{ "type": "genome", "identifier": "GCF_003026815.1", "organism": "Photobacterium damselae", "title": "Photobacterium damselae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "FDA/CFSAN", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003026815.1", "bioproject": "PRJNA224116", "biosample": "SAMN07327718", "wgs_master": "PYOG00000000.1", "refseq_category": "na", "taxid": "38293", "species_taxid": "38293", "organism_name": "Photobacterium damselae", "infraspecific_name": "strain=ATCC 33539", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/03/31", "asm_name": "ASM302681v1", "asm_submitter": "FDA/CFSAN", "gbrs_paired_asm": "GCA_003026815.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/026/815/GCF_003026815.1_ASM302681v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4914916", "genome_size_ungapped": "4914916", "gc_percent": "40.500000", "replicon_count": "0", "scaffold_count": "127", "contig_count": "127", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003026815.1-RS_2024_08_12", "annotation_date": "2024-08-12", "total_gene_count": "4492", "protein_coding_gene_count": "4235", "non_coding_gene_count": "155", "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 damselae" ], "sample_taxid": [ "38293" ], "sample_host_organism": [ "fish" ], "sample_host_organism_id": [], "sample_host_disease": [ "missing" ], "sample_host_disease_id": [], "sample_host_location": [ "USA", "USA:CA" ], "sample_host_location_id": [], "data_size": "1.397 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)": "4914916", "Number of Sequences": "127", "Longest Sequences (bp)": "627211", "N50 (bp)": "155188", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "40.5", "Number of CDSs": "4298", "Average Protein Length": "320.0", "Coding Ratio (%)": "84.0", "Number of rRNAs": "7", "Number of tRNAs": "129", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Photobacterium damselae", "strain": "strain=ATCC 33539", "accession": "GCA_003026815.1", "taxid": 38293, "species_taxid": 38293, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1576, "total_fragments": 1579, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Photobacterium damselae subsp. damselae", "strain": "strain=CIP 102761", "accession": "GCA_000176795.1", "taxid": 85581, "species_taxid": 38293, "relation_to_type": "type", "validated": true, "ani": 99.9952, "matched_fragments": 1574, "total_fragments": 1579, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Photobacterium damselae", "strain": "strain=NCTC11647", "accession": "GCA_900454585.1", "taxid": 38293, "species_taxid": 38293, "relation_to_type": "type", "validated": true, "ani": 99.9614, "matched_fragments": 1566, "total_fragments": 1579, "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": 79.8996, "matched_fragments": 442, "total_fragments": 1579, "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": 79.877, "matched_fragments": 442, "total_fragments": 1579, "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": 79.6164, "matched_fragments": 428, "total_fragments": 1579, "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": 79.2845, "matched_fragments": 422, "total_fragments": 1579, "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": 79.2174, "matched_fragments": 416, "total_fragments": 1579, "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": 79.1413, "matched_fragments": 282, "total_fragments": 1579, "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": 79.1322, "matched_fragments": 442, "total_fragments": 1579, "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": 78.9219, "matched_fragments": 163, "total_fragments": 1579, "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": 78.9093, "matched_fragments": 167, "total_fragments": 1579, "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": 78.9092, "matched_fragments": 164, "total_fragments": 1579, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio inusitatus", "strain": "strain=NBRC 102082", "accession": "GCA_006538525.1", "taxid": 413402, "species_taxid": 413402, "relation_to_type": "type", "validated": true, "ani": 78.8359, "matched_fragments": 121, "total_fragments": 1579, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio inusitatus", "strain": "strain=LMG 23434", "accession": "GCA_024346935.1", "taxid": 413402, "species_taxid": 413402, "relation_to_type": "type", "validated": true, "ani": 78.7876, "matched_fragments": 126, "total_fragments": 1579, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium phosphoreum", "strain": "strain=ATCC 11040", "accession": "GCA_000949955.1", "taxid": 659, "species_taxid": 659, "relation_to_type": "type", "validated": true, "ani": 78.7713, "matched_fragments": 393, "total_fragments": 1579, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio variabilis", "strain": "strain=CAIM 1454", "accession": "GCA_003263785.1", "taxid": 990271, "species_taxid": 990271, "relation_to_type": "type", "validated": true, "ani": 78.6348, "matched_fragments": 168, "total_fragments": 1579, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium indicum", "strain": "strain=ATCC 19614", "accession": "GCA_003026215.1", "taxid": 81447, "species_taxid": 81447, "relation_to_type": "type", "validated": true, "ani": 78.6111, "matched_fragments": 342, "total_fragments": 1579, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium frigidiphilum", "strain": "strain=JCM 12947", "accession": "GCA_003025615.1", "taxid": 264736, "species_taxid": 264736, "relation_to_type": "type", "validated": true, "ani": 78.5356, "matched_fragments": 328, "total_fragments": 1579, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio nitrifigilis", "strain": "strain=NFV-1", "accession": "GCA_015686695.1", "taxid": 2789781, "species_taxid": 2789781, "relation_to_type": "type", "validated": true, "ani": 77.8828, "matched_fragments": 152, "total_fragments": 1579, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003026815.1", "gtdb_species": "s__Photobacterium damselae", "ani": 100.0, "matched_fragments": 1576, "total_fragments": 1579, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.68", "min_intra_species_ani": "96.10", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.75", "num_clustered_genomes": 54, "status": "conclusive" }, { "accession": "GCF_000950415.1", "gtdb_species": "s__Photobacterium leiognathi", "ani": 79.8969, "matched_fragments": 442, "total_fragments": 1579, "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_003026105.1", "gtdb_species": "s__Photobacterium sp003026105", "ani": 79.7086, "matched_fragments": 399, "total_fragments": 1579, "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_000940995.1", "gtdb_species": "s__Photobacterium gaetbulicola", "ani": 79.6805, "matched_fragments": 223, "total_fragments": 1579, "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_009873615.1", "gtdb_species": "s__Photobacterium lucens", "ani": 79.5927, "matched_fragments": 431, "total_fragments": 1579, "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_003026495.1", "gtdb_species": "s__Photobacterium sanctipauli", "ani": 79.4296, "matched_fragments": 276, "total_fragments": 1579, "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": 79.3415, "matched_fragments": 335, "total_fragments": 1579, "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_003026365.1", "gtdb_species": "s__Photobacterium angustum", "ani": 79.271, "matched_fragments": 424, "total_fragments": 1579, "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_003026455.1", "gtdb_species": "s__Photobacterium rosenbergii", "ani": 79.1702, "matched_fragments": 268, "total_fragments": 1579, "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_000331515.1", "gtdb_species": "s__Photobacterium marinum", "ani": 79.1487, "matched_fragments": 281, "total_fragments": 1579, "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_000153325.1", "gtdb_species": "s__Photobacterium sp000153325", "ani": 79.0461, "matched_fragments": 389, "total_fragments": 1579, "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_001077885.1", "gtdb_species": "s__Photobacterium swingsii", "ani": 78.9594, "matched_fragments": 341, "total_fragments": 1579, "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": 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"coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Photobacterium", "damselae" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }