TB-Profiler

TB-Profiler result

Run: SRR25827886

Summary

Run ID: SRR25827886

Sample name:

Date: 03-02-2024 00:36:43

Number of reads: 20606511

Percentage reads mapped: 91.21

Strain: lineage3;lineage2.2.1

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 (0.88), rpoC p.Ile491Thr (0.58)
Isoniazid	R	katG p.Ser315Thr (0.76)
Ethambutol	R	embA c.-16C>T (0.57)
Pyrazinamide	R	pncA p.Ile5Ser (0.64)
Streptomycin	R	rpsL p.Lys43Arg (0.79)
Fluoroquinolones	R	gyrB p.Glu501Asp (0.73), gyrA p.Ala90Val (0.57), gyrA p.Asp94Gly (0.27)
Moxifloxacin	R	gyrB p.Glu501Asp (0.73), gyrA p.Ala90Val (0.57), gyrA p.Asp94Gly (0.27)
Ofloxacin	R	gyrB p.Glu501Asp (0.73), gyrA p.Ala90Val (0.57), gyrA p.Asp94Gly (0.27)
Levofloxacin	R	gyrB p.Glu501Asp (0.73), gyrA p.Ala90Val (0.57), gyrA p.Asp94Gly (0.27)
Ciprofloxacin	R	gyrB p.Glu501Asp (0.73), gyrA p.Ala90Val (0.57), gyrA p.Asp94Gly (0.27)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin	R	eis c.-12C>T (0.67)
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid	R	thyA p.Thr22Ala (0.70)
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	0.12
lineage2	East-Asian	Beijing	RD105	0.8
lineage2.2	East-Asian (Beijing)	Beijing-RD207	RD105;RD207	0.86
lineage2.2.1	East-Asian (Beijing)	Beijing-RD181	RD105;RD207;RD181	0.86

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
gyrB	6742	p.Glu501Asp	missense_variant	0.73	ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA	7570	p.Ala90Val	missense_variant	0.57	ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA	7582	p.Asp94Gly	missense_variant	0.27	ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB	761155	p.Ser450Leu	missense_variant	0.88	rifampicin
rpoC	764841	p.Ile491Thr	missense_variant	0.58	rifampicin
rpsL	781687	p.Lys43Arg	missense_variant	0.79	streptomycin
katG	2155168	p.Ser315Thr	missense_variant	0.76	isoniazid
pncA	2289228	p.Ile5Ser	missense_variant	0.64	pyrazinamide
eis	2715344	c.-12C>T	upstream_gene_variant	0.67	kanamycin
thyA	3074408	p.Thr22Ala	missense_variant	0.7	para-aminosalicylic_acid
embA	4243217	c.-16C>T	upstream_gene_variant	0.57	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
gyrB	5470	c.231C>T	synonymous_variant	0.83
gyrA	7362	p.Glu21Gln	missense_variant	1.0
gyrA	7585	p.Ser95Thr	missense_variant	1.0
gyrA	9304	p.Gly668Asp	missense_variant	1.0
fgd1	491290	p.Val170Met	missense_variant	0.75
fgd1	491742	c.960T>C	synonymous_variant	1.0
mshA	575907	p.Ala187Val	missense_variant	0.71
ccsA	620625	p.Ile245Met	missense_variant	0.85
rpoB	759746	c.-61C>T	upstream_gene_variant	0.15
rpoC	763031	c.-339T>C	upstream_gene_variant	1.0
mmpL5	775639	p.Ile948Val	missense_variant	1.0
mmpL5	776100	p.Thr794Ile	missense_variant	1.0
mmpL5	776182	p.Asp767Asn	missense_variant	0.64
mmpS5	779615	c.-710C>G	upstream_gene_variant	0.8
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0
Rv1258c	1406760	c.580_581insC	frameshift_variant	0.89
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0
rpsA	1834177	c.636A>C	synonymous_variant	0.89
tlyA	1917972	c.33A>G	synonymous_variant	1.0
katG	2154724	p.Arg463Leu	missense_variant	1.0
PPE35	2167926	p.Leu896Ser	missense_variant	1.0
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0
pncA	2289365	c.-125delC	upstream_gene_variant	0.43
thyX	3067949	c.-4C>T	upstream_gene_variant	0.67
ald	3086788	c.-32T>C	upstream_gene_variant	1.0
fprA	3473996	c.-11_-10insA	upstream_gene_variant	1.0
Rv3236c	3612813	p.Thr102Ala	missense_variant	0.92
embC	4241022	p.Ala387Val	missense_variant	0.8
embA	4242643	c.-590C>T	upstream_gene_variant	1.0
embA	4243460	c.228C>T	synonymous_variant	0.76
aftB	4267647	p.Asp397Gly	missense_variant	0.88
ethA	4326963	p.Leu171Phe	missense_variant	0.29
ethA	4327051	p.Tyr141*	stop_gained	0.29
whiB6	4338292	p.Ala77Val	missense_variant	0.88
whiB6	4338595	c.-75delG	upstream_gene_variant	1.0
gid	4407588	c.615A>G	synonymous_variant	1.0
gid	4407620	p.Tyr195His	missense_variant	0.94
gid	4407927	p.Glu92Asp	missense_variant	0.69