{ "type": "genome", "identifier": "GCF_002906655.1", "organism": "Vibrio hyugaensis", "title": "Vibrio hyugaensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Academia Sinica", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002906655.1", "bioproject": "PRJNA224116", "biosample": "SAMD00019133", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "1534743", "species_taxid": "1534743", "organism_name": "Vibrio hyugaensis", "infraspecific_name": "strain=090810a", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/01/17", "asm_name": "ASM290665v1", "asm_submitter": "Academia Sinica", "gbrs_paired_asm": "GCA_002906655.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/906/655/GCF_002906655.1_ASM290665v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5612082", "genome_size_ungapped": "5612082", "gc_percent": "45.000000", "replicon_count": "2", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002906655.1-RS_2024_04_22", "annotation_date": "2024-04-22", "total_gene_count": "5032", "protein_coding_gene_count": "4766", "non_coding_gene_count": "171", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-01-17", "dateModified": "2018-01-17", "datePublished": "2018-01-17", "_annotation": { "sample_count": 1, "sample_organism": [ "Vibrio hyugaensis" ], "sample_taxid": [ "1534743" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan:Miyazaki" ], "sample_host_location_id": [], "data_size": "1.590 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)": "5612082", "Number of Sequences": "2", "Longest Sequences (bp)": "3530957", "N50 (bp)": "3530957", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "45.0", "Number of CDSs": "4918", "Average Protein Length": "323.9", "Coding Ratio (%)": "85.1", "Number of rRNAs": "36", "Number of tRNAs": "130", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Vibrio hyugaensis", "strain": "strain=090810a", "accession": "GCA_002906655.1", "taxid": 1534743, "species_taxid": 1534743, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1867, "total_fragments": 1869, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Vibrio hyugaensis", "strain": "strain=090810a", "accession": "GCA_000818435.1", "taxid": 1534743, "species_taxid": 1534743, "relation_to_type": "type", "validated": true, "ani": 99.9829, "matched_fragments": 1786, "total_fragments": 1869, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Vibrio owensii", "strain": "strain=DY05", "accession": "GCA_000817815.1", "taxid": 696485, "species_taxid": 696485, "relation_to_type": "type", "validated": true, "ani": 89.7837, "matched_fragments": 1471, "total_fragments": 1869, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio campbellii", "strain": "strain=CAIM 519", "accession": "GCA_000334195.1", "taxid": 680, "species_taxid": 680, "relation_to_type": "type", "validated": true, "ani": 88.1781, "matched_fragments": 1258, "total_fragments": 1869, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio harveyi", "strain": "strain=NCTC12970", "accession": "GCA_900460165.1", "taxid": 669, "species_taxid": 669, "relation_to_type": "type", "validated": true, "ani": 87.873, "matched_fragments": 1432, "total_fragments": 1869, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio harveyi", "strain": "strain=ATCC 14126", "accession": "GCA_001263135.1", "taxid": 669, "species_taxid": 669, "relation_to_type": "type", "validated": true, "ani": 87.8067, "matched_fragments": 1363, "total_fragments": 1869, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio harveyi", "strain": "strain=NBRC 15634", "accession": "GCA_001591145.1", "taxid": 669, "species_taxid": 669, "relation_to_type": "type", "validated": true, "ani": 87.7439, "matched_fragments": 1388, "total_fragments": 1869, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio rotiferianus", "strain": "strain=CAIM 577", "accession": "GCA_002741985.1", "taxid": 190895, "species_taxid": 190895, "relation_to_type": "type", "validated": true, "ani": 87.508, "matched_fragments": 1228, "total_fragments": 1869, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio parahaemolyticus", "strain": "strain=NCTC10903", "accession": "GCA_900460535.1", "taxid": 670, "species_taxid": 670, "relation_to_type": "type", "validated": true, "ani": 83.9157, "matched_fragments": 1093, "total_fragments": 1869, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio natriegens", "strain": "strain=14048", "accession": "GCA_024508015.1", "taxid": 691, "species_taxid": 691, "relation_to_type": "type", "validated": true, "ani": 82.4036, "matched_fragments": 849, "total_fragments": 1869, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio panuliri", "strain": "strain=JCM 19500", "accession": "GCA_009938205.1", "taxid": 1381081, "species_taxid": 1381081, "relation_to_type": "type", "validated": true, "ani": 80.5903, "matched_fragments": 441, "total_fragments": 1869, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio panuliri", "strain": "strain=LBS 2", "accession": "GCA_008830195.1", "taxid": 1381081, "species_taxid": 1381081, "relation_to_type": "type", "validated": true, "ani": 80.5594, "matched_fragments": 438, "total_fragments": 1869, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio toranzoniae", "strain": "strain=CECT 7225", "accession": "GCA_024347655.1", "taxid": 1194427, "species_taxid": 1194427, "relation_to_type": "type", "validated": true, "ani": 80.0524, "matched_fragments": 516, "total_fragments": 1869, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio crassostreae", "strain": "strain=LMG 22240", "accession": "GCA_024347415.1", "taxid": 246167, "species_taxid": 246167, "relation_to_type": "type", "validated": true, "ani": 80.0468, "matched_fragments": 593, "total_fragments": 1869, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002906655.1", "gtdb_species": "s__Vibrio hyugaensis", "ani": 100.0, "matched_fragments": 1867, "total_fragments": 1869, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.28", "min_intra_species_ani": "97.73", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.90", "num_clustered_genomes": 6, "status": "conclusive" }, { "accession": "GCF_000400365.1", "gtdb_species": "s__Vibrio jasicida", "ani": 94.3334, "matched_fragments": 1585, "total_fragments": 1869, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.91", "min_intra_species_ani": "97.51", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 25, "status": "-" }, { "accession": "GCF_000817815.1", "gtdb_species": "s__Vibrio owensii", "ani": 89.8054, "matched_fragments": 1467, "total_fragments": 1869, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.72", "min_intra_species_ani": "96.06", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.79", "num_clustered_genomes": 29, "status": "-" }, { "accession": "GCF_002163755.1", "gtdb_species": "s__Vibrio campbellii", "ani": 88.287, "matched_fragments": 1344, "total_fragments": 1869, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.60", "min_intra_species_ani": "95.95", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.77", "num_clustered_genomes": 78, "status": "-" }, { "accession": "GCF_001591145.1", "gtdb_species": "s__Vibrio harveyi", "ani": 87.732, "matched_fragments": 1389, "total_fragments": 1869, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.80", "min_intra_species_ani": "98.53", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.89", "num_clustered_genomes": 41, "status": "-" }, { "accession": "GCF_002741985.1", "gtdb_species": "s__Vibrio rotiferianus", "ani": 87.4961, "matched_fragments": 1230, "total_fragments": 1869, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.35", "min_intra_species_ani": "95.73", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.85", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_003544875.1", "gtdb_species": "s__Vibrio alfacsensis", "ani": 84.9907, "matched_fragments": 1055, "total_fragments": 1869, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.49", "min_intra_species_ani": "96.49", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000171815.1", "gtdb_species": "s__Vibrio sp000171815", "ani": 84.3487, "matched_fragments": 914, "total_fragments": 1869, "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_900460535.1", "gtdb_species": "s__Vibrio parahaemolyticus", "ani": 83.8984, "matched_fragments": 1096, "total_fragments": 1869, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.33", "min_intra_species_ani": "97.74", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.76", "num_clustered_genomes": 1553, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.18, "cell_length": 0.215, "doubling_h": -0.527, "growth_tmp": 27.81, "optimum_tmp": 26.308, "optimum_ph": 7.4, "genome_size": 5639854.75, "gc_content": 44.989, "coding_genes": 4909.0, "rRNA16S_genes": 10.063, "tRNA_genes": 130.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.864, "range_salinity": 0.923, "facultative_respiration": 0.602, "anaerobic_respiration": 0.011, "aerobic_respiration": 0.386, "mesophilic_range_tmp": 0.976, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.023, "bacillus_cell_shape": 0.637, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.034, "vibrio_cell_shape": 0.327, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Vibrio", "hyugaensis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }