{ "type": "genome", "identifier": "GCF_000950415.1", "organism": "Photobacterium leiognathi", "title": "Photobacterium leiognathi", "description": "na", "data type": "Genome sequencing and assembly", "organization": "FDA/CFSAN", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000950415.1", "bioproject": "PRJNA224116", "biosample": "SAMN03295485", "wgs_master": "JZSK00000000.1", "refseq_category": "na", "taxid": "553611", "species_taxid": "553611", "organism_name": "Photobacterium leiognathi", "infraspecific_name": "strain=ATCC 25521", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/03/10", "asm_name": "CFSAN029437_01.0", "asm_submitter": "FDA/CFSAN", "gbrs_paired_asm": "GCA_000950415.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/950/415/GCF_000950415.1_CFSAN029437_01.0", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4607317", "genome_size_ungapped": "4607317", "gc_percent": "41.000000", "replicon_count": "0", "scaffold_count": "144", "contig_count": "144", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000950415.1-RS_2024_04_21", "annotation_date": "2024-04-21", "total_gene_count": "4244", "protein_coding_gene_count": "3994", "non_coding_gene_count": "92", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-03-10", "dateModified": "2015-03-10", "datePublished": "2015-03-10", "_annotation": { "sample_count": 1, "sample_organism": [ "Photobacterium leiognathi" ], "sample_taxid": [ "553611" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [ "missing" ], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.316 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)": "4607317", "Number of Sequences": "144", "Longest Sequences (bp)": "335027", "N50 (bp)": "87333", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "40.9", "Number of CDSs": "4180", "Average Protein Length": "307.5", "Coding Ratio (%)": "83.7", "Number of rRNAs": "6", "Number of tRNAs": "74", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Photobacterium leiognathi", "strain": "strain=ATCC 25521", "accession": "GCA_000950415.1", "taxid": 553611, "species_taxid": 553611, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1476, "total_fragments": 1478, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Photobacterium leiognathi", "strain": "strain=ATCC 25521", "accession": "GCA_003026235.1", "taxid": 553611, "species_taxid": 553611, "relation_to_type": "type", "validated": true, "ani": 99.9776, "matched_fragments": 1462, "total_fragments": 1478, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Photobacterium lucens", "strain": "strain=CAIM 1937", "accession": "GCA_009873615.1", "taxid": 2562949, "species_taxid": 2562949, "relation_to_type": "type", "validated": true, "ani": 93.1253, "matched_fragments": 1115, "total_fragments": 1478, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium angustum", "strain": "strain=ATCC 25915", "accession": "GCA_003026365.1", "taxid": 661, "species_taxid": 661, "relation_to_type": "type", "validated": true, "ani": 84.7128, "matched_fragments": 1100, "total_fragments": 1478, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium angustum", "strain": "strain=ATCC 25915", "accession": "GCA_000950005.1", "taxid": 661, "species_taxid": 661, "relation_to_type": "type", "validated": true, "ani": 84.7074, "matched_fragments": 1082, "total_fragments": 1478, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium toruni", "strain": "strain=CECT 9189", "accession": "GCA_024529955.1", "taxid": 1935446, "species_taxid": 1935446, "relation_to_type": "type", "validated": true, "ani": 80.5831, "matched_fragments": 549, "total_fragments": 1478, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium kishitanii", "strain": "strain=ATCC:BAA-1194", "accession": "GCA_003026355.1", "taxid": 318456, "species_taxid": 318456, "relation_to_type": "type", "validated": true, "ani": 80.2574, "matched_fragments": 579, "total_fragments": 1478, "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": 79.5981, "matched_fragments": 387, "total_fragments": 1478, "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": 79.2402, "matched_fragments": 401, "total_fragments": 1478, "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": 78.5692, "matched_fragments": 198, "total_fragments": 1478, "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": 78.3673, "matched_fragments": 240, "total_fragments": 1478, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000950415.1", "gtdb_species": "s__Photobacterium leiognathi", "ani": 100.0, "matched_fragments": 1476, "total_fragments": 1478, "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": "conclusive" }, { "accession": "GCF_009873615.1", "gtdb_species": "s__Photobacterium lucens", "ani": 93.1253, "matched_fragments": 1115, "total_fragments": 1478, "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_003026105.1", "gtdb_species": "s__Photobacterium sp003026105", "ani": 84.8224, "matched_fragments": 1078, "total_fragments": 1478, "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_003026365.1", "gtdb_species": "s__Photobacterium angustum", "ani": 84.7057, "matched_fragments": 1101, "total_fragments": 1478, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.76", "min_intra_species_ani": "95.45", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.87", "num_clustered_genomes": 27, "status": "-" }, { "accession": "GCF_000153325.1", "gtdb_species": "s__Photobacterium sp000153325", "ani": 84.114, "matched_fragments": 1050, "total_fragments": 1478, "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": 80.5096, "matched_fragments": 600, "total_fragments": 1478, "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": 0.204, "cell_length": 0.505, "doubling_h": 0.223, "growth_tmp": 29.0, "optimum_tmp": 25.035, "optimum_ph": 7.25, "genome_size": 4669182.0, "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": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "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", "leiognathi" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }