{ "type": "genome", "identifier": "GCF_001029455.1", "organism": "Photobacterium ganghwense", "title": "Photobacterium ganghwense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Technical University of Denmark", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001029455.1", "bioproject": "PRJNA224116", "biosample": "SAMN03702592", "wgs_master": "LDOU00000000.1", "refseq_category": "na", "taxid": "320778", "species_taxid": "320778", "organism_name": "Photobacterium ganghwense", "infraspecific_name": "strain=DSM 22954", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/06/18", "asm_name": "ASM102945v1", "asm_submitter": "Technical University of Denmark", "gbrs_paired_asm": "GCA_001029455.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/029/455/GCF_001029455.1_ASM102945v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5536932", "genome_size_ungapped": "5536932", "gc_percent": "50.500000", "replicon_count": "0", "scaffold_count": "120", "contig_count": "120", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001029455.1-RS_2024_05_17", "annotation_date": "2024-05-17", "total_gene_count": "5034", "protein_coding_gene_count": "4840", "non_coding_gene_count": "117", "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 ganghwense" ], "sample_taxid": [ "320778" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea: Ganghwa Island" ], "sample_host_location_id": [], "data_size": "1.580 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5536932", "Number of Sequences": "120", "Longest Sequences (bp)": "784732", "N50 (bp)": "301012", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "50.5", "Number of CDSs": "4924", "Average Protein Length": "311.7", "Coding Ratio (%)": "83.2", "Number of rRNAs": "3", "Number of tRNAs": "106", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Photobacterium ganghwense", "strain": "strain=DSM 22954", "accession": "GCA_001029455.1", "taxid": 320778, "species_taxid": 320778, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1815, "total_fragments": 1817, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Photobacterium ganghwense", "strain": "strain=JCM 12487", "accession": "GCA_003025595.1", "taxid": 320778, "species_taxid": 320778, "relation_to_type": "type", "validated": true, "ani": 99.9993, "matched_fragments": 1812, "total_fragments": 1817, "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": 80.1976, "matched_fragments": 549, "total_fragments": 1817, "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": 80.1747, "matched_fragments": 568, "total_fragments": 1817, "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": 80.1527, "matched_fragments": 392, "total_fragments": 1817, "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": 80.1258, "matched_fragments": 591, "total_fragments": 1817, "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": 80.0901, "matched_fragments": 585, "total_fragments": 1817, "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": 79.8594, "matched_fragments": 523, "total_fragments": 1817, "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": 79.8393, "matched_fragments": 515, "total_fragments": 1817, "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": 79.5884, "matched_fragments": 527, "total_fragments": 1817, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium proteolyticum", "strain": "strain=13-12", "accession": "GCA_001939735.1", "taxid": 1903952, "species_taxid": 1903952, "relation_to_type": "type", "validated": true, "ani": 79.4836, "matched_fragments": 543, "total_fragments": 1817, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium galatheae", "strain": "strain=DSM 100496", "accession": "GCA_023653475.1", "taxid": 1654360, "species_taxid": 1654360, "relation_to_type": "type", "validated": true, "ani": 78.8916, "matched_fragments": 414, "total_fragments": 1817, "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": 78.0444, "matched_fragments": 251, "total_fragments": 1817, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio tarriae", "strain": "strain=2521-89", "accession": "GCA_002216685.1", "taxid": 2014742, "species_taxid": 2014742, "relation_to_type": "type", "validated": true, "ani": 78.0422, "matched_fragments": 209, "total_fragments": 1817, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio albus", "strain": "strain=E4404", "accession": "GCA_003144035.1", "taxid": 2200953, "species_taxid": 2200953, "relation_to_type": "type", "validated": true, "ani": 77.9246, "matched_fragments": 185, "total_fragments": 1817, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio vulnificus", "strain": "strain=ATCC 27562", "accession": "GCA_000299635.1", "taxid": 672, "species_taxid": 672, "relation_to_type": "suspected-type", "validated": true, "ani": 77.8295, "matched_fragments": 161, "total_fragments": 1817, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003025595.1", "gtdb_species": "s__Photobacterium ganghwense", "ani": 99.9993, "matched_fragments": 1812, "total_fragments": 1817, "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", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.96", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_003026455.1", "gtdb_species": "s__Photobacterium rosenbergii", "ani": 80.1845, "matched_fragments": 567, "total_fragments": 1817, "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": 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"GCF_000331515.1", "gtdb_species": "s__Photobacterium marinum", "ani": 79.8493, "matched_fragments": 524, "total_fragments": 1817, "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_001029445.1", "gtdb_species": "s__Photobacterium aquae", "ani": 79.8471, "matched_fragments": 515, "total_fragments": 1817, "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": 79.7958, "matched_fragments": 539, "total_fragments": 1817, "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_009910675.1", "gtdb_species": "s__Photobacterium alginatilyticum", "ani": 79.5861, "matched_fragments": 529, "total_fragments": 1817, "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_003025555.1", "gtdb_species": 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sp018199995", "ani": 78.9966, "matched_fragments": 393, "total_fragments": 1817, "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_000425165.1", "gtdb_species": "s__Photobacterium halotolerans", "ani": 78.7225, "matched_fragments": 428, "total_fragments": 1817, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.98", "min_intra_species_ani": "97.78", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 4, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.097, "cell_length": 0.113, "doubling_h": 0.223, "growth_tmp": 28.0, "optimum_tmp": 35.0, "optimum_ph": 7.25, "genome_size": 5504645.0, "gc_content": 44.444, "coding_genes": 4615.291, "rRNA16S_genes": 15.0, "tRNA_genes": 173.333, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.666, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 0.833, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.166, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 1.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Photobacterium", "ganghwense" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }