TB-Profiler

TB-Profiler result

Run: ERR8025592

Summary

Run ID: ERR8025592

Sample name:

Date: 18-05-2023 02:54:03

Number of reads: 2847818

Percentage reads mapped: 99.54

Strain: lineage4.1.1.3

Drug-resistance: Pre-XDR-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), ahpC c.-48G>A (1.00)
Ethambutol	R	embA c.-16C>T (0.50), embB p.Met306Val (1.00)
Pyrazinamide	R	pncA p.Val139Met (1.00)
Streptomycin	R	rpsL p.Lys43Arg (1.00)
Fluoroquinolones	R	gyrA p.Ala90Val (1.00), gyrA p.Asp94Gly (0.56)
Moxifloxacin	R	gyrA p.Ala90Val (1.00), gyrA p.Asp94Gly (0.56)
Ofloxacin	R	gyrA p.Ala90Val (1.00), gyrA p.Asp94Gly (0.56)
Levofloxacin	R	gyrA p.Ala90Val (1.00), gyrA p.Asp94Gly (0.56)
Ciprofloxacin	R	gyrA p.Ala90Val (1.00), gyrA p.Asp94Gly (0.56)
Aminoglycosides	R	rrs n.1401A>G (1.00)
Amikacin	R	rrs n.1401A>G (1.00)
Capreomycin	R	rrs n.1401A>G (1.00)
Kanamycin	R	rrs n.1401A>G (1.00)
Cycloserine
Ethionamide	R	ethA c.597delC (1.00), ethA c.597delC (1.00)
Clofazimine
Para-aminosalicylic_acid	R	thyA p.Phe152Val (0.13)
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
lineage4.1	Euro-American	T;X;H	None	1.0
lineage4.1.1	Euro-American (X-type)	X1;X2;X3	None	1.0
lineage4.1.1.3	Euro-American (X-type)	X1;X3	RD193	1.0

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
gyrA	7570	p.Ala90Val	missense_variant	1.0	ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA	7582	p.Asp94Gly	missense_variant	0.56	ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB	761155	p.Ser450Leu	missense_variant	1.0	rifampicin
rpsL	781687	p.Lys43Arg	missense_variant	1.0	streptomycin
rrs	1473246	n.1401A>G	non_coding_transcript_exon_variant	1.0	kanamycin, capreomycin, aminoglycosides, amikacin
katG	2155167	p.Ser315Thr	missense_variant	1.0	isoniazid
pncA	2288827	p.Val139Met	missense_variant	1.0	pyrazinamide
ahpC	2726145	c.-48G>A	upstream_gene_variant	1.0	isoniazid
thyA	3074018	p.Phe152Val	missense_variant	0.13	para-aminosalicylic_acid
embA	4243217	c.-16C>T	upstream_gene_variant	0.5	ethambutol
embB	4247429	p.Met306Val	missense_variant	1.0	ethambutol
ethA	4326876	c.597delC	frameshift_variant	1.0	ethionamide, ethionamide

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
gyrB	6608	p.Val457Leu	missense_variant	1.0
gyrA	7362	p.Glu21Gln	missense_variant	1.0
gyrA	7585	p.Ser95Thr	missense_variant	1.0
gyrA	7678	p.Ala126Glu	missense_variant	0.44
gyrA	9304	p.Gly668Asp	missense_variant	1.0
rpoB	762478	p.Lys891Arg	missense_variant	0.48
rpoB	762480	p.Ile892Phe	missense_variant	0.5
rpoC	765150	p.Gly594Glu	missense_variant	1.0
rpoC	766916	p.Arg1183Ser	missense_variant	0.15
mmpL5	775639	p.Ile948Val	missense_variant	1.0
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0
rpsL	781469	c.-91C>T	upstream_gene_variant	0.17
rplC	801354	c.546G>A	synonymous_variant	1.0
fbiC	1304897	p.Leu656Gln	missense_variant	0.15
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0
rrs	1472536	n.691G>A	non_coding_transcript_exon_variant	0.13
rrs	1472741	n.896G>T	non_coding_transcript_exon_variant	0.13
tlyA	1917972	c.33A>G	synonymous_variant	1.0
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0
thyX	3067594	p.Val118Met	missense_variant	0.12
ald	3086788	c.-32T>C	upstream_gene_variant	1.0
ald	3087251	c.433_437dupGGCGC	frameshift_variant	1.0
Rv3083	3449084	p.Pro194Gln	missense_variant	0.12
Rv3083	3449616	p.Met371Ile	missense_variant	0.96
fprA	3473996	c.-11_-10insA	upstream_gene_variant	1.0
alr	3840423	p.Arg333Ile	missense_variant	0.13
embA	4242643	c.-590C>T	upstream_gene_variant	1.0
embC	4242803	p.Val981Leu	missense_variant	1.0
embB	4249408	c.2895G>A	synonymous_variant	1.0
aftB	4267754	p.Lys361Asn	missense_variant	0.12
whiB6	4338595	c.-75delG	upstream_gene_variant	1.0