{ "type": "genome", "identifier": "GCF_001650345.1", "organism": "Photobacterium jeanii", "title": "Photobacterium jeanii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Yantai Institute of Coastal Zone Research,Chinese Academy of Sciences", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001650345.1", "bioproject": "PRJNA224116", "biosample": "SAMN04571864", "wgs_master": "LVHF00000000.1", "refseq_category": "na", "taxid": "858640", "species_taxid": "858640", "organism_name": "Photobacterium jeanii", "infraspecific_name": "strain=R-40508", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/05/24", "asm_name": "ASM165034v1", "asm_submitter": "Yantai Institute of Coastal Zone Research,Chinese Academy of Sciences", "gbrs_paired_asm": "GCA_001650345.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/650/345/GCF_001650345.1_ASM165034v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5047042", "genome_size_ungapped": "5047042", "gc_percent": "45.000000", "replicon_count": "0", "scaffold_count": "33", "contig_count": "33", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-02-16", "total_gene_count": "4504", "protein_coding_gene_count": "4355", "non_coding_gene_count": "130", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-05-24", "dateModified": "2016-05-24", "datePublished": "2016-05-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Photobacterium jeanii" ], "sample_taxid": [ "858640" ], "sample_host_organism": [ "Palythoa caribaeorum" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Brazil: Preta Beach, Sao Sebastiao" ], "sample_host_location_id": [], "data_size": "1.437 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)": "5047042", "Number of Sequences": "33", "Longest Sequences (bp)": "1419180", "N50 (bp)": "501841", "Gap Ratio (%)": "0.000198", "GCcontent (%)": "45.1", "Number of CDSs": "4390", "Average Protein Length": "326.4", "Coding Ratio (%)": "85.2", "Number of rRNAs": "5", "Number of tRNAs": "119", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Photobacterium jeanii", "strain": "strain=R-40508", "accession": "GCA_001650345.1", "taxid": 858640, "species_taxid": 858640, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1664, "total_fragments": 1667, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Photobacterium jeanii", "strain": "strain=DSM 100339", "accession": "GCA_003025495.1", "taxid": 858640, "species_taxid": 858640, "relation_to_type": "type", "validated": true, "ani": 99.9973, "matched_fragments": 1659, "total_fragments": 1667, "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": 81.7383, "matched_fragments": 965, "total_fragments": 1667, "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": 81.6935, "matched_fragments": 957, "total_fragments": 1667, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium swingsii", "strain": "strain=CAIM 1393", "accession": "GCA_001077885.1", "taxid": 680026, "species_taxid": 680026, "relation_to_type": "type", "validated": true, "ani": 81.6326, "matched_fragments": 945, "total_fragments": 1667, "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": 81.3479, "matched_fragments": 946, "total_fragments": 1667, "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": 81.1623, "matched_fragments": 860, "total_fragments": 1667, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium leiognathi", "strain": "strain=ATCC 25521", "accession": "GCA_003026235.1", "taxid": 553611, "species_taxid": 553611, "relation_to_type": "type", "validated": true, "ani": 79.8843, "matched_fragments": 384, "total_fragments": 1667, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium rosenbergii", "strain": "strain=DSM 19138", "accession": "GCA_003026455.1", "taxid": 294936, "species_taxid": 294936, "relation_to_type": "type", "validated": true, "ani": 79.8316, "matched_fragments": 441, "total_fragments": 1667, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium leiognathi", "strain": "strain=ATCC 25521", "accession": "GCA_000950415.1", "taxid": 553611, "species_taxid": 553611, "relation_to_type": "type", "validated": true, "ani": 79.8121, "matched_fragments": 389, "total_fragments": 1667, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium lucens", "strain": "strain=CAIM 1937", "accession": "GCA_009873615.1", "taxid": 2562949, "species_taxid": 2562949, "relation_to_type": "type", "validated": true, "ani": 79.7245, "matched_fragments": 377, "total_fragments": 1667, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium alginatilyticum", "strain": "strain=P03D4", "accession": "GCA_009910675.1", "taxid": 1775171, "species_taxid": 