{ "type": "genome", "identifier": "GCF_003026455.1", "organism": "Photobacterium rosenbergii", "title": "Photobacterium rosenbergii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "FDA/CFSAN", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003026455.1", "bioproject": "PRJNA224116", "biosample": "SAMN07327748", "wgs_master": "PYMB00000000.1", "refseq_category": "reference genome", "taxid": "294936", "species_taxid": "294936", "organism_name": "Photobacterium rosenbergii", "infraspecific_name": "strain=DSM 19138", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/03/31", "asm_name": "ASM302645v1", "asm_submitter": "FDA/CFSAN", "gbrs_paired_asm": "GCA_003026455.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/026/455/GCF_003026455.1_ASM302645v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6354436", "genome_size_ungapped": "6354436", "gc_percent": "47.500000", "replicon_count": "0", "scaffold_count": "73", "contig_count": "73", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003026455.1-RS_2024_03_14", "annotation_date": "2024-03-14", "total_gene_count": "5862", "protein_coding_gene_count": "5652", "non_coding_gene_count": "176", "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 rosenbergii" ], "sample_taxid": [ "294936" ], "sample_host_organism": [ "missing" ], "sample_host_organism_id": [], "sample_host_disease": [ "missing" ], "sample_host_disease_id": [], "sample_host_location": [ "Australia" ], "sample_host_location_id": [], "data_size": "1.820 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)": "6354436", "Number of Sequences": "73", "Longest Sequences (bp)": "1525449", "N50 (bp)": "230668", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "47.6", "Number of CDSs": "5678", "Average Protein Length": "317.3", "Coding Ratio (%)": "85.1", "Number of rRNAs": "3", "Number of tRNAs": "152", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Photobacterium rosenbergii", "strain": "strain=DSM 19138", "accession": "GCA_003026455.1", "taxid": 294936, "species_taxid": 294936, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2082, "total_fragments": 2085, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Photobacterium gaetbulicola", "strain": "strain=DSM 26887", "accession": "GCA_003025515.1", "taxid": 1295392, "species_taxid": 1295392, "relation_to_type": "type", "validated": true, "ani": 84.7691, "matched_fragments": 1314, "total_fragments": 2085, "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": 84.7628, "matched_fragments": 1332, "total_fragments": 2085, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium lutimaris", "strain": "strain=JCM 13586", "accession": "GCA_003025555.1", "taxid": 388278, "species_taxid": 388278, "relation_to_type": "type", "validated": true, "ani": 83.4345, "matched_fragments": 1225, "total_fragments": 2085, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium sanctipauli", "strain": "strain=A-394", "accession": "GCA_000730475.1", "taxid": 1342794, "species_taxid": 1342794, "relation_to_type": "type", "validated": true, "ani": 81.0546, "matched_fragments": 584, "total_fragments": 2085, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium sanctipauli", "strain": "strain=DSM 100436", "accession": "GCA_003026495.1", "taxid": 1342794, "species_taxid": 1342794, "relation_to_type": "type", "validated": true, "ani": 80.7821, "matched_fragments": 818, "total_fragments": 2085, "ani_threshold": 95, "status": "below_threshold" }, { "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": 80.4302, "matched_fragments": 561, "total_fragments": 2085, "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": 79.9964, "matched_fragments": 610, "total_fragments": 2085, "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": 79.7403, "matched_fragments": 453, "total_fragments": 2085, "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": 79.3734, "matched_fragments": 435, "total_fragments": 2085, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio pelagius", "strain": "strain=ATCC 25916", "accession": "GCA_024347575.1", "taxid": 28169, "species_taxid": 28169, "relation_to_type": "type", "validated": true, "ani": 78.5246, "matched_fragments": 219, "total_fragments": 2085, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio spartinae", "strain": "strain=CECT 9026", "accession": "GCA_024347135.1", "taxid": 1918945, "species_taxid": 1918945, "relation_to_type": "type", "validated": true, "ani": 77.3652, "matched_fragments": 83, "total_fragments": 2085, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003026455.1", "gtdb_species": "s__Photobacterium rosenbergii", "ani": 100.0, "matched_fragments": 2082, "total_fragments": 2085, "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": "conclusive" }, { "accession": "GCF_000940995.1", "gtdb_species": "s__Photobacterium gaetbulicola", "ani": 84.7677, "matched_fragments": 1331, "total_fragments": 2085, "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": 83.4252, "matched_fragments": 1227, "total_fragments": 2085, "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_003026495.1", "gtdb_species": "s__Photobacterium sanctipauli", "ani": 80.7811, "matched_fragments": 819, "total_fragments": 2085, "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_001029445.1", "gtdb_species": "s__Photobacterium aquae", "ani": 80.4302, "matched_fragments": 561, "total_fragments": 2085, "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_001029435.1", "gtdb_species": "s__Photobacterium aphoticum", "ani": 80.3725, "matched_fragments": 626, "total_fragments": 2085, "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": "-" }, { "accession": "GCF_000331515.1", "gtdb_species": "s__Photobacterium marinum", "ani": 80.0757, "matched_fragments": 528, "total_fragments": 2085, "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": 80.0008, "matched_fragments": 609, "total_fragments": 2085, "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": 79.7382, "matched_fragments": 451, "total_fragments": 2085, "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": 0.176, "cell_length": 0.477, "doubling_h": 0.223, "growth_tmp": 28.0, "optimum_tmp": 25.0, "optimum_ph": 7.25, "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": 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", "rosenbergii" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }