{ "type": "genome", "identifier": "GCF_024346715.1", "organism": "Photobacterium swingsii", "title": "Photobacterium swingsii", "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_024346715.1", "bioproject": "PRJNA224116", "biosample": "SAMD00393679", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "680026", "species_taxid": "680026", "organism_name": "Photobacterium swingsii", "infraspecific_name": "strain=CECT 7576", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/07/13", "asm_name": "ASM2434671v1", "asm_submitter": "Laboratory of Microbiology, Division of Marine Life Science, Faculty of Fisheries Sciences, Hokkaido University", "gbrs_paired_asm": "GCA_024346715.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/024/346/715/GCF_024346715.1_ASM2434671v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5650079", "genome_size_ungapped": "5650079", "gc_percent": "44.000000", "replicon_count": "2", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_024346715.1-RS_2024_10_11", "annotation_date": "2024-10-11", "total_gene_count": "5038", "protein_coding_gene_count": "4778", "non_coding_gene_count": "233", "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": [ "Photobacterium swingsii" ], "sample_taxid": [ "680026" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Spain:Canary Islands" ], "sample_host_location_id": [], "data_size": "1.597 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)": "5650079", "Number of Sequences": "2", "Longest Sequences (bp)": "3818500", "N50 (bp)": "3818500", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "43.8", "Number of CDSs": "4848", "Average Protein Length": "327.3", "Coding Ratio (%)": "84.3", "Number of rRNAs": "52", "Number of tRNAs": "177", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Photobacterium swingsii", "strain": "strain=CECT 7576", "accession": "GCA_024346715.1", "taxid": 680026, "species_taxid": 680026, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1879, "total_fragments": 1882, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Photobacterium swingsii", "strain": "strain=DSM 24669", "accession": "GCA_003026435.1", "taxid": 680026, "species_taxid": 680026, "relation_to_type": "type", "validated": true, "ani": 99.9859, "matched_fragments": 1824, "total_fragments": 1882, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Photobacterium swingsii", "strain": "strain=CAIM 1393", "accession": "GCA_001077885.1", "taxid": 680026, "species_taxid": 680026, "relation_to_type": "type", "validated": true, "ani": 99.9516, "matched_fragments": 1797, "total_fragments": 1882, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Photobacterium sanguinicancri", "strain": "strain=CECT 7579", "accession": "GCA_024346675.1", "taxid": 875932, "species_taxid": 875932, "relation_to_type": "type", "validated": true, "ani": 86.5961, "matched_fragments": 1539, "total_fragments": 1882, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium sanguinicancri", "strain": "strain=CAIM 1827", "accession": "GCA_002265265.1", "taxid": 875932, "species_taxid": 875932, "relation_to_type": "type", "validated": true, "ani": 86.3761, "matched_fragments": 1347, "total_fragments": 1882, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio marisflavi", "strain": "strain=CECT 7928", "accession": "GCA_921294215.1", "taxid": 1216040, "species_taxid": 1216040, "relation_to_type": "type", "validated": true, "ani": 80.1256, "matched_fragments": 151, "total_fragments": 1882, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aliivibrio fischeri", "strain": "strain=DSM 507", "accession": "GCA_023983475.1", "taxid": 668, "species_taxid": 668, "relation_to_type": 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"min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_002265265.1", "gtdb_species": "s__Photobacterium sanguinicancri", "ani": 86.3585, "matched_fragments": 1350, "total_fragments": 1882, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.87", "min_intra_species_ani": "97.87", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001650345.1", "gtdb_species": "s__Photobacterium jeanii", "ani": 81.732, "matched_fragments": 948, "total_fragments": 1882, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", 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"N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_000950415.1", "gtdb_species": "s__Photobacterium leiognathi", "ani": 79.6617, "matched_fragments": 391, "total_fragments": 1882, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.11", "min_intra_species_ani": "96.59", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 15, "status": "-" }, { "accession": "GCF_000153325.1", "gtdb_species": "s__Photobacterium sp000153325", "ani": 79.5354, "matched_fragments": 369, "total_fragments": 1882, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "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_001939735.1", "gtdb_species": "s__Photobacterium proteolyticum", "ani": 79.4519, "matched_fragments": 452, "total_fragments": 1882, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "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_003026455.1", "gtdb_species": "s__Photobacterium rosenbergii", "ani": 79.4295, "matched_fragments": 416, "total_fragments": 1882, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.32", "min_intra_species_ani": "95.32", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.83", 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1, "status": "-" }, { "accession": "GCF_900185615.1", "gtdb_species": "s__Photobacterium malacitanum", "ani": 79.3649, "matched_fragments": 338, "total_fragments": 1882, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.08", "min_intra_species_ani": "95.06", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_000331515.1", "gtdb_species": "s__Photobacterium marinum", "ani": 79.2729, "matched_fragments": 395, "total_fragments": 1882, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.66", "min_intra_species_ani": "96.66", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003026285.1", "gtdb_species": "s__Photobacterium profundum", "ani": 79.2518, "matched_fragments": 544, "total_fragments": 1882, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.97", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002954455.1", "gtdb_species": "s__Photobacterium aquimaris", "ani": 79.2284, "matched_fragments": 340, "total_fragments": 1882, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.51", "min_intra_species_ani": "95.34", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.87", "num_clustered_genomes": 6, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.006, "cell_length": 0.34, "doubling_h": 0.223, "growth_tmp": 25.0, "optimum_tmp": 30.0, "optimum_ph": 7.25, "genome_size": 5515952.0, "gc_content": 43.69, "coding_genes": 4615.291, "rRNA16S_genes": 15.0, "tRNA_genes": 173.333, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.916, "range_salinity": 0.666, "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": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 1.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Photobacterium", "swingsii" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }