{ "type": "genome", "identifier": "GCF_003025575.1", "organism": "Photobacterium aphoticum", "title": "Photobacterium aphoticum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "FDA/CFSAN", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003025575.1", "bioproject": "PRJNA224116", "biosample": "SAMN07327753", "wgs_master": "PYMF00000000.1", "refseq_category": "na", "taxid": "754436", "species_taxid": "754436", "organism_name": "Photobacterium aphoticum", "infraspecific_name": "strain=DSM 25995", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/03/31", "asm_name": "ASM302557v1", "asm_submitter": "FDA/CFSAN", "gbrs_paired_asm": "GCA_003025575.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/025/575/GCF_003025575.1_ASM302557v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5240783", "genome_size_ungapped": "5240783", "gc_percent": "49.500000", "replicon_count": "0", "scaffold_count": "246", "contig_count": "246", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003025575.1-RS_2024_05_17", "annotation_date": "2024-05-17", "total_gene_count": "4885", "protein_coding_gene_count": "4597", "non_coding_gene_count": "184", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-03-31", "dateModified": "2018-03-31", "datePublished": "2018-03-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Photobacterium aphoticum" ], "sample_taxid": [ "754436" ], "sample_host_organism": [ "missing" ], "sample_host_organism_id": [], "sample_host_disease": [ "missing" ], "sample_host_disease_id": [], "sample_host_location": [ "Spain" ], "sample_host_location_id": [], "data_size": "1.500 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)": "5240783", "Number of Sequences": "246", "Longest Sequences (bp)": "388535", "N50 (bp)": "66367", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "49.6", "Number of CDSs": "4452", "Average Protein Length": "312.0", "Coding Ratio (%)": "79.5", "Number of rRNAs": "5", "Number of tRNAs": "161", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Photobacterium aphoticum", "strain": "strain=DSM 25995", "accession": "GCA_003025575.1", "taxid": 754436, "species_taxid": 754436, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1617, "total_fragments": 1625, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Photobacterium aphoticum", "strain": "strain=KCTC 23057", "accession": "GCA_014652075.1", "taxid": 754436, "species_taxid": 754436, "relation_to_type": "type", "validated": true, "ani": 99.9839, "matched_fragments": 1615, "total_fragments": 1625, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Photobacterium aphoticum", "strain": "strain=DSM 25995", "accession": "GCA_001029435.1", "taxid": 754436, "species_taxid": 754436, "relation_to_type": "type", "validated": true, "ani": 99.9806, "matched_fragments": 1601, "total_fragments": 1625, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Photobacterium aquae", "strain": "strain=CGMCC 1.12159", "accession": "GCA_001029445.1", "taxid": 1195763, "species_taxid": 1195763, "relation_to_type": "type", "validated": true, "ani": 80.597, "matched_fragments": 557, "total_fragments": 1625, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium gaetbulicola", "strain": "strain=DSM 26887", "accession": "GCA_003025515.1", "taxid": 1295392, "species_taxid": 1295392, "relation_to_type": "type", "validated": true, "ani": 80.4415, "matched_fragments": 585, "total_fragments": 1625, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium gaetbulicola", "strain": "strain=Gung47", "accession": "GCA_000940995.1", "taxid": 1295392, "species_taxid": 1295392, "relation_to_type": "type", "validated": true, "ani": 80.4156, "matched_fragments": 599, "total_fragments": 1625, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium ganghwense", "strain": "strain=JCM 12487", "accession": "GCA_003025595.1", "taxid": 320778, "species_taxid": 320778, "relation_to_type": "type", "validated": true, "ani": 80.0716, "matched_fragments": 568, "total_fragments": 1625, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium ganghwense", "strain": "strain=DSM 22954", "accession": "GCA_001029455.1", "taxid": 320778, "species_taxid": 320778, "relation_to_type": "type", "validated": true, "ani": 79.9369, "matched_fragments": 577, "total_fragments": 1625, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium marinum", "strain": "strain=AK15", "accession": "GCA_000331515.1", "taxid": 1056511, "species_taxid": 1056511, "relation_to_type": "type", "validated": true, "ani": 79.8707, "matched_fragments": 444, "total_fragments": 1625, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium jeanii", "strain": "strain=R-40508", "accession": "GCA_001650345.1", "taxid": 858640, "species_taxid": 858640, "relation_to_type": "type", "validated": true, "ani": 79.6442, "matched_fragments": 424, "total_fragments": 1625, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium swingsii", "strain": "strain=CECT 7576", "accession": "GCA_024346715.1", "taxid": 680026, "species_taxid": 680026, "relation_to_type": "type", "validated": true, "ani": 79.3714, "matched_fragments": 391, "total_fragments": 1625, "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": 79.1559, "matched_fragments": 365, "total_fragments": 1625, "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": 78.5562, "matched_fragments": 184, "total_fragments": 1625, "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": 78.5455, "matched_fragments": 188, "total_fragments": 1625, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium salinisoli", "strain": "strain=LAM9072", "accession": "GCA_003614885.1", "taxid": 1616783, "species_taxid": 1616783, "relation_to_type": "type", "validated": true, "ani": 78.3482, "matched_fragments": 296, "total_fragments": 1625, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001029435.1", "gtdb_species": "s__Photobacterium aphoticum", "ani": 99.9806, "matched_fragments": 1601, "total_fragments": 1625, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.09", "min_intra_species_ani": "97.29", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.93", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_001029445.1", "gtdb_species": "s__Photobacterium aquae", "ani": 80.597, "matched_fragments": 557, "total_fragments": 1625, "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": 80.5462, "matched_fragments": 571, "total_fragments": 1625, "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_003026495.1", "gtdb_species": "s__Photobacterium sanctipauli", "ani": 80.4484, "matched_fragments": 549, "total_fragments": 1625, "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_000940995.1", "gtdb_species": "s__Photobacterium gaetbulicola", "ani": 80.4139, "matched_fragments": 601, "total_fragments": 1625, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.90", "min_intra_species_ani": "95.81", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003025555.1", "gtdb_species": "s__Photobacterium lutimaris", "ani": 80.2229, "matched_fragments": 583, "total_fragments": 1625, "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_009910675.1", "gtdb_species": "s__Photobacterium alginatilyticum", "ani": 80.0841, "matched_fragments": 462, "total_fragments": 1625, "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_003025595.1", "gtdb_species": "s__Photobacterium ganghwense", "ani": 80.0761, "matched_fragments": 567, "total_fragments": 1625, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.50", "min_intra_species_ani": "98.82", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.96", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000331515.1", "gtdb_species": "s__Photobacterium marinum", "ani": 79.8688, "matched_fragments": 444, "total_fragments": 1625, "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_001939735.1", "gtdb_species": "s__Photobacterium proteolyticum", "ani": 79.84, "matched_fragments": 473, "total_fragments": 1625, "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_001650345.1", "gtdb_species": "s__Photobacterium jeanii", "ani": 79.6416, "matched_fragments": 425, "total_fragments": 1625, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.006, "cell_length": 0.34, "doubling_h": 0.223, "growth_tmp": 28.0, "optimum_tmp": 25.035, "optimum_ph": 7.25, "genome_size": 5329349.0, "gc_content": 44.444, "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": 0.666, "anaerobic_respiration": 0.066, "aerobic_respiration": 0.266, "mesophilic_range_tmp": 0.833, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.166, "bacillus_cell_shape": 0.666, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.333, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Photobacterium", "aphoticum" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }