TB-Profiler

TB-Profiler result

Run: ERR9806778

Summary

Run ID: ERR9806778

Sample name:

Date: 18-05-2023 14:44:57

Number of reads: 88574

Percentage reads mapped: 97.38

Strain: lineage4.9

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes

Drug	Resistance	Supporting mutations
Rifampicin	R	rpoB p.Ser450Leu (1.00)
Isoniazid	R	katG p.Ser315Thr (1.00)
Ethambutol	R	embB p.Met306Ile (1.00)
Pyrazinamide
Streptomycin	R	rrs n.878G>A (1.00)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine	R	ald c.464delG (1.00)
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid

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

Lineage	Family	Main Spoligotype	RDs	Frequency
lineage4	Euro-American	LAM;T;S;X;H	None	1.0
lineage4.9	Euro-American (H37Rv-like)	T1	None	0.95
lineage4.1.1.3	Euro-American (X-type)	X1;X3	RD193	0.07

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
rpoB	761155	p.Ser450Leu	missense_variant	1.0	rifampicin
rrs	1472723	n.878G>A	non_coding_transcript_exon_variant	1.0	streptomycin
katG	2155168	p.Ser315Thr	missense_variant	1.0	isoniazid
ald	3087278	c.464delG	frameshift_variant	1.0	cycloserine
embB	4247431	p.Met306Ile	missense_variant	1.0	ethambutol

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
gyrA	7362	p.Glu21Gln	missense_variant	1.0
gyrA	7585	p.Ser95Thr	missense_variant	1.0
gyrA	9304	p.Gly668Asp	missense_variant	1.0
rpoB	762285	p.Arg827Cys	missense_variant	1.0
rpoC	765150	p.Gly594Glu	missense_variant	1.0
mmpL5	775639	p.Ile948Val	missense_variant	1.0
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0
rpsL	781435	c.-125G>C	upstream_gene_variant	1.0
fbiC	1302885	c.-46G>A	upstream_gene_variant	0.5
PPE35	2169122	c.1491C>G	synonymous_variant	0.5
PPE35	2169125	p.Val496Ile	missense_variant	0.5
PPE35	2169131	c.1482C>T	synonymous_variant	0.5
PPE35	2169134	c.1479G>A	synonymous_variant	0.5
fprA	3473996	c.-11_-10insA	upstream_gene_variant	1.0
embA	4242643	c.-590C>T	upstream_gene_variant	1.0
embC	4242803	p.Val981Leu	missense_variant	1.0