{ "type": "genome", "identifier": "GCF_900454585.1", "organism": "Photobacterium damselae", "title": "Photobacterium damselae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "SC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900454585.1", "bioproject": "PRJNA224116", "biosample": "SAMEA4362424", "wgs_master": "UATL00000000.1", "refseq_category": "na", "taxid": "38293", "species_taxid": "38293", "organism_name": "Photobacterium damselae", "infraspecific_name": "strain=NCTC11647", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/06/29", "asm_name": "49950_G01", "asm_submitter": "SC", "gbrs_paired_asm": "GCA_900454585.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/454/585/GCF_900454585.1_49950_G01", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5058754", "genome_size_ungapped": "5058754", "gc_percent": "41.000000", "replicon_count": "0", "scaffold_count": "11", "contig_count": "11", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-03-03", "total_gene_count": "4590", "protein_coding_gene_count": "4208", "non_coding_gene_count": "287", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-06-29", "dateModified": "2018-06-29", "datePublished": "2018-06-29", "_annotation": { "sample_count": 1, "sample_organism": [ "Photobacterium damselae" ], "sample_taxid": [ "38293" ], "sample_host_organism": [ "Fish (Damsel Fish)" ], "sample_host_organism_id": [], "sample_host_disease": [ "disease" ], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.419 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)": "5058754", "Number of Sequences": "11", "Longest Sequences (bp)": "2798225", "N50 (bp)": "2798225", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "40.8", "Number of CDSs": "4369", "Average Protein Length": "319.5", "Coding Ratio (%)": "82.8", "Number of rRNAs": "68", "Number of tRNAs": "206", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Photobacterium damselae", "strain": "strain=NCTC11647", "accession": "GCA_900454585.1", "taxid": 38293, "species_taxid": 38293, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1677, "total_fragments": 1680, "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": 99.992, "matched_fragments": 1644, "total_fragments": 1680, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Photobacterium damselae", "strain": "strain=ATCC 33539", "accession": "GCA_003026815.1", "taxid": 38293, "species_taxid": 38293, "relation_to_type": "type", "validated": true, "ani": 99.9452, "matched_fragments": 1558, "total_fragments": 1680, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Vibrio inusitatus", "strain": "strain=LMG 23434", "accession": "GCA_024346935.1", "taxid": 413402, "species_taxid": 413402, "relation_to_type": "type", "validated": true, "ani": 80.4522, "matched_fragments": 148, "total_fragments": 1680, "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": 80.3324, "matched_fragments": 189, "total_fragments": 1680, "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": 80.0106, "matched_fragments": 177, "total_fragments": 1680, "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": 79.8654, "matched_fragments": 447, "total_fragments": 1680, "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": 79.8041, "matched_fragments": 464, "total_fragments": 1680, "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": 79.7791, "matched_fragments": 169, "total_fragments": 1680, "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": 79.7078, "matched_fragments": 458, "total_fragments": 1680, "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": 79.5513, "matched_fragments": 436, "total_fragments": 1680, "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": 79.424, "matched_fragments": 417, "total_fragments": 1680, "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": 79.3559, "matched_fragments": 175, "total_fragments": 1680, "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": 79.2436, "matched_fragments": 414, "total_fragments": 1680, "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": 79.0357, "matched_fragments": 288, "total_fragments": 1680, "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": 78.739, "matched_fragments": 130, "total_fragments": 1680, "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": 78.7341, "matched_fragments": 404, "total_fragments": 1680, "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": 78.5661, "matched_fragments": 358, "total_fragments": 1680, "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": 78.4618, "matched_fragments": 167, "total_fragments": 1680, "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": 78.4612, "matched_fragments": 349, "total_fragments": 1680, "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": 99.9452, "matched_fragments": 1558, "total_fragments": 1680, "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_000940995.1", "gtdb_species": "s__Photobacterium gaetbulicola", "ani": 80.0025, "matched_fragments": 260, "total_fragments": 1680, "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", 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"0.92", "min_intra_species_af": "0.87", "num_clustered_genomes": 27, "status": "-" }, { "accession": "GCF_000153325.1", "gtdb_species": "s__Photobacterium sp000153325", "ani": 79.3156, "matched_fragments": 394, "total_fragments": 1680, "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_003026495.1", "gtdb_species": "s__Photobacterium sanctipauli", "ani": 79.2452, "matched_fragments": 290, "total_fragments": 1680, "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": 79.2065, "matched_fragments": 270, "total_fragments": 1680, "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_900233005.1", "gtdb_species": "s__Vibrio tapetis", "ani": 79.1417, "matched_fragments": 174, "total_fragments": 1680, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "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": 79.0957, "matched_fragments": 355, "total_fragments": 1680, "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_000331515.1", "gtdb_species": "s__Photobacterium marinum", "ani": 79.0725, "matched_fragments": 285, "total_fragments": 1680, "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", 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"bacillus_cell_shape": 1.0, "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": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }