TB-Profiler

TB-Profiler result

Run: SRR6824546

Summary

Run ID: SRR6824546

Sample name:

Date: 20-10-2023 19:49:28

Number of reads: 16414399

Percentage reads mapped: 98.8

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.Ser450Leu (0.97), rpoC p.Gly332Arg (0.98)
Isoniazid	R	fabG1 c.-15C>T (0.98), inhA p.Ile194Thr (0.96), katG p.Trp191Arg (0.96)
Ethambutol	R	embB p.Gln497Arg (0.99)
Pyrazinamide
Streptomycin	R	rpsL p.Lys43Arg (0.98)
Fluoroquinolones	R	gyrA p.Asp94Gly (0.96)
Moxifloxacin	R	gyrA p.Asp94Gly (0.96)
Ofloxacin	R	gyrA p.Asp94Gly (0.96)
Levofloxacin	R	gyrA p.Asp94Gly (0.96)
Ciprofloxacin	R	gyrA p.Asp94Gly (0.96)
Aminoglycosides	R	rrs n.1401A>G (0.98)
Amikacin	R	rrs n.1401A>G (0.98)
Capreomycin	R	rrs n.1401A>G (0.98)
Kanamycin	R	rrs n.1401A>G (0.98)
Cycloserine
Ethionamide	R	fabG1 c.-15C>T (0.98), inhA p.Ile194Thr (0.96)
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	0.98
lineage2.2	East-Asian (Beijing)	Beijing-RD207	RD105;RD207	0.98
lineage2.2.1	East-Asian (Beijing)	Beijing-RD181	RD105;RD207;RD181	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	0.96	ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB	761155	p.Ser450Leu	missense_variant	0.97	rifampicin
rpoC	764363	p.Gly332Arg	missense_variant	0.98	rifampicin
rpsL	781687	p.Lys43Arg	missense_variant	0.98	streptomycin
rrs	1473246	n.1401A>G	non_coding_transcript_exon_variant	0.98	kanamycin, capreomycin, aminoglycosides, amikacin
fabG1	1673425	c.-15C>T	upstream_gene_variant	0.98	isoniazid, ethionamide
inhA	1674782	p.Ile194Thr	missense_variant	0.96	isoniazid, ethionamide
katG	2155541	p.Trp191Arg	missense_variant	0.96	isoniazid
embB	4248003	p.Gln497Arg	missense_variant	0.99	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
fgd1	491742	c.960T>C	synonymous_variant	0.98
mshA	575907	p.Ala187Val	missense_variant	0.98
ccsA	620625	p.Ile245Met	missense_variant	0.98
rpoC	763031	c.-339T>C	upstream_gene_variant	1.0
mmpL5	775639	p.Ile948Val	missense_variant	1.0
mmpL5	776100	p.Thr794Ile	missense_variant	0.98
mmpL5	776182	p.Asp767Asn	missense_variant	0.98
mmpR5	779164	p.Ala59Thr	missense_variant	0.99
mmpS5	779615	c.-710C>G	upstream_gene_variant	0.97
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0
Rv1258c	1406760	c.580_581insC	frameshift_variant	0.98
Rv1258c	1406885	c.456G>A	synonymous_variant	0.99
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0
rrl	1474298	n.641T>C	non_coding_transcript_exon_variant	0.33
rpsA	1834177	c.636A>C	synonymous_variant	0.99
tlyA	1917972	c.33A>G	synonymous_variant	1.0
katG	2154724	p.Arg463Leu	missense_variant	0.98
PPE35	2167926	p.Leu896Ser	missense_variant	0.98
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0
pncA	2288944	p.Thr100Pro	missense_variant	0.96
ald	3086788	c.-32T>C	upstream_gene_variant	0.99
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	4243460	c.228C>T	synonymous_variant	0.99
aftB	4267647	p.Asp397Gly	missense_variant	0.98
ethA	4327498	c.-25G>A	upstream_gene_variant	0.98
whiB6	4338593	c.-73delT	upstream_gene_variant	1.0
whiB6	4338596	c.-75G>C	upstream_gene_variant	1.0
gid	4407588	c.615A>G	synonymous_variant	0.99
gid	4407927	p.Glu92Asp	missense_variant	0.98