_variant	1.0	levofloxacin	Not assoc w R
gyrB	5520	p.Pro94Leu	missense_variant	1.0	moxifloxacin	Not assoc w R
gyrB	7222	c.1983C>T	synonymous_variant	1.0	levofloxacin	Not assoc w R
gyrB	7222	c.1983C>T	synonymous_variant	1.0	moxifloxacin	Not assoc w R
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
gyrA	9304	p.Gly668Asp	missense_variant	1.0	levofloxacin	Not assoc w R
gyrA	9304	p.Gly668Asp	missense_variant	1.0	moxifloxacin	Not assoc w R
rpoC	764995	c.1626C>G	synonymous_variant	1.0	rifampicin	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
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472337	n.492C>T	non_coding_transcript_exon_variant	1.0	kanamycin	Not assoc w R
					capreomycin	Not assoc w R
					streptomycin	Not assoc w R - Interim
					amikacin	Not assoc w R
tsnR	1854300	p.Leu232Pro	missense_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
pncA	2288895	c.338_346delGCACGCCAC	disruptive_inframe_deletion	0.33	pyrazinamide	Not assoc w R - Interim
thyA	3073868	p.Thr202Ala	missense_variant	1.0	para-aminosalicylic_acid
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
mtrB	3625065	p.Met517Leu	missense_variant	1.0	rifampicin	Not assoc w R
mtrB	3625065	p.Met517Leu	missense_variant	1.0	bedaquiline	Uncertain significance
clpC1	4038287	c.2418C>T	synonymous_variant	1.0	pyrazinamide	Not assoc w R
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
whiB6	4338732	c.-211C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					amikacin
gid	4408156	p.Leu16Arg	missense_variant	1.0	streptomycin	Not assoc w R