{ "type": "genome", "identifier": "GCF_002849855.1", "organism": "Vibrio azureus", "title": "Vibrio azureus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Atmosphere and Ocean Research Institute, The University of Tokyo", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002849855.1", "bioproject": "PRJNA224116", "biosample": "SAMN06105395", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "512649", "species_taxid": "512649", "organism_name": "Vibrio azureus", "infraspecific_name": "strain=LC2-005", "isolate": "na", "version_status": "latest", "assembly_level": "Chromosome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/01/03", "asm_name": "ASM284985v1", "asm_submitter": "Atmosphere and Ocean Research Institute, The University of Tokyo", "gbrs_paired_asm": "GCA_002849855.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/849/855/GCF_002849855.1_ASM284985v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4833901", "genome_size_ungapped": "4833501", "gc_percent": "42.500000", "replicon_count": "4", "scaffold_count": "4", "contig_count": "4", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-03-05", "total_gene_count": "4322", "protein_coding_gene_count": "4099", "non_coding_gene_count": "149", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-01-03", "dateModified": "2018-01-03", "datePublished": "2018-01-03", "_annotation": { "sample_count": 1, "sample_organism": [ "Vibrio azureus" ], "sample_taxid": [ "512649" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan: Kuroshio region" ], "sample_host_location_id": [], "data_size": "1.371 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)": "4833501", "Number of Sequences": "4", "Longest Sequences (bp)": "3027709", "N50 (bp)": "3027709", "Gap Ratio (%)": "0.000021", "GCcontent (%)": "42.3", "Number of CDSs": "4190", "Average Protein Length": "320.9", "Coding Ratio (%)": "83.5", "Number of rRNAs": "31", "Number of tRNAs": "116", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Vibrio azureus", "strain": "strain=LC2-005", "accession": "GCA_002849855.1", "taxid": 512649, "species_taxid": 512649, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1610, "total_fragments": 1610, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Vibrio azureus", "strain": "strain=NBRC 104587", "accession": "GCA_000467165.1", "taxid": 512649, "species_taxid": 512649, "relation_to_type": "type", "validated": true, "ani": 99.9109, "matched_fragments": 1478, "total_fragments": 1610, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Vibrio azureus", "strain": "strain=NBRC 104587", "accession": "GCA_000400265.1", "taxid": 512649, "species_taxid": 512649, "relation_to_type": "type", "validated": true, "ani": 99.8259, "matched_fragments": 1338, "total_fragments": 1610, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Vibrio sagamiensis", "strain": "strain=NBRC 104589", "accession": "GCA_000400425.1", "taxid": 512650, "species_taxid": 512650, "relation_to_type": "type", "validated": true, "ani": 91.1642, "matched_fragments": 1131, "total_fragments": 1610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio sagamiensis", "strain": "strain=NBRC 104589", "accession": "GCA_007990935.1", "taxid": 512650, "species_taxid": 512650, "relation_to_type": "type", "validated": true, "ani": 91.1401, "matched_fragments": 1141, "total_fragments": 1610, "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": 82.0436, "matched_fragments": 504, "total_fragments": 1610, "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": 81.6605, "matched_fragments": 492, "total_fragments": 1610, "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": 80.9022, "matched_fragments": 459, "total_fragments": 1610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio fortis", "strain": "strain=LMG 21557", "accession": "GCA_024347475.1", "taxid": 212667, "species_taxid": 212667, "relation_to_type": "type", "validated": true, "ani": 80.6419, "matched_fragments": 317, "total_fragments": 1610, "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": 80.4516, "matched_fragments": 285, "total_fragments": 1610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio celticus", "strain": "strain=CECT 7224", "accession": "GCA_024347335.1", "taxid": 446372, "species_taxid": 446372, "relation_to_type": "type", "validated": true, "ani": 80.1066, "matched_fragments": 309, "total_fragments": 1610, "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": 80.0997, "matched_fragments": 280, "total_fragments": 1610, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002849855.1", "gtdb_species": "s__Vibrio azureus", "ani": 100.0, "matched_fragments": 1610, "total_fragments": 1610, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "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": 3, "status": "conclusive" }, { "accession": "GCF_007990935.1", "gtdb_species": "s__Vibrio sagamiensis", "ani": 91.1547, "matched_fragments": 1140, "total_fragments": 1610, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.95", "min_intra_species_ani": "99.91", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.96", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002163755.1", "gtdb_species": "s__Vibrio campbellii", "ani": 82.5886, "matched_fragments": 525, "total_fragments": 1610, "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_002906655.1", "gtdb_species": "s__Vibrio hyugaensis", "ani": 81.8872, "matched_fragments": 536, "total_fragments": 1610, "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": "-" }, { "accession": "GCF_002741985.1", "gtdb_species": "s__Vibrio rotiferianus", "ani": 81.6605, "matched_fragments": 492, "total_fragments": 1610, "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": 81.559, "matched_fragments": 478, "total_fragments": 1610, "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_000817815.1", "gtdb_species": "s__Vibrio owensii", "ani": 81.5508, "matched_fragments": 518, "total_fragments": 1610, "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_001591145.1", "gtdb_species": "s__Vibrio harveyi", "ani": 81.5003, "matched_fragments": 513, "total_fragments": 1610, "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_000400365.1", "gtdb_species": "s__Vibrio jasicida", "ani": 81.3935, "matched_fragments": 518, "total_fragments": 1610, "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_002608565.1", "gtdb_species": "s__Vibrio sp002608565", "ani": 81.1027, "matched_fragments": 475, "total_fragments": 1610, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.42", "min_intra_species_ani": "99.42", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000830505.1", "gtdb_species": "s__Vibrio mytili", "ani": 80.1827, "matched_fragments": 385, "total_fragments": 1610, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.18, "cell_length": 0.215, "doubling_h": -0.527, "growth_tmp": 28.0, "optimum_tmp": 23.5, "optimum_ph": 7.4, "genome_size": 4751195.667, "gc_content": 42.21, "coding_genes": 4624.827, "rRNA16S_genes": 10.063, "tRNA_genes": 116.411, "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": 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": [ "Vibrio", "azureus" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }