TB-Profiler

TB-Profiler result

Run: ERR4799128

Summary

Run ID: ERR4799128

Sample name:

Date: 20-10-2023 03:28:58

Number of reads: 4093654

Percentage reads mapped: 99.58

Strain: lineage3.1.2.1

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.Gly279Asp (0.74), katG p.Trp107Arg (0.21)
Ethambutol	R	embB p.Met306Ile (0.15)
Pyrazinamide	R	pncA p.Thr142Ala (0.37), pncA p.Trp68Arg (0.18)
Streptomycin
Fluoroquinolones	R	gyrA p.Asp94Gly (0.21)
Moxifloxacin	R	gyrA p.Asp94Gly (0.21)
Ofloxacin	R	gyrA p.Asp94Gly (0.21)
Levofloxacin	R	gyrA p.Asp94Gly (0.21)
Ciprofloxacin	R	gyrA p.Asp94Gly (0.21)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
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
lineage3	East-African-Indian	CAS	RD750	0.99
lineage3.1	East-African-Indian	Non-CAS1-Delhi	RD750	0.98
lineage3.1.2	East-African-Indian	CAS;CAS2	RD750	0.99
lineage3.1.2.1	East-African-Indian	CAS2	RD750	0.98

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	7582	p.Asp94Gly	missense_variant	0.21	ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB	761155	p.Ser450Leu	missense_variant	1.0	rifampicin
katG	2155276	p.Gly279Asp	missense_variant	0.74	isoniazid
katG	2155793	p.Trp107Arg	missense_variant	0.21	isoniazid
pncA	2288818	p.Thr142Ala	missense_variant	0.37	pyrazinamide
pncA	2289040	p.Trp68Arg	missense_variant	0.18	pyrazinamide
embB	4247431	p.Met306Ile	missense_variant	0.15	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	0.99
fgd1	491742	c.960T>C	synonymous_variant	1.0
rpoB	759746	c.-61C>T	upstream_gene_variant	0.98
rpoC	762434	c.-936T>G	upstream_gene_variant	0.97
rpoC	763031	c.-339T>C	upstream_gene_variant	1.0
rpoC	764712	p.Ala448Val	missense_variant	0.16
rpoC	764819	p.Trp484Gly	missense_variant	0.14
rpoC	765860	p.Phe831Val	missense_variant	0.15
rpoC	766487	p.Pro1040Ala	missense_variant	0.33
mmpL5	775639	p.Ile948Val	missense_variant	1.0
mmpL5	776100	p.Thr794Ile	missense_variant	1.0
mmpS5	778941	c.-36A>G	upstream_gene_variant	0.97
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0
rrl	1475988	n.2331A>G	non_coding_transcript_exon_variant	1.0
rpsA	1833677	p.Val46Met	missense_variant	0.99
tlyA	1917972	c.33A>G	synonymous_variant	1.0
katG	2154724	p.Arg463Leu	missense_variant	0.99
PPE35	2167926	p.Leu896Ser	missense_variant	1.0
PPE35	2168604	p.Pro670Leu	missense_variant	0.97
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0
pncA	2289047	c.195C>T	synonymous_variant	1.0
pncA	2289365	c.-125delC	upstream_gene_variant	0.98
ahpC	2726105	c.-88G>A	upstream_gene_variant	0.97
ald	3086788	c.-32T>C	upstream_gene_variant	1.0
fprA	3473996	c.-11_-10insA	upstream_gene_variant	1.0
embC	4242075	p.Arg738Gln	missense_variant	0.97
embA	4242643	c.-590C>T	upstream_gene_variant	0.99
whiB6	4338595	c.-75delG	upstream_gene_variant	1.0
whiB6	4338599	c.-78A>C	upstream_gene_variant	0.99
gid	4407588	c.615A>G	synonymous_variant	1.0