hamronize_summarize: test-data/hamronized

comparison test-data/hamronized_rgi.json @ 0:ef76d74a7171 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"

author	iuc
date	Tue, 16 Mar 2021 12:39:05 +0000
parents
children

comparison

equal deleted inserted replaced

-1:000000000000	0:ef76d74a7171
	1 [{"input_file_name": "rgi_report", "gene_symbol": "oqxA", "gene_name": "resistance-nodulation-cell division (RND) antibiotic efflux pump", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3003922", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "100.0", "input_sequence_id": "NODE_1_length_803036_cov_42.265_33", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "30758", "input_gene_stop": "31933", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "fluoroquinolone antibiotic; glycylcycline; tetracycline antibiotic; diaminopyrimidine antibiotic; nitrofuran antibiotic", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic efflux"}, {"input_file_name": "rgi_report", "gene_symbol": "oqxB", "gene_name": "resistance-nodulation-cell division (RND) antibiotic efflux pump", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3003923", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "99.52", "input_sequence_id": "NODE_1_length_803036_cov_42.265_34", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "31957", "input_gene_stop": "35109", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "fluoroquinolone antibiotic; glycylcycline; tetracycline antibiotic; diaminopyrimidine antibiotic; nitrofuran antibiotic", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic efflux"}, {"input_file_name": "rgi_report", "gene_symbol": "emrR", "gene_name": "major facilitator superfamily (MFS) antibiotic efflux pump", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3000516", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "92.57", "input_sequence_id": "NODE_1_length_803036_cov_42.265_80", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "79380", "input_gene_stop": "79910", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "fluoroquinolone antibiotic", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic efflux"}, {"input_file_name": "rgi_report", "gene_symbol": "Klebsiella pneumoniae KpnG", "gene_name": "major facilitator superfamily (MFS) antibiotic efflux pump", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3004588", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "99.74", "input_sequence_id": "NODE_1_length_803036_cov_42.265_81", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "80036", "input_gene_stop": "81208", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "macrolide antibiotic; fluoroquinolone antibiotic; aminoglycoside antibiotic; carbapenem; cephalosporin; penam; peptide antibiotic; penem", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic efflux"}, {"input_file_name": "rgi_report", "gene_symbol": "Klebsiella pneumoniae KpnH", "gene_name": "major facilitator superfamily (MFS) antibiotic efflux pump", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3004597", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "94.02", "input_sequence_id": "NODE_1_length_803036_cov_42.265_82", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "81224", "input_gene_stop": "82762", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "macrolide antibiotic; fluoroquinolone antibiotic; aminoglycoside antibiotic; carbapenem; cephalosporin; penam; peptide antibiotic; penem", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic efflux"}, {"input_file_name": "rgi_report", "gene_symbol": "mdtB", "gene_name": "resistance-nodulation-cell division (RND) antibiotic efflux pump", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3000793", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "90.1", "input_sequence_id": "NODE_3_length_454317_cov_40.2449_14", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "17656", "input_gene_stop": "20778", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "aminocoumarin antibiotic", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic efflux"}, {"input_file_name": "rgi_report", "gene_symbol": "mdtC", "gene_name": "resistance-nodulation-cell division (RND) antibiotic efflux pump", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3000794", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "91.41", "input_sequence_id": "NODE_3_length_454317_cov_40.2449_15", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "20779", "input_gene_stop": "23856", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "aminocoumarin antibiotic", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic efflux"}, {"input_file_name": "rgi_report", "gene_symbol": "baeR", "gene_name": "resistance-nodulation-cell division (RND) antibiotic efflux pump", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3000828", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "90.83", "input_sequence_id": "NODE_3_length_454317_cov_40.2449_18", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "26745", "input_gene_stop": "27467", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "aminoglycoside antibiotic; aminocoumarin antibiotic", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic efflux"}, {"input_file_name": "rgi_report", "gene_symbol": "acrD", "gene_name": "resistance-nodulation-cell division (RND) antibiotic efflux pump", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3000491", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "90.94", "input_sequence_id": "NODE_3_length_454317_cov_40.2449_285", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "330238", "input_gene_stop": "333351", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "aminoglycoside antibiotic", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic efflux"}, {"input_file_name": "rgi_report", "gene_symbol": "FosA6", "gene_name": "fosfomycin thiol transferase", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3004111", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "97.84", "input_sequence_id": "NODE_4_length_367278_cov_42.3139_12", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "14037", "input_gene_stop": "14456", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "fosfomycin", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic inactivation"}, {"input_file_name": "rgi_report", "gene_symbol": "Klebsiella pneumoniae acrA", "gene_name": "resistance-nodulation-cell division (RND) antibiotic efflux pump", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3004041", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "95.24", "input_sequence_id": "NODE_6_length_262587_cov_42.4347_106 ", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "86156", "input_gene_stop": "87349", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "99.75", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "fluoroquinolone antibiotic; cephalosporin; glycylcycline; penam; tetracycline antibiotic; rifamycin antibiotic; phenicol antibiotic; triclosan", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic efflux"}, {"input_file_name": "rgi_report", "gene_symbol": "acrB", "gene_name": "resistance-nodulation-cell division (RND) antibiotic efflux pump", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3000216", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "91.52", "input_sequence_id": "NODE_6_length_262587_cov_42.4347_107", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "87372", "input_gene_stop": "90518", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "99.9", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "fluoroquinolone antibiotic; cephalosporin; glycylcycline; penam; tetracycline antibiotic; rifamycin antibiotic; phenicol antibiotic; triclosan", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic efflux"}, {"input_file_name": "rgi_report", "gene_symbol": "Escherichia coli ampH beta-lactamase", "gene_name": "ampC-type beta-lactamase", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3004612", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "85.71", "input_sequence_id": "NODE_6_length_262587_cov_42.4347_234", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "216120", "input_gene_stop": "217280", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "100.26", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "cephalosporin; penam", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic inactivation"}, {"input_file_name": "rgi_report", "gene_symbol": "msbA", "gene_name": "ATP-binding cassette (ABC) antibiotic efflux pump", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3003950", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "92.78", "input_sequence_id": "NODE_8_length_247415_cov_40.5207_219", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "227800", "input_gene_stop": "229548", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "-", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "nitroimidazole antibiotic", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic efflux"}, {"input_file_name": "rgi_report", "gene_symbol": "CRP", "gene_name": "resistance-nodulation-cell division (RND) antibiotic efflux pump", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3000518", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "99.05", "input_sequence_id": "NODE_9_length_203843_cov_42.4911_20", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "15303", "input_gene_stop": "15935", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "macrolide antibiotic; fluoroquinolone antibiotic; penam", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic efflux"}, {"input_file_name": "rgi_report", "gene_symbol": "PmrF", "gene_name": "pmr phosphoethanolamine transferase", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3003578", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "83.69", "input_sequence_id": "NODE_9_length_203843_cov_42.4911_123", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "130217", "input_gene_stop": "131200", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "-", "coverage_depth": "", "coverage_percentage": "101.55", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "peptide antibiotic", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic target alteration"}, {"input_file_name": "rgi_report", "gene_symbol": "marA", "gene_name": "resistance-nodulation-cell division (RND) antibiotic efflux pump; General Bacterial Porin with reduced permeability to beta-lactams", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3000263", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "92.74", "input_sequence_id": "NODE_11_length_157792_cov_39.2115_112", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "108413", "input_gene_stop": "108787", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "97.64", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "fluoroquinolone antibiotic; monobactam; carbapenem; cephalosporin; glycylcycline; cephamycin; penam; tetracycline antibiotic; rifamycin antibiotic; phenicol antibiotic; triclosan; penem", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic efflux; reduced permeability to antibiotic"}, {"input_file_name": "rgi_report", "gene_symbol": "SHV-11", "gene_name": "SHV beta-lactamase", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3001070", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "100.0", "input_sequence_id": "NODE_11_length_157792_cov_39.2115_132", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "128890", "input_gene_stop": "129750", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "carbapenem; cephalosporin; penam", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic inactivation"}, {"input_file_name": "rgi_report", "gene_symbol": "CBP-1", "gene_name": "CBP beta-lactamase", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3004764", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "100.0", "input_sequence_id": "NODE_19_length_86672_cov_43.8582_38 ", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "39587", "input_gene_stop": "39811", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "-", "coverage_depth": "", "coverage_percentage": "24.03", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "penam", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic inactivation"}, {"input_file_name": "rgi_report", "gene_symbol": "Escherichia coli mdfA", "gene_name": "major facilitator superfamily (MFS) antibiotic efflux pump", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3001328", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "85.61", "input_sequence_id": "NODE_21_length_66123_cov_41.3566_52", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "60858", "input_gene_stop": "62090", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "tetracycline antibiotic; benzalkonium chloride; rhodamine", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic efflux"}, {"input_file_name": "rgi_report", "gene_symbol": "Klebsiella pneumoniae KpnE", "gene_name": "major facilitator superfamily (MFS) antibiotic efflux pump", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3004580", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "99.17", "input_sequence_id": "NODE_27_length_37761_cov_37.6839_21", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "25311", "input_gene_stop": "25673", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "macrolide antibiotic; aminoglycoside antibiotic; cephalosporin; tetracycline antibiotic; peptide antibiotic; rifamycin antibiotic", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic efflux"}, {"input_file_name": "rgi_report", "gene_symbol": "Klebsiella pneumoniae KpnF", "gene_name": "major facilitator superfamily (MFS) antibiotic efflux pump", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3004583", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "100.0", "input_sequence_id": "NODE_27_length_37761_cov_37.6839_22", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "25660", "input_gene_stop": "25989", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "macrolide antibiotic; aminoglycoside antibiotic; cephalosporin; tetracycline antibiotic; peptide antibiotic; rifamycin antibiotic", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic efflux"}, {"input_file_name": "rgi_report", "gene_symbol": "AAC(3)-IId", "gene_name": "AAC(3)", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3004623", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "100.0", "input_sequence_id": "NODE_39_length_11164_cov_23.0187_6", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "4569", "input_gene_stop": "5429", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "aminoglycoside antibiotic", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic inactivation"}, {"input_file_name": "rgi_report", "gene_symbol": "rmtC", "gene_name": "16S rRNA methyltransferase (G1405)", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3000861", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "100.0", "input_sequence_id": "NODE_40_length_7360_cov_24.8738_6", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "6358", "input_gene_stop": "7203", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "-", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "aminoglycoside antibiotic", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic target alteration"}, {"input_file_name": "rgi_report", "gene_symbol": "NDM-1", "gene_name": "NDM beta-lactamase", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3000589", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "100.0", "input_sequence_id": "NODE_44_length_4295_cov_23.2123_1", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "301", "input_gene_stop": "1113", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "carbapenem; cephalosporin; cephamycin; penam", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic inactivation"}, {"input_file_name": "rgi_report", "gene_symbol": "BRP(MBL)", "gene_name": "Bleomycin resistant protein", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3001205", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "100.0", "input_sequence_id": "NODE_44_length_4295_cov_23.2123_2 ", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "1222", "input_gene_stop": "1482", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "71.07", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "glycopeptide antibiotic", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic inactivation"}, {"input_file_name": "rgi_report", "gene_symbol": "DHA-7", "gene_name": "DHA beta-lactamase", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3002136", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "100.0", "input_sequence_id": "NODE_44_length_4295_cov_23.2123_3 ", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "1846", "input_gene_stop": "2862", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "-", "coverage_depth": "", "coverage_percentage": "89.18", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "cephalosporin; cephamycin", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic inactivation"}, {"input_file_name": "rgi_report", "gene_symbol": "CTX-M-15", "gene_name": "CTX-M beta-lactamase", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3001878", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "100.0", "input_sequence_id": "NODE_47_length_3813_cov_27.9457_4", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "2763", "input_gene_stop": "3638", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "-", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "cephalosporin", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic inactivation"}, {"input_file_name": "rgi_report", "gene_symbol": "OXA-1", "gene_name": "OXA beta-lactamase", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3001396", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "100.0", "input_sequence_id": "NODE_51_length_1731_cov_22.5767_1", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "196", "input_gene_stop": "1026", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "cephalosporin; penam", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic inactivation"}, {"input_file_name": "rgi_report", "gene_symbol": "catB3", "gene_name": "chloramphenicol acetyltransferase (CAT)", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3002676", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "100.0", "input_sequence_id": "NODE_51_length_1731_cov_22.5767_2 ", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "1164", "input_gene_stop": "1712", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "86.67", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "phenicol antibiotic", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic inactivation"}, {"input_file_name": "rgi_report", "gene_symbol": "AAC(6')-Ib-cr", "gene_name": "AAC(6')", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3002547", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "95.45", "input_sequence_id": "NODE_54_length_1272_cov_25.1921_2 ", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "1130", "input_gene_stop": "1270", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "23.62", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "fluoroquinolone antibiotic; aminoglycoside antibiotic", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic inactivation"}, {"input_file_name": "rgi_report", "gene_symbol": "sul1", "gene_name": "sulfonamide resistant sul", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3000410", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "100.0", "input_sequence_id": "NODE_57_length_1134_cov_34.8908_1", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "25", "input_gene_stop": "864", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "-", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "sulfonamide antibiotic", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic target replacement"}, {"input_file_name": "rgi_report", "gene_symbol": "AAC(6')-Ib10", "gene_name": "AAC(6')", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3002581", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "100.0", "input_sequence_id": "NODE_69_length_625_cov_55.4398_1", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "63", "input_gene_stop": "623", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "-", "coverage_depth": "", "coverage_percentage": "91.63", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "aminoglycoside antibiotic", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic inactivation"}, {"input_file_name": "rgi_report", "gene_symbol": "AAC(6')-Ib-cr", "gene_name": "AAC(6')", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3002547", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "100.0", "input_sequence_id": "NODE_185_length_335_cov_33.8077_1 ", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "172", "input_gene_stop": "333", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "27.14", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "fluoroquinolone antibiotic; aminoglycoside antibiotic", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic inactivation"}]

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

Mercurial > repos > iuc > hamronize_summarize

comparison test-data/hamronized_rgi.json @ 0:ef76d74a7171 draft