{ "type": "genome", "identifier": "GCF_001029445.1", "organism": "Photobacterium aquae", "title": "Photobacterium aquae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Technical University of Denmark", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001029445.1", "bioproject": "PRJNA224116", "biosample": "SAMN03702590", "wgs_master": "LDOT00000000.1", "refseq_category": "reference genome", "taxid": "1195763", "species_taxid": "1195763", "organism_name": "Photobacterium aquae", "infraspecific_name": "strain=CGMCC 1.12159", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/06/18", "asm_name": "ASM102944v1", "asm_submitter": "Technical University of Denmark", "gbrs_paired_asm": "GCA_001029445.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/029/445/GCF_001029445.1_ASM102944v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5078735", "genome_size_ungapped": "5078735", "gc_percent": "49.000000", "replicon_count": "0", "scaffold_count": "112", "contig_count": "112", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001029445.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "4670", "protein_coding_gene_count": "4486", "non_coding_gene_count": "120", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-06-18", "dateModified": "2015-06-18", "datePublished": "2015-06-18", "_annotation": { "sample_count": 1, "sample_organism": [ "Photobacterium aquae" ], "sample_taxid": [ "1195763" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Tianjin" ], "sample_host_location_id": [], "data_size": "1.452 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)": "5078735", "Number of Sequences": "112", "Longest Sequences (bp)": "709976", "N50 (bp)": "183567", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "49.1", "Number of CDSs": "4524", "Average Protein Length": "315.2", "Coding Ratio (%)": "84.2", "Number of rRNAs": "3", "Number of tRNAs": "109", "Number of CRISPRs": "4" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "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": 100.0, "matched_fragments": 1646, "total_fragments": 1651, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Photobacterium aphoticum", "strain": "strain=DSM 25995", "accession": "GCA_003025575.1", "taxid": 754436, "species_taxid": 754436, "relation_to_type": "type", "validated": true, "ani": 80.6139, "matched_fragments": 563, "total_fragments": 1651, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium aphoticum", "strain": "strain=DSM 25995", "accession": "GCA_001029435.1", "taxid": 754436, "species_taxid": 754436, "relation_to_type": "type", "validated": true, "ani": 80.5321, "matched_fragments": 594, "total_fragments": 1651, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium aphoticum", "strain": "strain=KCTC 23057", "accession": "GCA_014652075.1", "taxid": 754436, "species_taxid": 754436, "relation_to_type": "type", "validated": true, "ani": 80.4693, "matched_fragments": 594, "total_fragments": 1651, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium gaetbulicola", "strain": "strain=DSM 26887", "accession": "GCA_003025515.1", "taxid": 1295392, "species_taxid": 1295392, "relation_to_type": "type", "validated": true, "ani": 80.3455, "matched_fragments": 580, "total_fragments": 1651, "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": 80.3241, "matched_fragments": 549, "total_fragments": 1651, "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": 80.3162, "matched_fragments": 586, "total_fragments": 1651, "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": 80.1858, "matched_fragments": 393, "total_fragments": 1651, "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": 79.9794, "matched_fragments": 536, "total_fragments": 1651, "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": 79.8283, "matched_fragments": 525, "total_fragments": 1651, "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": 79.7816, "matched_fragments": 526, "total_fragments": 1651, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium alginatilyticum", "strain": "strain=P03D4", "accession": "GCA_009910675.1", "taxid": 1775171, "species_taxid": 1775171, "relation_to_type": "type", "validated": true, "ani": 79.5906, "matched_fragments": 514, "total_fragments": 1651, "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": 79.5062, "matched_fragments": 482, "total_fragments": 1651, "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": 79.0621, "matched_fragments": 332, "total_fragments": 1651, "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": 78.7837, "matched_fragments": 319, "total_fragments": 1651, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio splendidus", "strain": "strain=LMG 19031", "accession": "GCA_024347615.1", "taxid": 29497, "species_taxid": 29497, "relation_to_type": "type", "validated": true, "ani": 78.0408, "matched_fragments": 154, "total_fragments": 1651, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium salinisoli", "strain": "strain=LAM9072", "accession": "GCA_003614885.1", "taxid": 1616783, "species_taxid": 1616783, "relation_to_type": "type", "validated": true, "ani": 77.9492, "matched_fragments": 281, "total_fragments": 1651, "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": 77.8337, "matched_fragments": 162, "total_fragments": 1651, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001029445.1", "gtdb_species": "s__Photobacterium aquae", "ani": 100.0, "matched_fragments": 1646, "total_fragments": 1651, "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_001029435.1", "gtdb_species": "s__Photobacterium aphoticum", "ani": 80.5267, "matched_fragments": 594, "total_fragments": 1651, "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_003026455.1", "gtdb_species": "s__Photobacterium rosenbergii", "ani": 80.3269, "matched_fragments": 548, "total_fragments": 1651, "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", 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"mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_003025555.1", "gtdb_species": "s__Photobacterium lutimaris", "ani": 79.9019, "matched_fragments": 573, "total_fragments": 1651, "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_003025595.1", "gtdb_species": "s__Photobacterium ganghwense", "ani": 79.8396, "matched_fragments": 523, "total_fragments": 1651, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.50", "min_intra_species_ani": "98.82", 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"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": 79.4971, "matched_fragments": 483, "total_fragments": 1651, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.006, "cell_length": 0.34, "doubling_h": 0.223, "growth_tmp": 24.368, "optimum_tmp": 25.035, "optimum_ph": 7.25, "genome_size": 5060549.0, "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": 0.666, "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", "aquae" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }