{ "type": "genome", "identifier": "GCF_000280495.2", "organism": "Kosakonia radicincitans DSM 16656", "title": "Kosakonia radicincitans DSM 16656", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Leibniz-Institute of Vegetable and Ornamental Crpos", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000280495.2", "bioproject": "PRJNA224116", "biosample": "SAMN02470245", "wgs_master": "na", "refseq_category": "na", "taxid": "1177180", "species_taxid": "283686", "organism_name": "Kosakonia radicincitans DSM 16656", "infraspecific_name": "strain=DSM 16656", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/04/03", "asm_name": "ASM28049v2", "asm_submitter": "Leibniz-Institute of Vegetable and Ornamental Crpos", "gbrs_paired_asm": "GCA_000280495.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/280/495/GCF_000280495.2_ASM28049v2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6122453", "genome_size_ungapped": "6122453", "gc_percent": "53.500000", "replicon_count": "3", "scaffold_count": "3", "contig_count": "3", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000280495.2-RS_2024_07_08", "annotation_date": "2024-07-08", "total_gene_count": "5934", "protein_coding_gene_count": "5729", "non_coding_gene_count": "116", "pubmed_id": "22965092" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-04-03", "dateModified": "2017-04-03", "datePublished": "2017-04-03", "_annotation": { "sample_count": 1, "sample_organism": [ "Kosakonia radicincitans DSM 16656" ], "sample_taxid": [ "1177180" ], "sample_host_organism": [ "winter wheat" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Germany" ], "sample_host_location_id": [], "data_size": "1.730 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "6122453", "Number of Sequences": "3", "Longest Sequences (bp)": "5817639", "N50 (bp)": "5817639", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "53.7", "Number of CDSs": "5809", "Average Protein Length": "308.4", "Coding Ratio (%)": "87.8", "Number of rRNAs": "22", "Number of tRNAs": "82", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Kosakonia oryzae", "strain": "strain=CGMCC 1.7012", "accession": "GCA_900112145.1", "taxid": 497725, "species_taxid": 497725, "relation_to_type": "type", "validated": true, "ani": 95.7256, "matched_fragments": 1686, "total_fragments": 2039, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Kosakonia oryzae", "strain": "strain=Ola 51", "accession": "GCA_001658025.2", "taxid": 497725, "species_taxid": 497725, "relation_to_type": "type", "validated": true, "ani": 95.7251, "matched_fragments": 1707, "total_fragments": 2039, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Kosakonia oryziphila", "strain": "strain=REICA_142", "accession": "GCA_900094795.1", "taxid": 1005667, "species_taxid": 1005667, "relation_to_type": "type", "validated": true, "ani": 93.2297, "matched_fragments": 1330, "total_fragments": 2039, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kosakonia arachidis", "strain": "strain=Ah-143", "accession": "GCA_900116535.1", "taxid": 551989, "species_taxid": 551989, "relation_to_type": "type", "validated": true, "ani": 92.7772, "matched_fragments": 1480, "total_fragments": 2039, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kosakonia sacchari", "strain": "strain=SP1", "accession": "GCA_000300455.4", "taxid": 1158459, "species_taxid": 1158459, "relation_to_type": "type", "validated": true, "ani": 85.1585, "matched_fragments": 1289, "total_fragments": 2039, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kosakonia sacchari", "strain": "strain=CGMCC 1.12102", "accession": "GCA_900100995.1", "taxid": 1158459, "species_taxid": 1158459, "relation_to_type": "type", "validated": true, "ani": 85.0084, "matched_fragments": 1274, "total_fragments": 2039, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kosakonia oryzendophytica", "strain": "strain=REICA_082", "accession": "GCA_900094925.1", "taxid": 1005665, "species_taxid": 1005665, "relation_to_type": "type", "validated": true, "ani": 84.1333, "matched_fragments": 1240, "total_fragments": 2039, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kosakonia cowanii", "strain": "strain=888-76", "accession": "GCA_001975225.1", "taxid": 208223, "species_taxid": 208223, "relation_to_type": "type", "validated": true, "ani": 83.7777, "matched_fragments": 1170, "total_fragments": 2039, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter roggenkampii", "strain": "strain=DSM 16690", "accession": "GCA_024390995.1", "taxid": 1812935, "species_taxid": 1812935, "relation_to_type": "type", "validated": true, "ani": 81.5932, "matched_fragments": 928, "total_fragments": 2039, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter hormaechei", "strain": "strain=FDAARGOS 1433", "accession": "GCA_019048245.1", "taxid": 158836, "species_taxid": 158836, "relation_to_type": "suspected-type", "validated": true, "ani": 81.589, "matched_fragments": 927, "total_fragments": 2039, "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": 81.5611, "matched_fragments": 913, "total_fragments": 2039, "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": 81.2819, "matched_fragments": 878, "total_fragments": 2039, "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": 81.2448, "matched_fragments": 918, "total_fragments": 2039, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Klebsiella pneumoniae", "strain": "strain=PartO-Kpneumoniae-RM8376", "accession": "GCA_022869665.1", "taxid": 573, "species_taxid": 573, "relation_to_type": "type", "validated": true, "ani": 81.151, "matched_fragments": 872, "total_fragments": 2039, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pantoea cypripedii", "strain": "strain=LMG 2657", "accession": "GCA_002095535.1", "taxid": 55209, "species_taxid": 55209, "relation_to_type": "type", "validated": true, "ani": 79.3576, "matched_fragments": 594, "total_fragments": 2039, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mixta gaviniae", "strain": "strain=DSM 22758", "accession": "GCA_002953195.1", "taxid": 665914, "species_taxid": 665914, "relation_to_type": "type", "validated": true, "ani": 79.2643, "matched_fragments": 602, "total_fragments": 2039, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pantoea deleyi", "strain": "strain=LMG24200", "accession": "GCA_022647325.1", "taxid": 470932, "species_taxid": 470932, "relation_to_type": "type", "validated": true, "ani": 78.795, "matched_fragments": 517, "total_fragments": 2039, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pantoea deleyi", "strain": "strain=LMG 24200", "accession": "GCA_006494415.1", "taxid": 470932, "species_taxid": 470932, "relation_to_type": "type", "validated": true, "ani": 78.5508, "matched_fragments": 505, "total_fragments": 2039, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pantoea deleyi", "strain": "strain=LMG 24200", "accession": "GCA_002095375.1", "taxid": 470932, "species_taxid": 470932, "relation_to_type": "type", "validated": true, "ani": 78.5264, "matched_fragments": 476, "total_fragments": 2039, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pantoea conspicua", "strain": "strain=LMG 24534", "accession": "GCA_002095315.1", "taxid": 472705, "species_taxid": 472705, "relation_to_type": "type", "validated": true, "ani": 78.3719, "matched_fragments": 483, "total_fragments": 2039, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Edwardsiella piscicida", "strain": "strain=ACC35.1", "accession": "GCA_001896205.1", "taxid": 1263550, "species_taxid": 1263550, "relation_to_type": "reftype", "validated": true, "ani": 78.0154, "matched_fragments": 351, "total_fragments": 2039, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoduganella ginsengisoli", "strain": "strain=KCTC 42409", "accession": "GCA_009720865.1", "taxid": 1462440, "species_taxid": 1462440, "relation_to_type": "type", "validated": true, "ani": 74.966, "matched_fragments": 52, "total_fragments": 2039, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000280495.2", "gtdb_species": "s__Kosakonia radicincitans", "ani": 100.0, "matched_fragments": 2037, "total_fragments": 2039, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia", "ani_circumscription_radius": 95.7299, "mean_intra_species_ani": "99.26", "min_intra_species_ani": "99.13", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.93", "num_clustered_genomes": 14, "status": "inconclusive" }, { "accession": "GCA_009929615.1", "gtdb_species": "s__Frisingicoccus sp009929615", "ani": 97.6158, "matched_fragments": 61, "total_fragments": 2039, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Frisingicoccus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.91", "min_intra_species_ani": "99.91", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "inconclusive" }, { "accession": "GCF_001658025.2", "gtdb_species": "s__Kosakonia oryzae", "ani": 95.7271, "matched_fragments": 1708, "total_fragments": 2039, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia", "ani_circumscription_radius": 95.7299, "mean_intra_species_ani": "98.47", "min_intra_species_ani": "96.95", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_900109485.1", "gtdb_species": "s__Kosakonia sacchari_B", "ani": 95.5795, "matched_fragments": 1644, "total_fragments": 2039, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia", "ani_circumscription_radius": 95.7228, "mean_intra_species_ani": "98.05", "min_intra_species_ani": "98.05", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_018261615.1", "gtdb_species": "s__Kosakonia sp018261615", "ani": 93.6588, "matched_fragments": 1347, "total_fragments": 2039, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia", "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_900094795.1", "gtdb_species": "s__Kosakonia oryziphila", "ani": 93.2066, "matched_fragments": 1332, "total_fragments": 2039, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia", "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_900116535.1", "gtdb_species": "s__Kosakonia arachidis", "ani": 92.7771, "matched_fragments": 1480, "total_fragments": 2039, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia", "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_000300455.3", "gtdb_species": "s__Kosakonia sacchari", "ani": 85.1536, "matched_fragments": 1290, "total_fragments": 2039, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.35", "min_intra_species_ani": "95.81", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.92", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_009363175.1", "gtdb_species": "s__Citrobacter_A telavivensis", "ani": 82.6737, "matched_fragments": 949, "total_fragments": 2039, "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_006711645.1", "gtdb_species": "s__Klebsiella electrica", "ani": 82.2507, "matched_fragments": 953, "total_fragments": 2039, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.88", "min_intra_species_ani": "98.54", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.85", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_014168815.1", "gtdb_species": "s__Kluyvera ascorbata_B", "ani": 82.2449, "matched_fragments": 904, "total_fragments": 2039, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.36", "min_intra_species_ani": "99.08", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.88", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_000025565.1", "gtdb_species": "s__Enterobacter cloacae", "ani": 82.1918, "matched_fragments": 987, "total_fragments": 2039, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.05", "min_intra_species_ani": "95.14", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.80", "num_clustered_genomes": 129, "status": "-" }, { "accession": "GCF_001521715.1", "gtdb_species": "s__Enterobacter asburiae", "ani": 81.7254, "matched_fragments": 920, "total_fragments": 2039, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 96.8818, "mean_intra_species_ani": "98.42", "min_intra_species_ani": "96.92", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.84", "num_clustered_genomes": 32, "status": "-" }, { "accession": "GCF_002939185.1", "gtdb_species": "s__Enterobacter sichuanensis", "ani": 81.2483, "matched_fragments": 924, "total_fragments": 2039, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.38", "min_intra_species_ani": "97.99", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.85", "num_clustered_genomes": 19, "status": "-" }, { "accession": "GCF_007680145.1", "gtdb_species": "s__Pseudescherichia sp002298805", "ani": 80.9891, "matched_fragments": 877, "total_fragments": 2039, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pseudescherichia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.55", "min_intra_species_ani": "96.56", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 13, "status": "-" }, { "accession": "GCF_005671395.1", "gtdb_species": "s__Jejubacter calystegiae", "ani": 79.5545, "matched_fragments": 612, "total_fragments": 2039, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Jejubacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.55", "min_intra_species_ani": "98.55", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002095535.1", "gtdb_species": "s__Pantoea cypripedii", "ani": 79.3447, "matched_fragments": 596, "total_fragments": 2039, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001922585.1", "gtdb_species": "s__1-19 sp001922585", "ani": 78.5161, "matched_fragments": 430, "total_fragments": 2039, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__1-19", "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.168, "cell_length": 0.248, "doubling_h": null, "growth_tmp": 30.0, "optimum_tmp": 29.0, "optimum_ph": 6.916, "genome_size": 5824844.222, "gc_content": 53.558, "coding_genes": 5330.333, "rRNA16S_genes": 7.0, "tRNA_genes": 82.5, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Kosakonia", "radicincitans", "DSM", "16656" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }