TB-Profiler

TB-Profiler result

Run: SRR998739

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: SRR998739

Sample name:

Date: 2024-10-04T17:07:25.054390

Number of reads: 960378

Percentage reads mapped: 91.06

Median coverage: 23.0

Strain: lineage4.1.3

Spoligotype:

Drug-resistance: Sensitive

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

Lineage	Family	RDs	Frequency
lineage4.1.3	Euro-American	None	1.0
lineage4.1	Euro-American	None	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
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
gyrA	9557	c.2256G>C	synonymous_variant	1.0	levofloxacin	Not assoc w R - Interim
gyrA	9557	c.2256G>C	synonymous_variant	1.0	moxifloxacin	Not assoc w R - Interim
Rv0565c	657269	p.Ser68Pro	missense_variant	1.0	ethionamide	Uncertain significance
rpoC	765150	p.Gly594Glu	missense_variant	1.0	rifampicin	Not assoc w R
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
rpsL	781421	c.-139C>A	upstream_gene_variant	0.96	streptomycin	Uncertain significance
fbiC	1304610	c.1680C>T	synonymous_variant	1.0	pretomanid
					delamanid	Not assoc w R - Interim
					clofazimine	Not assoc w R - Interim
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
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	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
lpqB	3623291	c.1620C>A	synonymous_variant	1.0	rifampicin	Not assoc w R - Interim
lpqB	3623291	c.1620C>A	synonymous_variant	1.0	bedaquiline	Not assoc w R - Interim
lpqB	3624660	p.Ala84Gly	missense_variant	1.0	rifampicin	Uncertain significance
lpqB	3624660	p.Ala84Gly	missense_variant	1.0	bedaquiline	Uncertain significance
mtrB	3625065	p.Met517Leu	missense_variant	1.0	rifampicin	Not assoc w R
mtrB	3625065	p.Met517Leu	missense_variant	1.0	bedaquiline	Uncertain significance
embC	4239595	c.-268T>C	upstream_gene_variant	1.0	ethambutol	Uncertain significance
embC	4242803	p.Val981Leu	missense_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