{ "type": "genome", "identifier": "GCF_001077885.1", "organism": "Photobacterium swingsii", "title": "Photobacterium swingsii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "CIAD, A.C.", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001077885.1", "bioproject": "PRJNA224116", "biosample": "SAMN03766180", "wgs_master": "LELC00000000.1", "refseq_category": "na", "taxid": "680026", "species_taxid": "680026", "organism_name": "Photobacterium swingsii", "infraspecific_name": "strain=CAIM 1393", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/07/14", "asm_name": "CAIM1393T.ver1", "asm_submitter": "CIAD, A.C.", "gbrs_paired_asm": "GCA_001077885.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/077/885/GCF_001077885.1_CAIM1393T.ver1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5523519", "genome_size_ungapped": "5523519", "gc_percent": "43.500000", "replicon_count": "0", "scaffold_count": "98", "contig_count": "98", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001077885.1-RS_2024_03_29", "annotation_date": "2024-03-29", "total_gene_count": "5056", "protein_coding_gene_count": "4461", "non_coding_gene_count": "70", "pubmed_id": "20228205" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-07-14", "dateModified": "2015-07-14", "datePublished": "2015-07-14", "_annotation": { "sample_count": 1, "sample_organism": [ "Photobacterium swingsii" ], "sample_taxid": [ "680026" ], "sample_host_organism": [ "Maja brachydactyla" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Spain: Canary Islands" ], "sample_host_location_id": [], "data_size": "1.579 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": 30.0, "max": 30.0 }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5523519", "Number of Sequences": "98", "Longest Sequences (bp)": "535680", "N50 (bp)": "175448", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "43.7", "Number of CDSs": "5369", "Average Protein Length": "290.8", "Coding Ratio (%)": "84.8", "Number of rRNAs": "3", "Number of tRNAs": "61", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Photobacterium swingsii", "strain": "strain=CAIM 1393", "accession": "GCA_001077885.1", "taxid": 680026, "species_taxid": 680026, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1797, "total_fragments": 1800, "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": 99.9772, "matched_fragments": 1800, "total_fragments": 1800, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Photobacterium swingsii", "strain": "strain=CECT 7576", "accession": "GCA_024346715.1", "taxid": 680026, "species_taxid": 680026, "relation_to_type": "type", "validated": true, "ani": 99.9768, "matched_fragments": 1799, "total_fragments": 1800, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Photobacterium sanguinicancri", "strain": "strain=CAIM 1827", "accession": "GCA_002265265.1", "taxid": 875932, "species_taxid": 875932, "relation_to_type": "type", "validated": true, "ani": 86.3839, "matched_fragments": 1317, "total_fragments": 1800, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium sanguinicancri", "strain": "strain=CECT 7579", "accession": "GCA_024346675.1", "taxid": 875932, "species_taxid": 875932, "relation_to_type": "type", "validated": true, "ani": 86.3215, "matched_fragments": 1486, "total_fragments": 1800, "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": "suspected-type", "validated": true, "ani": 78.294, "matched_fragments": 224, "total_fragments": 1800, "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": 77.8545, "matched_fragments": 125, "total_fragments": 1800, "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": 77.5715, "matched_fragments": 160, "total_fragments": 1800, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001077885.1", "gtdb_species": "s__Photobacterium swingsii", "ani": 100.0, "matched_fragments": 1797, "total_fragments": 1800, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_002265265.1", "gtdb_species": "s__Photobacterium sanguinicancri", "ani": 86.4057, "matched_fragments": 1314, "total_fragments": 1800, "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": 81.8174, "matched_fragments": 926, "total_fragments": 1800, "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", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000950415.1", "gtdb_species": "s__Photobacterium leiognathi", "ani": 79.6703, "matched_fragments": 377, "total_fragments": 1800, 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"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_003026105.1", "gtdb_species": "s__Photobacterium sp003026105", "ani": 79.3993, "matched_fragments": 341, "total_fragments": 1800, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.17", "min_intra_species_ani": "99.06", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.95", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_001939735.1", "gtdb_species": "s__Photobacterium proteolyticum", "ani": 79.3483, "matched_fragments": 420, "total_fragments": 1800, "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": 79.3405, "matched_fragments": 399, "total_fragments": 1800, "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", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000153325.1", "gtdb_species": "s__Photobacterium sp000153325", "ani": 79.2355, "matched_fragments": 338, "total_fragments": 1800, "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_900185615.1", "gtdb_species": "s__Photobacterium malacitanum", "ani": 79.2177, "matched_fragments": 321, "total_fragments": 1800, "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_003026215.1", "gtdb_species": "s__Photobacterium indicum", "ani": 79.185, "matched_fragments": 512, "total_fragments": 1800, "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_002954455.1", "gtdb_species": "s__Photobacterium aquimaris", "ani": 79.1348, "matched_fragments": 326, "total_fragments": 1800, "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": "-" }, { "accession": "GCF_003026285.1", "gtdb_species": "s__Photobacterium profundum", "ani": 79.0359, "matched_fragments": 513, "total_fragments": 1800, "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": "-" } ] }, "_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": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }