{ "type": "genome", "identifier": "GCA_937949795.1", "organism": "uncultured Citrobacter sp.", "title": "uncultured Citrobacter sp.", "description": "derived from environmental source; derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "European Bioinformatics Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCA_937949795.1", "bioproject": "PRJEB51075", "biosample": "SAMEA14085423", "wgs_master": "CALECJ000000000.1", "refseq_category": "na", "taxid": "200446", "species_taxid": "200446", "organism_name": "uncultured Citrobacter sp.", "infraspecific_name": "", "isolate": "ERR912191_bin.60_CONCOCT_v1.1_MAG", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2023/01/12", "asm_name": "ERR912191_bin.60_CONCOCT_v1.1_MAG", "submitter": "European Bioinformatics Institute", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/937/949/795/GCA_937949795.1_ERR912191_bin.60_CONCOCT_v1.1_MAG", "excluded_from_refseq": "derived from environmental source; derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2023-01-12", "dateModified": "2023-01-12", "datePublished": "2023-01-12", "_annotation": { "sample_count": 1, "sample_organism": [ "uncultured Citrobacter sp." ], "sample_taxid": [ "200446" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "United Kingdom" ], "sample_host_location_id": [], "data_size": "1.317 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 98.96, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "4643552", "Number of Sequences": "17", "Longest Sequences (bp)": "1008888", "N50 (bp)": "653157", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "53.7", "Number of CDSs": "4289", "Average Protein Length": "320.5", "Coding Ratio (%)": "88.8", "Number of rRNAs": "1", "Number of tRNAs": "66", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Citrobacter youngae", "strain": "strain=NCTC13709", "accession": "GCA_900638065.1", "taxid": 133448, "species_taxid": 133448, "relation_to_type": "type", "validated": true, "ani": 84.437, "matched_fragments": 1073, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter amalonaticus", "strain": "strain=FDAARGOS_1489", "accession": "GCA_020099335.1", "taxid": 35703, "species_taxid": 35703, "relation_to_type": "type", "validated": true, "ani": 84.3934, "matched_fragments": 1090, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter amalonaticus", "strain": "strain=JCM 1661", "accession": "GCA_018323885.1", "taxid": 35703, "species_taxid": 35703, "relation_to_type": "type", "validated": true, "ani": 84.3731, "matched_fragments": 1108, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter rodentium", "strain": "strain=DSM 16636", "accession": "GCA_015965555.1", "taxid": 67825, "species_taxid": 67825, "relation_to_type": "type", "validated": true, "ani": 84.3642, "matched_fragments": 1032, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter braakii", "strain": "strain=FDAARGOS 1421", "accession": "GCA_019048805.1", "taxid": 57706, "species_taxid": 57706, "relation_to_type": "type", "validated": true, "ani": 84.3345, "matched_fragments": 1090, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter braakii", "strain": "strain=ATCC 51113", "accession": "GCA_002075345.1", "taxid": 57706, "species_taxid": 57706, "relation_to_type": "type", "validated": true, "ani": 84.3301, "matched_fragments": 1077, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter rodentium", "strain": "strain=ATCC 51116", "accession": "GCA_015965415.1", "taxid": 67825, "species_taxid": 67825, "relation_to_type": "type", "validated": true, "ani": 84.3182, "matched_fragments": 1037, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter arsenatis", "strain": "strain=LY-1", "accession": "GCA_004353845.1", "taxid": 2546350, "species_taxid": 2546350, "relation_to_type": "type", "validated": true, "ani": 84.3084, "matched_fragments": 1124, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter rodentium", "strain": "strain=DSM 16636", "accession": "GCA_021278985.1", "taxid": 67825, "species_taxid": 67825, "relation_to_type": "type", "validated": true, "ani": 84.301, "matched_fragments": 1065, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter farmeri", "strain": "strain=FDAARGOS 1423", "accession": "GCA_019048065.1", "taxid": 67824, "species_taxid": 67824, "relation_to_type": "type", "validated": true, "ani": 84.2942, "matched_fragments": 1086, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter rodentium", "strain": "strain=NBRC 105723", "accession": "GCA_000759815.1", "taxid": 67825, "species_taxid": 67825, "relation_to_type": "type", "validated": true, "ani": 84.2559, "matched_fragments": 1043, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salmonella enterica subsp. diarizonae", "strain": "strain=CCUG30040", "accession": "GCA_016030095.1", "taxid": 59204, "species_taxid": 28901, "relation_to_type": "type", "validated": true, "ani": 83.8406, "matched_fragments": 1007, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salmonella enterica subsp. enterica", "strain": "strain=PartC-Senterica-RM8376", "accession": "GCA_022869965.1", "taxid": 59201, "species_taxid": 28901, "relation_to_type": "suspected-type", "validated": true, "ani": 83.8125, "matched_fragments": 1001, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salmonella enterica subsp. diarizonae", "strain": "strain=CCUG 30040T", "accession": "GCA_008692785.1", "taxid": 59204, "species_taxid": 28901, "relation_to_type": "type", "validated": true, "ani": 83.7657, "matched_fragments": 1025, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salmonella enterica subsp. houtenae", "strain": "strain=CCUG 30041T", "accession": "GCA_008692755.1", "taxid": 59205, "species_taxid": 28901, "relation_to_type": "type", "validated": true, "ani": 83.6891, "matched_fragments": 979, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salmonella enterica subsp. indica", "strain": "strain=CCUG30038", "accession": "GCA_018033035.1", "taxid": 59207, "species_taxid": 28901, "relation_to_type": "type", "validated": true, "ani": 83.649, "matched_fragments": 999, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salmonella bongori", "strain": "strain=NCTC 12419", "accession": "GCA_000252995.1", "taxid": 54736, "species_taxid": 54736, "relation_to_type": "type", "validated": true, "ani": 83.17, "matched_fragments": 959, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Escherichia coli", "strain": "strain=DSM 30083", "accession": "GCA_024519395.1", "taxid": 562, "species_taxid": 562, "relation_to_type": "neotype", "validated": true, "ani": 83.0123, "matched_fragments": 981, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Escherichia coli", "strain": "strain=ATCC 11775", "accession": "GCA_003697165.2", "taxid": 562, "species_taxid": 562, "relation_to_type": "neotype", "validated": true, "ani": 82.9718, "matched_fragments": 969, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Escherichia coli", "strain": "strain=ATCC 11775", "accession": "GCA_000734955.1", "taxid": 562, "species_taxid": 562, "relation_to_type": "neotype", "validated": true, "ani": 82.9612, "matched_fragments": 961, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Escherichia coli", "strain": "strain=DSM 30083", "accession": "GCA_000690815.1", "taxid": 562, "species_taxid": 562, "relation_to_type": "neotype", "validated": true, "ani": 82.9412, "matched_fragments": 971, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shigella flexneri 2a", "strain": "strain=ATCC 29903", "accession": "GCA_002950215.1", "taxid": 42897, "species_taxid": 623, "relation_to_type": "type", "validated": true, "ani": 82.8594, "matched_fragments": 936, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shigella dysenteriae", "strain": "strain=ATCC 13313", "accession": "GCA_002949675.1", "taxid": 622, "species_taxid": 622, "relation_to_type": "suspected-type", "validated": true, "ani": 82.7219, "matched_fragments": 896, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shigella dysenteriae", "strain": "strain=NCTC4837", "accession": "GCA_900457215.1", "taxid": 622, "species_taxid": 622, "relation_to_type": "suspected-type", "validated": true, "ani": 82.7001, "matched_fragments": 900, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Escherichia fergusonii", "strain": "strain=FDAARGOS_1499", "accession": "GCA_020097475.1", "taxid": 564, "species_taxid": 564, "relation_to_type": "type", "validated": true, "ani": 82.6519, "matched_fragments": 889, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Klebsiella indica", "strain": "strain=TOUT106", "accession": "GCA_005860775.1", "taxid": 2582917, "species_taxid": 2582917, "relation_to_type": "type", "validated": true, "ani": 82.5597, "matched_fragments": 817, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter wuhouensis", "strain": "strain=WCHEW120002", "accession": "GCA_004331265.1", "taxid": 2529381, "species_taxid": 2529381, "relation_to_type": "type", "validated": true, "ani": 82.0512, "matched_fragments": 919, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter sichuanensis", "strain": "strain=WCHECL1597", "accession": "GCA_025002605.1", "taxid": 2071710, "species_taxid": 2071710, "relation_to_type": "type", "validated": true, "ani": 82.049, "matched_fragments": 917, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudocitrobacter corydidari", "strain": "", "accession": "GCA_021172065.1", "taxid": 2891570, "species_taxid": 2891570, "relation_to_type": "type", "validated": true, "ani": 82.042, "matched_fragments": 916, "total_fragments": 1538, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 98.96, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_900446925.1", "gtdb_species": "s__Citrobacter_B koseri", "ani": 98.7195, "matched_fragments": 1435, "total_fragments": 1538, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.74", "min_intra_species_ani": "98.70", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.91", "num_clustered_genomes": 109, "status": "conclusive" }, { "accession": "GCF_016811995.1", "gtdb_species": "s__Citrobacter sp016811995", "ani": 84.7887, "matched_fragments": 1076, "total_fragments": 1538, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.97", "min_intra_species_ani": "95.97", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002918555.1", "gtdb_species": "s__Citrobacter_C amalonaticus_A", "ani": 84.7323, "matched_fragments": 1118, "total_fragments": 1538, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_C", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000155975.1", "gtdb_species": "s__Citrobacter portucalensis_A", "ani": 84.5399, "matched_fragments": 1099, "total_fragments": 1538, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000981805.1", "gtdb_species": "s__Citrobacter_A amalonaticus_C", "ani": 84.5319, "matched_fragments": 1114, "total_fragments": 1538, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_010231475.1", "gtdb_species": "s__Citrobacter sp010231475", "ani": 84.477, "matched_fragments": 1044, "total_fragments": 1538, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_009363175.1", "gtdb_species": "s__Citrobacter_A telavivensis", "ani": 84.4638, "matched_fragments": 1106, "total_fragments": 1538, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_018323885.1", "gtdb_species": "s__Citrobacter_A amalonaticus", "ani": 84.3642, "matched_fragments": 1109, "total_fragments": 1538, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.67", "min_intra_species_ani": "95.02", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.83", "num_clustered_genomes": 59, "status": "-" }, { "accession": "GCF_019048065.1", "gtdb_species": "s__Citrobacter_A farmeri", "ani": 84.2788, "matched_fragments": 1088, "total_fragments": 1538, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.22", "min_intra_species_ani": "96.70", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 16, "status": "-" }, { "accession": "GCF_000759815.1", "gtdb_species": "s__Citrobacter_A rodentium", "ani": 84.2508, "matched_fragments": 1044, "total_fragments": 1538, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.96", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.96", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000759835.1", "gtdb_species": "s__Citrobacter_A sedlakii", "ani": 83.9217, "matched_fragments": 1074, "total_fragments": 1538, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.16", "min_intra_species_ani": "99.00", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.93", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_000006945.2", "gtdb_species": "s__Salmonella enterica", "ani": 83.81, "matched_fragments": 1012, "total_fragments": 1538, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella", "ani_circumscription_radius": 95.0604, "mean_intra_species_ani": "98.80", "min_intra_species_ani": "95.43", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.81", "num_clustered_genomes": 12285, "status": "-" }, { "accession": "GCF_008692785.1", "gtdb_species": "s__Salmonella diarizonae", "ani": 83.7589, "matched_fragments": 1026, "total_fragments": 1538, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella", "ani_circumscription_radius": 95.0604, "mean_intra_species_ani": "98.90", "min_intra_species_ani": "95.36", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.81", "num_clustered_genomes": 98, "status": "-" }, { "accession": "GCA_900478215.1", "gtdb_species": "s__Salmonella houtenae", "ani": 83.6735, "matched_fragments": 980, "total_fragments": 1538, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.09", "min_intra_species_ani": "96.71", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.89", "num_clustered_genomes": 62, "status": "-" }, { "accession": "GCF_003697165.2", "gtdb_species": "s__Escherichia coli", "ani": 82.9806, "matched_fragments": 968, "total_fragments": 1538, "gtdb_taxonomy": 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