{ "type": "genome", "identifier": "GCF_024346875.1", "organism": "Vibrio gallicus", "title": "Vibrio gallicus", "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_024346875.1", "bioproject": "PRJNA224116", "biosample": "SAMD00393684", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "190897", "species_taxid": "190897", "organism_name": "Vibrio gallicus", "infraspecific_name": "strain=CIP 107863", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/07/13", "asm_name": "ASM2434687v1", "asm_submitter": "Laboratory of Microbiology, Division of Marine Life Science, Faculty of Fisheries Sciences, Hokkaido University", "gbrs_paired_asm": "GCA_024346875.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/024/346/875/GCF_024346875.1_ASM2434687v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3518157", "genome_size_ungapped": "3518157", "gc_percent": "44.000000", "replicon_count": "2", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_024346875.1-RS_2024_10_11", "annotation_date": "2024-10-11", "total_gene_count": "3229", "protein_coding_gene_count": "3071", "non_coding_gene_count": "127", "pubmed_id": "34905112" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-07-13", "dateModified": "2022-07-13", "datePublished": "2022-07-13", "_annotation": { "sample_count": 1, "sample_organism": [ "Vibrio gallicus" ], "sample_taxid": [ "190897" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "France:Brest" ], "sample_host_location_id": [], "data_size": "0.997 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)": "3518157", "Number of Sequences": "2", "Longest Sequences (bp)": "2528163", "N50 (bp)": "2528163", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "43.8", "Number of CDSs": "3098", "Average Protein Length": "326.8", "Coding Ratio (%)": "86.3", "Number of rRNAs": "28", "Number of tRNAs": "96", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Vibrio gallicus", "strain": "strain=CIP 107863", "accession": "GCA_024346875.1", "taxid": 190897, "species_taxid": 190897, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1170, "total_fragments": 1171, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Vibrio inusitatus", "strain": "strain=LMG 23434", "accession": "GCA_024346935.1", "taxid": 413402, "species_taxid": 413402, "relation_to_type": "type", "validated": true, "ani": 81.0192, "matched_fragments": 353, "total_fragments": 1171, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio comitans", "strain": "strain=LMG 23416", "accession": "GCA_024346835.1", "taxid": 413401, "species_taxid": 413401, "relation_to_type": "type", "validated": true, "ani": 80.965, "matched_fragments": 366, "total_fragments": 1171, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio superstes", "strain": "strain=G3-29", "accession": "GCA_003569005.1", "taxid": 198815, "species_taxid": 198815, "relation_to_type": "type", "validated": true, "ani": 80.9489, "matched_fragments": 354, "total_fragments": 1171, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio superstes", "strain": "strain=NBRC 103154", "accession": "GCA_007990955.1", "taxid": 198815, "species_taxid": 198815, "relation_to_type": "type", "validated": true, "ani": 80.831, "matched_fragments": 341, "total_fragments": 1171, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio ishigakensis", "strain": "strain=JCM 19231", "accession": "GCA_024347675.1", "taxid": 1481914, "species_taxid": 1481914, "relation_to_type": "type", "validated": true, "ani": 80.5667, "matched_fragments": 475, "total_fragments": 1171, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio rarus", "strain": "strain=LMG 23674", "accession": "GCA_024347075.1", "taxid": 413403, "species_taxid": 413403, "relation_to_type": "type", "validated": true, "ani": 80.5146, "matched_fragments": 312, "total_fragments": 1171, "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": 80.4626, "matched_fragments": 343, "total_fragments": 1171, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio comitans", "strain": "strain=NBRC 102076", "accession": "GCA_006538565.1", "taxid": 413401, "species_taxid": 413401, "relation_to_type": "type", "validated": true, "ani": 80.3715, "matched_fragments": 344, "total_fragments": 1171, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio inusitatus", "strain": "strain=NBRC 102082", "accession": "GCA_006538525.1", "taxid": 413402, "species_taxid": 413402, "relation_to_type": "type", "validated": true, "ani": 80.2697, "matched_fragments": 328, "total_fragments": 1171, "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": 79.8552, "matched_fragments": 184, "total_fragments": 1171, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio ezurae", "strain": "strain=NBRC 102218", "accession": "GCA_000467185.1", "taxid": 252583, "species_taxid": 252583, "relation_to_type": "type", "validated": true, "ani": 79.6423, "matched_fragments": 301, "total_fragments": 1171, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio ezurae", "strain": "strain=HDS1-1", "accession": "GCA_003568985.1", "taxid": 252583, "species_taxid": 252583, "relation_to_type": "type", "validated": true, "ani": 79.6287, "matched_fragments": 317, "total_fragments": 1171, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio marinisediminis", "strain": "strain=404", "accession": "GCA_014050145.1", "taxid": 2758441, "species_taxid": 2758441, "relation_to_type": "type", "validated": true, "ani": 78.9128, "matched_fragments": 169, "total_fragments": 1171, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio rhodolitus", "strain": "strain=G98", "accession": "GCA_003350325.1", "taxid": 2231649, "species_taxid": 2231649, "relation_to_type": "type", "validated": true, "ani": 78.8778, "matched_fragments": 173, "total_fragments": 1171, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aliivibrio fischeri", "strain": "strain=ATCC 7744", "accession": "GCA_016464335.1", "taxid": 668, "species_taxid": 668, "relation_to_type": "suspected-type", "validated": true, "ani": 78.6149, "matched_fragments": 169, "total_fragments": 1171, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001677275.1", "gtdb_species": "s__Vibrio breoganii", "ani": 81.8712, "matched_fragments": 367, "total_fragments": 1171, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.22", "min_intra_species_ani": "96.88", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.86", "num_clustered_genomes": 59, "status": "-" }, { "accession": "GCF_003569005.1", "gtdb_species": "s__Vibrio superstes", "ani": 80.9167, "matched_fragments": 353, "total_fragments": 1171, "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": 2, "status": "-" }, { "accession": "GCF_006538565.1", "gtdb_species": "s__Vibrio comitans", "ani": 80.3715, "matched_fragments": 344, "total_fragments": 1171, "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_006538525.1", "gtdb_species": "s__Vibrio inusitatus", "ani": 80.253, "matched_fragments": 329, "total_fragments": 1171, "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": "GCA_000830415.1", "gtdb_species": "s__Vibrio ishigakensis", "ani": 80.0661, "matched_fragments": 430, "total_fragments": 1171, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.42", "min_intra_species_ani": "95.17", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000496695.1", "gtdb_species": "s__Vibrio halioticoli", "ani": 79.805, "matched_fragments": 306, "total_fragments": 1171, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.64", "min_intra_species_ani": "97.31", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002218045.2", "gtdb_species": "s__Vibrio rumoiensis", "ani": 79.7618, "matched_fragments": 165, "total_fragments": 1171, "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_009938205.1", "gtdb_species": "s__Vibrio panuliri", "ani": 79.6752, "matched_fragments": 182, "total_fragments": 1171, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.52", "min_intra_species_ani": "98.57", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.94", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_001676025.1", "gtdb_species": "s__Vibrio sp001676025", "ani": 79.6243, "matched_fragments": 336, "total_fragments": 1171, "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": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000467185.1", "gtdb_species": "s__Vibrio ezurae", "ani": 79.617, "matched_fragments": 303, "total_fragments": 1171, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "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_000189275.1", "gtdb_species": "s__Vibrio sinaloensis_B", "ani": 79.1092, "matched_fragments": 170, "total_fragments": 1171, "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_009811315.1", "gtdb_species": "s__Vibrio atypicus", "ani": 79.0959, "matched_fragments": 191, "total_fragments": 1171, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.15", "min_intra_species_ani": "97.15", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000222605.1", "gtdb_species": "s__Vibrio ichthyoenteri", "ani": 79.0322, "matched_fragments": 164, "total_fragments": 1171, "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_004551525.1", "gtdb_species": "s__Vibrio ouci", "ani": 79.0004, "matched_fragments": 199, "total_fragments": 1171, "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_014694375.1", "gtdb_species": "s__Vibrio sp014694375", "ani": 79.0001, "matched_fragments": 121, "total_fragments": 1171, "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_014050145.1", "gtdb_species": "s__Vibrio marinisediminis", "ani": 78.9324, "matched_fragments": 167, "total_fragments": 1171, "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_003350325.1", "gtdb_species": "s__Vibrio rhodolitus", "ani": 78.8667, "matched_fragments": 171, "total_fragments": 1171, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.24", "min_intra_species_ani": "97.24", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_001874155.1", "gtdb_species": "s__Vibrio sp001874155", "ani": 78.7264, "matched_fragments": 142, "total_fragments": 1171, "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_009727955.1", "gtdb_species": "s__Aliivibrio fischeri_A", "ani": 78.6023, "matched_fragments": 168, "total_fragments": 1171, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio", "ani_circumscription_radius": 95.1568, "mean_intra_species_ani": "98.75", "min_intra_species_ani": "97.87", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.92", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_016464335.1", "gtdb_species": "s__Aliivibrio fischeri", "ani": 78.5895, "matched_fragments": 169, "total_fragments": 1171, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio", "ani_circumscription_radius": 95.1568, "mean_intra_species_ani": "96.45", "min_intra_species_ani": "95.48", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.84", "num_clustered_genomes": 60, "status": "-" }, { "accession": "GCF_015223435.1", "gtdb_species": "s__Vibrio hibernica", "ani": 78.3967, "matched_fragments": 123, "total_fragments": 1171, "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": -0.26, "cell_length": 0.322, "doubling_h": -0.527, "growth_tmp": 25.0, "optimum_tmp": 22.5, "optimum_ph": 7.4, "genome_size": 4870437.62, "gc_content": 44.906, "coding_genes": 4624.827, "rRNA16S_genes": 10.063, "tRNA_genes": 116.411, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "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": 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", "gallicus" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }