TB-Profiler

TB-Profiler result

Run: SRR1225522

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: SRR1225522

Sample name:

Date: 2024-10-04T04:05:44.100172

Number of reads: 3553160

Percentage reads mapped: 99.4

Median coverage: 19.0

Strain: lineage4.1.2.1

Spoligotype:

Drug-resistance: RR-TB

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

Lineage	Family	RDs	Frequency
lineage4.1	Euro-American	None	0.84
lineage4.1.2	Euro-American	None	0.85
lineage4.1.2.1	Euro-American (Haarlem)	RD182	0.67
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
rifampicin	rpoB	p.Ser450Leu	Assoc w R
isoniazid
ethambutol	embB	p.Gln497Arg	Assoc w R
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
rpoB	761155	p.Ser450Leu	missense_variant	1.0	rifampicin	Assoc w R
embB	4248003	p.Gln497Arg	missense_variant	1.0	ethambutol	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	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
mshA	575679	p.Asn111Ser	missense_variant	0.93	isoniazid	Not assoc w R
mshA	575679	p.Asn111Ser	missense_variant	0.93	ethionamide	Not assoc w R
rpoB	760115	c.309C>T	synonymous_variant	1.0	rifampicin	Not assoc w R
rpoC	765150	p.Gly594Glu	missense_variant	1.0	rifampicin	Not assoc w R
rpoC	766740	p.Val1124Gly	missense_variant	0.9	rifampicin	Uncertain significance
mmpL5	775639	p.Ile948Val	missense_variant	0.96	bedaquiline	Not assoc w R - Interim
mmpL5	775639	p.Ile948Val	missense_variant	0.96	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
inhA	1674917	p.Ala239Val	missense_variant	1.0	isoniazid	Uncertain significance
inhA	1674917	p.Ala239Val	missense_variant	1.0	ethionamide	Uncertain significance
tsnR	1854300	p.Leu232Pro	missense_variant	1.0	linezolid	Not assoc w R
tlyA	1917972	c.33A>G	synonymous_variant	0.96	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
kasA	2518076	c.-39C>T	upstream_gene_variant	0.99	isoniazid
mtrB	3625065	p.Met517Leu	missense_variant	1.0	rifampicin	Not assoc w R
mtrB	3625065	p.Met517Leu	missense_variant	1.0	bedaquiline	Uncertain significance
mtrB	3626093	p.Gly174Ala	missense_variant	1.0	rifampicin	Uncertain significance
mtrB	3626093	p.Gly174Ala	missense_variant	1.0	bedaquiline	Uncertain significance
alr	3841001	p.Glu140Asp	missense_variant	1.0	cycloserine
embC	4239298	c.-565C>T	upstream_gene_variant	1.0	ethambutol	Not assoc w R
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
embC	4242803	p.Val981Leu	missense_variant	1.0	ethambutol	Not assoc w R
gid	4407967	p.Leu79Trp	missense_variant	1.0	streptomycin	Uncertain significance