TB-Profiler

TB-Profiler result

Run: SRR16087967

Summary

Run ID: SRR16087967

Sample name:

Date: 20-01-2024 16:58:30

Number of reads: 2666271

Percentage reads mapped: 99.62

Strain: 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.Leu430Pro (0.85), rpoB p.Asp435Gly (0.84), rpoB p.Ser450Phe (0.21)
Isoniazid	R	inhA c.-154G>A (0.81), katG p.Ser315Thr (1.00)
Ethambutol
Pyrazinamide	R	pncA p.Gln141Pro (0.25), pncA c.75dupC (0.79), pncA c.75dupC (0.79)
Streptomycin	R	rpsL p.Lys43Arg (0.21), rrs n.517C>T (0.70)
Fluoroquinolones	R	gyrA p.Ala90Val (0.99)
Moxifloxacin	R	gyrA p.Ala90Val (0.99)
Ofloxacin	R	gyrA p.Ala90Val (0.99)
Levofloxacin	R	gyrA p.Ala90Val (0.99)
Ciprofloxacin	R	gyrA p.Ala90Val (0.99)
Aminoglycosides
Amikacin	R	eis c.-14C>T (0.80)
Capreomycin
Kanamycin	R	eis c.-14C>T (0.80), eis c.-37G>T (0.17)
Cycloserine
Ethionamide	R	inhA c.-154G>A (0.81), ethA c.768delG (0.90), ethA c.768delG (0.90), ethA p.Trp69* (0.15)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid

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

Lineage	Family	Main Spoligotype	RDs	Frequency
lineage2	East-Asian	Beijing	RD105	1.0
lineage2.2	East-Asian (Beijing)	Beijing-RD207	RD105;RD207	1.0
lineage2.2.1	East-Asian (Beijing)	Beijing-RD181	RD105;RD207;RD181	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	0.99	ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB	761095	p.Leu430Pro	missense_variant	0.85	rifampicin
rpoB	761110	p.Asp435Gly	missense_variant	0.84	rifampicin
rpoB	761155	p.Ser450Phe	missense_variant	0.21	rifampicin
rpsL	781687	p.Lys43Arg	missense_variant	0.21	streptomycin
rrs	1472362	n.517C>T	non_coding_transcript_exon_variant	0.7	streptomycin
inhA	1674048	c.-154G>A	upstream_gene_variant	0.81	isoniazid, ethionamide
katG	2155168	p.Ser315Thr	missense_variant	1.0	isoniazid
pncA	2288820	p.Gln141Pro	missense_variant	0.25	pyrazinamide
pncA	2289166	c.75dupC	frameshift_variant	0.79	pyrazinamide, pyrazinamide
eis	2715346	c.-14C>T	upstream_gene_variant	0.8	kanamycin, amikacin
eis	2715369	c.-37G>T	upstream_gene_variant	0.17	kanamycin
ethA	4326705	c.768delG	frameshift_variant	0.9	ethionamide, ethionamide
ethA	4327267	p.Trp69*	stop_gained	0.15	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
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	491742	c.960T>C	synonymous_variant	1.0
mshA	575907	p.Ala187Val	missense_variant	1.0
ccsA	620625	p.Ile245Met	missense_variant	1.0
rpoC	763031	c.-339T>C	upstream_gene_variant	1.0
rpoC	766645	p.Glu1092Asp	missense_variant	0.84
mmpL5	775639	p.Ile948Val	missense_variant	1.0
mmpL5	776100	p.Thr794Ile	missense_variant	0.99
mmpL5	776182	p.Asp767Asn	missense_variant	0.99
mmpR5	779266	p.Phe93Leu	missense_variant	0.87
mmpS5	779615	c.-710C>G	upstream_gene_variant	1.0
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0
Rv1258c	1406760	c.580_581insC	frameshift_variant	1.0
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0
rpsA	1834177	c.636A>C	synonymous_variant	0.99
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
Rv2752c	3067187	c.-997_-996insG	upstream_gene_variant	0.16
ald	3086731	c.-89A>G	upstream_gene_variant	0.25
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	0.99
embA	4242643	c.-590C>T	upstream_gene_variant	1.0
embA	4243190	c.-43G>C	upstream_gene_variant	0.76
embA	4243346	c.114A>G	synonymous_variant	0.19
embA	4243460	c.228C>T	synonymous_variant	1.0
aftB	4267647	p.Asp397Gly	missense_variant	1.0
whiB6	4338371	p.Thr51Pro	missense_variant	0.17
whiB6	4338563	c.-42G>T	upstream_gene_variant	0.79
whiB6	4338595	c.-75delG	upstream_gene_variant	1.0
gid	4407588	c.615A>G	synonymous_variant	1.0
gid	4407927	p.Glu92Asp	missense_variant	0.98