view test-data/concatenated_abricate_reports.tsv @ 1:c9129ecc609d draft default tip

"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
author public-health-bioinformatics
date Thu, 19 Dec 2019 18:22:33 -0500
parents 62019f5116f8
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#FILE	SEQUENCE	START	END	STRAND	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION	PRODUCT	RESISTANCE
#FILE	SEQUENCE	START	END	STRAND	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION	PRODUCT	RESISTANCE
plasmid_1550	SRR9113487.fasta|65_length=4058_depth=2.47x	2638	3513	-	CTX-M-15	1-876/876	===============	0/0	100.00	100.00	card	AY044436:1436-2312	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
plasmid_1550	SRR9113487.fasta|77_length=2186_depth=3.14x	1	442	-	catB3	1-442/633	===========....	0/0	69.83	100.00	card	JX101693.1:58201-58834	catB3 is a plasmid or chromosome-encoded variant of the cat gene found in Salmonella typhimurium Acinetobacter baumannii and Escherichia coli	phenicol
plasmid_1550	SRR9113487.fasta|77_length=2186_depth=3.14x	580	1410	-	OXA-1	1-831/831	===============	0/0	100.00	100.00	card	JN420336.1:1400-2231	OXA-1 is a beta-lactamase found in E. coli	penam/cephalosporin
plasmid_1550	SRR9113487.fasta|77_length=2186_depth=3.14x	1475	2124	-	OXA-368	2072-2721/2721	...........====	0/0	23.89	99.08	card	KT736121.1:1-2722	OXA-368 is a beta-lactamase found in Aeromonas sobria. From the Lahey list of OXA beta-lactamases.	cephalosporin/penam
#FILE	SEQUENCE	START	END	STRAND	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION	PRODUCT	RESISTANCE
plasmid_2719	SRR9113487.fasta|53_length=9674_depth=5.42x	496	1308	+	NDM-5	1-813/813	===============	0/0	100.00	100.00	card	JN104597:115-928	New Delhi beta-lactamase NDM-5.	cephamycin/penam/cephalosporin/carbapenem
plasmid_2719	SRR9113487.fasta|53_length=9674_depth=5.42x	1312	1677	+	determinant_of_bleomycin_resistance	1-366/366	===============	0/0	100.00	100.00	card	KC503911.1:9884-10250	A novel bleomycin resistance protein encoded by a metallo-beta-lactamase-associated ble gene. Expression of BRP(MBL) confers resistance to bleomycin and bleomycin-like antibiotics in Enterobacteriaceae and Acinetobacter where it is co-expressed with an MBL and controlled by the same promoter region.	glycopeptide
plasmid_2719	SRR9113487.fasta|53_length=9674_depth=5.42x	5621	6460	-	sul1	1-840/840	===============	0/0	100.00	100.00	card	JF969163:1054-1894	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
plasmid_2719	SRR9113487.fasta|53_length=9674_depth=5.42x	6965	7744	-	aadA2	1-780/780	===============	0/0	100.00	99.87	card	AF156486:5013-5793	aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp.	aminoglycoside
plasmid_2719	SRR9113487.fasta|53_length=9674_depth=5.42x	8164	8661	-	dfrA12	1-498/498	===============	0/0	100.00	100.00	card	GU585907.1:21606-22104	dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
plasmid_2719	SRR9113487.fasta|53_length=9674_depth=5.42x	8662	8910	-	AAC(6')-Ib7	1-249/980	====...........	0/0	25.41	98.80	card	Y11946.1:1-981	AAC(6')-Ib7 is a plasmid-encoded aminoglycoside acetyltransferase in E. cloacae and C. freundii	aminoglycoside
#FILE	SEQUENCE	START	END	STRAND	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION	PRODUCT	RESISTANCE
plasmid_739	SRR9113487.fasta|58_length=8070_depth=5.28x	70	972	+	mphA	1-903/906	===============	0/0	99.67	100.00	card	D16251.1:1626-2532	The mphA gene encodes for resistance enzyme MPH(2')-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2'-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
plasmid_739	SRR9113487.fasta|58_length=8070_depth=5.28x	5102	5962	+	TEM-1	1-861/861	===============	0/0	100.00	99.88	card	AL513383:161911-162772	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	penam/cephalosporin/penem/monobactam
plasmid_739	SRR9113487.fasta|58_length=8070_depth=5.28x	6132	6887	+	rmtB	1-756/756	===============	0/0	100.00	100.00	card	AM886293.1:116480-117236	RmtB is a 16S rRNA methyltransferase that targets mature or nearly mature 30S subunits. It transfers a methyl group from S-adenosyl-L-methionine to N7-G1405 of the 16S rRNA an aminoglycoside binding site.	aminoglycoside
#FILE	SEQUENCE	START	END	STRAND	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION	PRODUCT	RESISTANCE
#FILE	SEQUENCE	START	END	STRAND	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION	PRODUCT	RESISTANCE