1775171, "relation_to_type": "type", "validated": true, "ani": 79.5291, "matched_fragments": 431, "total_fragments": 1667, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium proteolyticum", "strain": "strain=13-12", "accession": "GCA_001939735.1", "taxid": 1903952, "species_taxid": 1903952, "relation_to_type": "type", "validated": true, "ani": 79.5012, "matched_fragments": 443, "total_fragments": 1667, "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": 79.0595, "matched_fragments": 205, "total_fragments": 1667, "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": 78.9275, "matched_fragments": 204, "total_fragments": 1667, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio furnissii", "strain": "strain=PartQ-Vfurnissii-RM8376", "accession": "GCA_022869905.1", "taxid": 29494, "species_taxid": 29494, "relation_to_type": "type", "validated": true, "ani": 77.8229, "matched_fragments": 196, "total_fragments": 1667, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001650345.1", "gtdb_species": "s__Photobacterium jeanii", "ani": 100.0, "matched_fragments": 1664, "total_fragments": 1667, "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": "conclusive" }, { "accession": "GCF_001077885.1", "gtdb_species": "s__Photobacterium swingsii", "ani": 81.652, "matched_fragments": 942, "total_fragments": 1667, "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": "-" }, { "accession": "GCF_002265265.1", "gtdb_species": "s__Photobacterium sanguinicancri", "ani": 81.1477, "matched_fragments": 862, "total_fragments": 1667, "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_003026495.1", "gtdb_species": "s__Photobacterium sanctipauli", "ani": 79.8641, "matched_fragments": 459, "total_fragments": 1667, "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": 79.8288, "matched_fragments": 442, "total_fragments": 1667, "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_000950415.1", "gtdb_species": "s__Photobacterium leiognathi", "ani": 79.8185, "matched_fragments": 388, "total_fragments": 1667, "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_009873615.1", "gtdb_species": "s__Photobacterium lucens", "ani": 79.7116, "matched_fragments": 378, "total_fragments": 1667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.83", "min_intra_species_ani": "97.58", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.94", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_001029435.1", "gtdb_species": "s__Photobacterium aphoticum", "ani": 79.5538, "matched_fragments": 457, "total_fragments": 1667, "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", 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"min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_001939735.1", "gtdb_species": "s__Photobacterium proteolyticum", "ani": 79.503, "matched_fragments": 442, "total_fragments": 1667, "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": 79.4991, "matched_fragments": 426, "total_fragments": 1667, "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_003026475.1", "gtdb_species": "s__Photobacterium lipolyticum", "ani": 79.1579, "matched_fragments": 432, "total_fragments": 1667, "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_002954725.1", "gtdb_species": "s__Photobacterium phosphoreum", "ani": 79.0563, "matched_fragments": 285, "total_fragments": 1667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.41", "min_intra_species_ani": "96.65", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.88", "num_clustered_genomes": 23, "status": "-" }, { "accession": "GCF_000695255.1", "gtdb_species": "s__Photobacterium galatheae", "ani": 78.7847, "matched_fragments": 170, "total_fragments": 1667, "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_003026395.1", "gtdb_species": "s__Photobacterium iliopiscarium", "ani": 78.6711, "matched_fragments": 306, "total_fragments": 1667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.31", "min_intra_species_ani": "98.95", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 7, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": 0.0, "cell_length": 0.301, "doubling_h": 0.223, "growth_tmp": 28.0, "optimum_tmp": 27.5, "optimum_ph": 7.0, "genome_size": 5044823.821, "gc_content": 44.444, "coding_genes": 4615.291, "rRNA16S_genes": 15.0, "tRNA_genes": 173.333, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.666, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 0.833, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.166, "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", "jeanii" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }