{ "type": "genome", "identifier": "GCF_002218025.2", "organism": "Vibrio casei", "title": "Vibrio casei", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Laboratory of Microbiology, Division of Marine Life Science, Faculty of Fisheries Sciences, Hokkaido University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002218025.2", "bioproject": "PRJNA224116", "biosample": "SAMD00080446", "wgs_master": "na", "refseq_category": "na", "taxid": "673372", "species_taxid": "673372", "organism_name": "Vibrio casei", "infraspecific_name": "strain=DSM 22364", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/06/06", "asm_name": "ASM221802v2", "asm_submitter": "Laboratory of Microbiology, Division of Marine Life Science, Faculty of Fisheries Sciences, Hokkaido University", "gbrs_paired_asm": "GCA_002218025.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/218/025/GCF_002218025.2_ASM221802v2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4140771", "genome_size_ungapped": "4140771", "gc_percent": "40.500000", "replicon_count": "5", "scaffold_count": "5", "contig_count": "5", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002218025.2-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "3877", "protein_coding_gene_count": "3635", "non_coding_gene_count": "122", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-06-06", "dateModified": "2018-06-06", "datePublished": "2018-06-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Vibrio casei" ], "sample_taxid": [ "673372" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.170 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)": "4140771", "Number of Sequences": "5", "Longest Sequences (bp)": "2756634", "N50 (bp)": "2756634", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "40.7", "Number of CDSs": "3847", "Average Protein Length": "305.6", "Coding Ratio (%)": "85.2", "Number of rRNAs": "25", "Number of tRNAs": "93", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Vibrio casei", "strain": "strain=DSM 22364", "accession": "GCA_002218025.2", "taxid": 673372, "species_taxid": 673372, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1377, "total_fragments": 1378, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Vibrio litoralis", "strain": "strain=DSM 17657", "accession": "GCA_000426765.1", "taxid": 335972, "species_taxid": 335972, "relation_to_type": "type", "validated": true, "ani": 82.7366, "matched_fragments": 652, "total_fragments": 1378, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio rumoiensis", "strain": "strain=FERM P-14531", "accession": "GCA_002218045.2", "taxid": 76258, "species_taxid": 76258, "relation_to_type": "type", "validated": true, "ani": 81.9695, "matched_fragments": 641, "total_fragments": 1378, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio algivorus", "strain": "strain=SA2", "accession": "GCA_002218005.2", "taxid": 1667024, "species_taxid": 1667024, "relation_to_type": "type", "validated": true, "ani": 81.6723, "matched_fragments": 609, "total_fragments": 1378, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio hibernica", "strain": "strain=B1.19", "accession": "GCA_015223435.1", "taxid": 2587465, "species_taxid": 2587465, "relation_to_type": "type", "validated": true, "ani": 81.3182, "matched_fragments": 471, "total_fragments": 1378, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio gangliei", "strain": "strain=SZDIS-1", "accession": "GCA_002934045.1", "taxid": 2077090, "species_taxid": 2077090, "relation_to_type": "type", "validated": true, "ani": 80.1221, "matched_fragments": 511, "total_fragments": 1378, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio aphrogenes", "strain": "strain=CA-1004", "accession": "GCA_002157735.2", "taxid": 1891186, "species_taxid": 1891186, "relation_to_type": "type", "validated": true, "ani": 80.0788, "matched_fragments": 492, "total_fragments": 1378, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio algicola", "strain": "strain=SM1977", "accession": "GCA_009601765.2", "taxid": 2662262, "species_taxid": 2662262, "relation_to_type": "type", "validated": true, "ani": 80.0776, "matched_fragments": 431, "total_fragments": 1378, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio neonatus", "strain": "strain=JCM 21521", "accession": "GCA_024346975.1", "taxid": 278860, "species_taxid": 278860, "relation_to_type": "type", "validated": true, "ani": 79.7995, "matched_fragments": 175, "total_fragments": 1378, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio splendidus", "strain": "strain=LMG 19031", "accession": "GCA_024347615.1", "taxid": 29497, "species_taxid": 29497, "relation_to_type": "type", "validated": true, "ani": 79.7438, "matched_fragments": 221, "total_fragments": 1378, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio cyclitrophicus", "strain": "strain=LMG 21359", "accession": "GCA_024347435.1", "taxid": 47951, "species_taxid": 47951, "relation_to_type": "type", "validated": true, "ani": 79.6047, "matched_fragments": 223, "total_fragments": 1378, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium phosphoreum", "strain": "strain=ATCC 11040", "accession": "GCA_000949955.1", "taxid": 659, "species_taxid": 659, "relation_to_type": "type", "validated": true, "ani": 77.6037, "matched_fragments": 162, "total_fragments": 1378, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002218025.2", "gtdb_species": "s__Vibrio casei", "ani": 100.0, "matched_fragments": 1378, "total_fragments": 1378, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.63", "min_intra_species_ani": "99.33", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.89", "num_clustered_genomes": 5, "status": "conclusive" }, { "accession": "GCF_000426765.1", "gtdb_species": "s__Vibrio litoralis", "ani": 82.746, "matched_fragments": 651, "total_fragments": 1378, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.36", "min_intra_species_ani": "97.06", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002218045.2", "gtdb_species": "s__Vibrio rumoiensis", "ani": 81.9536, "matched_fragments": 643, "total_fragments": 1378, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "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_000286955.2", "gtdb_species": "s__Vibrio rumoiensis_A", "ani": 81.8558, "matched_fragments": 735, "total_fragments": 1378, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "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_002218005.2", "gtdb_species": "s__Vibrio algivorus", "ani": 81.5471, "matched_fragments": 607, "total_fragments": 1378, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.65", "min_intra_species_ani": "98.65", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014694375.1", "gtdb_species": "s__Vibrio sp014694375", "ani": 81.4392, "matched_fragments": 552, "total_fragments": 1378, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "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_015223435.1", "gtdb_species": "s__Vibrio hibernica", "ani": 81.3182, "matched_fragments": 471, "total_fragments": 1378, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "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_002157735.2", "gtdb_species": "s__Vibrio aphrogenes", "ani": 80.1189, "matched_fragments": 495, "total_fragments": 1378, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "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_002934045.1", "gtdb_species": "s__Vibrio gangliei", "ani": 80.1094, "matched_fragments": 511, "total_fragments": 1378, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "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_009601765.2", "gtdb_species": "s__Vibrio sp009601765", "ani": 80.077, "matched_fragments": 431, "total_fragments": 1378, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.01", "min_intra_species_ani": "99.01", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.125, "cell_length": 0.197, "doubling_h": -0.527, "growth_tmp": 29.0, "optimum_tmp": 30.0, "optimum_ph": 7.25, "genome_size": 4077845.0, "gc_content": 40.738, "coding_genes": 3607.0, "rRNA16S_genes": 10.063, "tRNA_genes": 93.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.923, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 0.976, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.023, "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": [ "Vibrio", "casei" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }