{ "type": "genome", "identifier": "GCF_001939735.1", "organism": "Photobacterium proteolyticum", "title": "Photobacterium proteolyticum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Yantai Institute of Coastal Zone Research,Chinese Academy of Sciences", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001939735.1", "bioproject": "PRJNA224116", "biosample": "SAMN05792409", "wgs_master": "MJIL00000000.1", "refseq_category": "reference genome", "taxid": "1903952", "species_taxid": "1903952", "organism_name": "Photobacterium proteolyticum", "infraspecific_name": "strain=13-12", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/01/09", "asm_name": "ASM193973v1", "asm_submitter": "Yantai Institute of Coastal Zone Research,Chinese Academy of Sciences", "gbrs_paired_asm": "GCA_001939735.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/939/735/GCF_001939735.1_ASM193973v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6484429", "genome_size_ungapped": "6484299", "gc_percent": "48.000000", "replicon_count": "0", "scaffold_count": "101", "contig_count": "101", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001939735.1-RS_2024_05_03", "annotation_date": "2024-05-03", "total_gene_count": "5780", "protein_coding_gene_count": "5528", "non_coding_gene_count": "153", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-01-09", "dateModified": "2017-01-09", "datePublished": "2017-01-09", "_annotation": { "sample_count": 1, "sample_organism": [ "Photobacterium proteolyticum" ], "sample_taxid": [ "1903952" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Laizhou Bay, Bohai Sea" ], "sample_host_location_id": [], "data_size": "1.857 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 2.08, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "6484429", "Number of Sequences": "101", "Longest Sequences (bp)": "368175", "N50 (bp)": "174031", "Gap Ratio (%)": "0.002730", "GCcontent (%)": "47.9", "Number of CDSs": "5614", "Average Protein Length": "323.5", "Coding Ratio (%)": "84.0", "Number of rRNAs": "4", "Number of tRNAs": "141", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Photobacterium proteolyticum", "strain": "strain=13-12", "accession": "GCA_001939735.1", "taxid": 1903952, "species_taxid": 1903952, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2110, "total_fragments": 2113, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Photobacterium alginatilyticum", "strain": "strain=P03D4", "accession": "GCA_009910675.1", "taxid": 1775171, "species_taxid": 1775171, "relation_to_type": "type", "validated": true, "ani": 93.7725, "matched_fragments": 1769, "total_fragments": 2113, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium chitinilyticum", "strain": "strain=BEI247", "accession": "GCA_004104355.1", "taxid": 2485123, "species_taxid": 2485123, "relation_to_type": "type", "validated": true, "ani": 83.4864, "matched_fragments": 1331, "total_fragments": 2113, "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": 80.6687, "matched_fragments": 761, "total_fragments": 2113, "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": 80.3996, "matched_fragments": 459, "total_fragments": 2113, "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": 80.3256, "matched_fragments": 617, "total_fragments": 2113, "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": 80.1478, "matched_fragments": 591, "total_fragments": 2113, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium aphoticum", "strain": "strain=DSM 25995", "accession": "GCA_003025575.1", "taxid": 754436, "species_taxid": 754436, "relation_to_type": "type", "validated": true, "ani": 79.9612, "matched_fragments": 470, "total_fragments": 2113, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium jeanii", "strain": "strain=DSM 100339", "accession": "GCA_003025495.1", "taxid": 858640, "species_taxid": 858640, "relation_to_type": "type", "validated": true, "ani": 79.6934, "matched_fragments": 443, "total_fragments": 2113, "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": 79.6859, "matched_fragments": 420, "total_fragments": 2113, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium ganghwense", "strain": "strain=JCM 12487", "accession": "GCA_003025595.1", "taxid": 320778, "species_taxid": 320778, "relation_to_type": "type", "validated": true, "ani": 79.5797, "matched_fragments": 537, "total_fragments": 2113, "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": 79.5608, "matched_fragments": 443, "total_fragments": 2113, "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": 79.5406, "matched_fragments": 437, "total_fragments": 2113, "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": 79.539, "matched_fragments": 527, "total_fragments": 2113, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium ganghwense", "strain": "strain=DSM 22954", "accession": "GCA_001029455.1", "taxid": 320778, "species_taxid": 320778, "relation_to_type": "type", "validated": true, "ani": 79.463, "matched_fragments": 546, "total_fragments": 2113, "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": 79.3449, "matched_fragments": 435, "total_fragments": 2113, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio fortis", "strain": "strain=LMG 21557", "accession": "GCA_024347475.1", "taxid": 212667, "species_taxid": 212667, "relation_to_type": "type", "validated": true, "ani": 78.6376, "matched_fragments": 174, "total_fragments": 2113, "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": 77.7284, "matched_fragments": 191, "total_fragments": 2113, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter sichuanensis", "strain": "strain=WCHECL1597", "accession": "GCA_025002605.1", "taxid": 2071710, "species_taxid": 2071710, "relation_to_type": "type", "validated": true, "ani": 76.2941, "matched_fragments": 91, "total_fragments": 2113, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 2.08, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001939735.1", "gtdb_species": "s__Photobacterium proteolyticum", "ani": 100.0, "matched_fragments": 2110, "total_fragments": 2113, "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": "conclusive" }, { "accession": "GCF_009910675.1", "gtdb_species": "s__Photobacterium alginatilyticum", "ani": 93.769, "matched_fragments": 1770, "total_fragments": 2113, "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_004104355.1", "gtdb_species": "s__Photobacterium chitinilyticum", "ani": 83.4928, "matched_fragments": 1329, "total_fragments": 2113, "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_000331515.1", "gtdb_species": "s__Photobacterium marinum", "ani": 80.6524, "matched_fragments": 763, "total_fragments": 2113, "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": 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aquae", "ani": 79.5339, "matched_fragments": 528, "total_fragments": 2113, "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": 79.3414, "matched_fragments": 437, "total_fragments": 2113, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.006, "cell_length": 0.34, 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