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view test-data/hamronized_rgi.tsv @ 4:f8bcc852f6b3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d
author iuc
date Fri, 09 Feb 2024 21:27:25 +0000
parents ef76d74a7171
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input_file_name	gene_symbol	gene_name	reference_database_id	reference_database_version	reference_accession	analysis_software_name	analysis_software_version	sequence_identity	input_sequence_id	input_protein_start	input_protein_stop	input_gene_start	input_gene_stop	reference_protein_start	reference_protein_stop	reference_gene_start	reference_gene_stop	strand_orientation	coverage_depth	coverage_percentage	coverage_ratio	reference_gene_length	reference_protein_length	input_gene_length	input_protein_length	drug_class	antimicrobial_agent	resistance_mechanism
rgi_report	oqxA	resistance-nodulation-cell division (RND) antibiotic efflux pump	CARD	card_v1	3003922	rgi	rgi_v1	100.0	NODE_1_length_803036_cov_42.265_33			30758	31933					+		100.0						fluoroquinolone antibiotic; glycylcycline; tetracycline antibiotic; diaminopyrimidine antibiotic; nitrofuran antibiotic		antibiotic efflux
rgi_report	oqxB	resistance-nodulation-cell division (RND) antibiotic efflux pump	CARD	card_v1	3003923	rgi	rgi_v1	99.52	NODE_1_length_803036_cov_42.265_34			31957	35109					+		100.0						fluoroquinolone antibiotic; glycylcycline; tetracycline antibiotic; diaminopyrimidine antibiotic; nitrofuran antibiotic		antibiotic efflux
rgi_report	emrR	major facilitator superfamily (MFS) antibiotic efflux pump	CARD	card_v1	3000516	rgi	rgi_v1	92.57	NODE_1_length_803036_cov_42.265_80			79380	79910					+		100.0						fluoroquinolone antibiotic		antibiotic efflux
rgi_report	Klebsiella pneumoniae KpnG	major facilitator superfamily (MFS) antibiotic efflux pump	CARD	card_v1	3004588	rgi	rgi_v1	99.74	NODE_1_length_803036_cov_42.265_81			80036	81208					+		100.0						macrolide antibiotic; fluoroquinolone antibiotic; aminoglycoside antibiotic; carbapenem; cephalosporin; penam; peptide antibiotic; penem		antibiotic efflux
rgi_report	Klebsiella pneumoniae KpnH	major facilitator superfamily (MFS) antibiotic efflux pump	CARD	card_v1	3004597	rgi	rgi_v1	94.02	NODE_1_length_803036_cov_42.265_82			81224	82762					+		100.0						macrolide antibiotic; fluoroquinolone antibiotic; aminoglycoside antibiotic; carbapenem; cephalosporin; penam; peptide antibiotic; penem		antibiotic efflux
rgi_report	mdtB	resistance-nodulation-cell division (RND) antibiotic efflux pump	CARD	card_v1	3000793	rgi	rgi_v1	90.1	NODE_3_length_454317_cov_40.2449_14			17656	20778					+		100.0						aminocoumarin antibiotic		antibiotic efflux
rgi_report	mdtC	resistance-nodulation-cell division (RND) antibiotic efflux pump	CARD	card_v1	3000794	rgi	rgi_v1	91.41	NODE_3_length_454317_cov_40.2449_15			20779	23856					+		100.0						aminocoumarin antibiotic		antibiotic efflux
rgi_report	baeR	resistance-nodulation-cell division (RND) antibiotic efflux pump	CARD	card_v1	3000828	rgi	rgi_v1	90.83	NODE_3_length_454317_cov_40.2449_18			26745	27467					+		100.0						aminoglycoside antibiotic; aminocoumarin antibiotic		antibiotic efflux
rgi_report	acrD	resistance-nodulation-cell division (RND) antibiotic efflux pump	CARD	card_v1	3000491	rgi	rgi_v1	90.94	NODE_3_length_454317_cov_40.2449_285			330238	333351					+		100.0						aminoglycoside antibiotic		antibiotic efflux
rgi_report	FosA6	fosfomycin thiol transferase	CARD	card_v1	3004111	rgi	rgi_v1	97.84	NODE_4_length_367278_cov_42.3139_12			14037	14456					+		100.0						fosfomycin		antibiotic inactivation
rgi_report	Klebsiella pneumoniae acrA	resistance-nodulation-cell division (RND) antibiotic efflux pump	CARD	card_v1	3004041	rgi	rgi_v1	95.24	NODE_6_length_262587_cov_42.4347_106 			86156	87349					+		99.75						fluoroquinolone antibiotic; cephalosporin; glycylcycline; penam; tetracycline antibiotic; rifamycin antibiotic; phenicol antibiotic; triclosan		antibiotic efflux
rgi_report	acrB	resistance-nodulation-cell division (RND) antibiotic efflux pump	CARD	card_v1	3000216	rgi	rgi_v1	91.52	NODE_6_length_262587_cov_42.4347_107			87372	90518					+		99.9						fluoroquinolone antibiotic; cephalosporin; glycylcycline; penam; tetracycline antibiotic; rifamycin antibiotic; phenicol antibiotic; triclosan		antibiotic efflux
rgi_report	Escherichia coli ampH beta-lactamase	ampC-type beta-lactamase	CARD	card_v1	3004612	rgi	rgi_v1	85.71	NODE_6_length_262587_cov_42.4347_234			216120	217280					+		100.26						cephalosporin; penam		antibiotic inactivation
rgi_report	msbA	ATP-binding cassette (ABC) antibiotic efflux pump	CARD	card_v1	3003950	rgi	rgi_v1	92.78	NODE_8_length_247415_cov_40.5207_219			227800	229548					-		100.0						nitroimidazole antibiotic		antibiotic efflux
rgi_report	CRP	resistance-nodulation-cell division (RND) antibiotic efflux pump	CARD	card_v1	3000518	rgi	rgi_v1	99.05	NODE_9_length_203843_cov_42.4911_20			15303	15935					+		100.0						macrolide antibiotic; fluoroquinolone antibiotic; penam		antibiotic efflux
rgi_report	PmrF	pmr phosphoethanolamine transferase	CARD	card_v1	3003578	rgi	rgi_v1	83.69	NODE_9_length_203843_cov_42.4911_123			130217	131200					-		101.55						peptide antibiotic		antibiotic target alteration
rgi_report	marA	resistance-nodulation-cell division (RND) antibiotic efflux pump; General Bacterial Porin with reduced permeability to beta-lactams	CARD	card_v1	3000263	rgi	rgi_v1	92.74	NODE_11_length_157792_cov_39.2115_112			108413	108787					+		97.64						fluoroquinolone antibiotic; monobactam; carbapenem; cephalosporin; glycylcycline; cephamycin; penam; tetracycline antibiotic; rifamycin antibiotic; phenicol antibiotic; triclosan; penem		antibiotic efflux; reduced permeability to antibiotic
rgi_report	SHV-11	SHV beta-lactamase	CARD	card_v1	3001070	rgi	rgi_v1	100.0	NODE_11_length_157792_cov_39.2115_132			128890	129750					+		100.0						carbapenem; cephalosporin; penam		antibiotic inactivation
rgi_report	CBP-1	CBP beta-lactamase	CARD	card_v1	3004764	rgi	rgi_v1	100.0	NODE_19_length_86672_cov_43.8582_38 			39587	39811					-		24.03						penam		antibiotic inactivation
rgi_report	Escherichia coli mdfA	major facilitator superfamily (MFS) antibiotic efflux pump	CARD	card_v1	3001328	rgi	rgi_v1	85.61	NODE_21_length_66123_cov_41.3566_52			60858	62090					+		100.0						tetracycline antibiotic; benzalkonium chloride; rhodamine		antibiotic efflux
rgi_report	Klebsiella pneumoniae KpnE	major facilitator superfamily (MFS) antibiotic efflux pump	CARD	card_v1	3004580	rgi	rgi_v1	99.17	NODE_27_length_37761_cov_37.6839_21			25311	25673					+		100.0						macrolide antibiotic; aminoglycoside antibiotic; cephalosporin; tetracycline antibiotic; peptide antibiotic; rifamycin antibiotic		antibiotic efflux
rgi_report	Klebsiella pneumoniae KpnF	major facilitator superfamily (MFS) antibiotic efflux pump	CARD	card_v1	3004583	rgi	rgi_v1	100.0	NODE_27_length_37761_cov_37.6839_22			25660	25989					+		100.0						macrolide antibiotic; aminoglycoside antibiotic; cephalosporin; tetracycline antibiotic; peptide antibiotic; rifamycin antibiotic		antibiotic efflux
rgi_report	AAC(3)-IId	AAC(3)	CARD	card_v1	3004623	rgi	rgi_v1	100.0	NODE_39_length_11164_cov_23.0187_6			4569	5429					+		100.0						aminoglycoside antibiotic		antibiotic inactivation
rgi_report	rmtC	16S rRNA methyltransferase (G1405)	CARD	card_v1	3000861	rgi	rgi_v1	100.0	NODE_40_length_7360_cov_24.8738_6			6358	7203					-		100.0						aminoglycoside antibiotic		antibiotic target alteration
rgi_report	NDM-1	NDM beta-lactamase	CARD	card_v1	3000589	rgi	rgi_v1	100.0	NODE_44_length_4295_cov_23.2123_1			301	1113					+		100.0						carbapenem; cephalosporin; cephamycin; penam		antibiotic inactivation
rgi_report	BRP(MBL)	Bleomycin resistant protein	CARD	card_v1	3001205	rgi	rgi_v1	100.0	NODE_44_length_4295_cov_23.2123_2 			1222	1482					+		71.07						glycopeptide antibiotic		antibiotic inactivation
rgi_report	DHA-7	DHA beta-lactamase	CARD	card_v1	3002136	rgi	rgi_v1	100.0	NODE_44_length_4295_cov_23.2123_3 			1846	2862					-		89.18						cephalosporin; cephamycin		antibiotic inactivation
rgi_report	CTX-M-15	CTX-M beta-lactamase	CARD	card_v1	3001878	rgi	rgi_v1	100.0	NODE_47_length_3813_cov_27.9457_4			2763	3638					-		100.0						cephalosporin		antibiotic inactivation
rgi_report	OXA-1	OXA beta-lactamase	CARD	card_v1	3001396	rgi	rgi_v1	100.0	NODE_51_length_1731_cov_22.5767_1			196	1026					+		100.0						cephalosporin; penam		antibiotic inactivation
rgi_report	catB3	chloramphenicol acetyltransferase (CAT)	CARD	card_v1	3002676	rgi	rgi_v1	100.0	NODE_51_length_1731_cov_22.5767_2 			1164	1712					+		86.67						phenicol antibiotic		antibiotic inactivation
rgi_report	AAC(6')-Ib-cr	AAC(6')	CARD	card_v1	3002547	rgi	rgi_v1	95.45	NODE_54_length_1272_cov_25.1921_2 			1130	1270					+		23.62						fluoroquinolone antibiotic; aminoglycoside antibiotic		antibiotic inactivation
rgi_report	sul1	sulfonamide resistant sul	CARD	card_v1	3000410	rgi	rgi_v1	100.0	NODE_57_length_1134_cov_34.8908_1			25	864					-		100.0						sulfonamide antibiotic		antibiotic target replacement
rgi_report	AAC(6')-Ib10	AAC(6')	CARD	card_v1	3002581	rgi	rgi_v1	100.0	NODE_69_length_625_cov_55.4398_1			63	623					-		91.63						aminoglycoside antibiotic		antibiotic inactivation
rgi_report	AAC(6')-Ib-cr	AAC(6')	CARD	card_v1	3002547	rgi	rgi_v1	100.0	NODE_185_length_335_cov_33.8077_1 			172	333					+		27.14						fluoroquinolone antibiotic; aminoglycoside antibiotic		antibiotic inactivation