{ "type": "genome", "identifier": "GCF_004104355.1", "organism": "Photobacterium chitinilyticum", "title": "Photobacterium chitinilyticum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Ocean University of China", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004104355.1", "bioproject": "PRJNA224116", "biosample": "SAMN10345552", "wgs_master": "RJLM00000000.1", "refseq_category": "reference genome", "taxid": "2485123", "species_taxid": "2485123", "organism_name": "Photobacterium chitinilyticum", "infraspecific_name": "strain=BEI247", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/01/17", "asm_name": "ASM410435v1", "asm_submitter": "Ocean University of China", "gbrs_paired_asm": "GCA_004104355.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/104/355/GCF_004104355.1_ASM410435v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5923999", "genome_size_ungapped": "5923999", "gc_percent": "46.500000", "replicon_count": "0", "scaffold_count": "295", "contig_count": "295", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004104355.1-RS_2024_08_05", "annotation_date": "2024-08-05", "total_gene_count": "5346", "protein_coding_gene_count": "5083", "non_coding_gene_count": "163", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-01-17", "dateModified": "2019-01-17", "datePublished": "2019-01-17", "_annotation": { "sample_count": 1, "sample_organism": [ "Photobacterium chitinilyticum" ], "sample_taxid": [ "2485123" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: South China Sea" ], "sample_host_location_id": [], "data_size": "1.700 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.75, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5923999", "Number of Sequences": "295", "Longest Sequences (bp)": "1470417", "N50 (bp)": "473535", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "46.4", "Number of CDSs": "5082", "Average Protein Length": "322.5", "Coding Ratio (%)": "83.0", "Number of rRNAs": "8", "Number of tRNAs": "138", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Photobacterium chitinilyticum", "strain": "strain=BEI247", "accession": "GCA_004104355.1", "taxid": 2485123, "species_taxid": 2485123, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1894, "total_fragments": 1896, "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": 83.7079, "matched_fragments": 1361, "total_fragments": 1896, "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": 83.4553, "matched_fragments": 1365, "total_fragments": 1896, "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": 80.2814, "matched_fragments": 766, "total_fragments": 1896, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium lipolyticum", "strain": "strain=DSM 16190", "accession": "GCA_003026475.1", "taxid": 266810, "species_taxid": 266810, "relation_to_type": "type", "validated": true, "ani": 80.1538, "matched_fragments": 611, "total_fragments": 1896, "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": 80.025, "matched_fragments": 414, "total_fragments": 1896, "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": 79.9939, "matched_fragments": 423, "total_fragments": 1896, "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": 79.727, "matched_fragments": 447, "total_fragments": 1896, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium swingsii", "strain": "strain=DSM 24669", "accession": "GCA_003026435.1", "taxid": 680026, "species_taxid": 680026, "relation_to_type": "type", "validated": true, "ani": 79.5849, "matched_fragments": 450, "total_fragments": 1896, "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": 79.5798, "matched_fragments": 492, "total_fragments": 1896, "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": 79.5345, "matched_fragments": 444, "total_fragments": 1896, "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": 79.4743, "matched_fragments": 441, "total_fragments": 1896, "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": 79.407, "matched_fragments": 454, "total_fragments": 1896, "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": 79.0266, "matched_fragments": 477, "total_fragments": 1896, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio natriegens", "strain": "strain=14048", "accession": "GCA_024508015.1", "taxid": 691, "species_taxid": 691, "relation_to_type": "type", "validated": true, "ani": 78.4908, "matched_fragments": 156, "total_fragments": 1896, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio chagasii", "strain": "strain=LMG 21353", "accession": "GCA_024347355.1", "taxid": 170679, "species_taxid": 170679, "relation_to_type": "suspected-type", "validated": true, "ani": 78.4533, "matched_fragments": 160, "total_fragments": 1896, "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": 77.6628, "matched_fragments": 159, "total_fragments": 1896, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.75, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004104355.1", "gtdb_species": "s__Photobacterium chitinilyticum", "ani": 100.0, "matched_fragments": 1894, "total_fragments": 1896, "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": 83.7182, "matched_fragments": 1360, "total_fragments": 1896, "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_001939735.1", "gtdb_species": "s__Photobacterium proteolyticum", "ani": 83.4553, "matched_fragments": 1365, "total_fragments": 1896, "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": 80.278, "matched_fragments": 766, "total_fragments": 1896, "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_003026475.1", "gtdb_species": "s__Photobacterium lipolyticum", "ani": 80.1334, "matched_fragments": 616, "total_fragments": 1896, "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_002265265.1", "gtdb_species": "s__Photobacterium sanguinicancri", "ani": 79.8698, "matched_fragments": 395, "total_fragments": 1896, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.87", "min_intra_species_ani": "97.87", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003026495.1", "gtdb_species": "s__Photobacterium sanctipauli", "ani": 79.859, "matched_fragments": 565, "total_fragments": 1896, "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_003026215.1", "gtdb_species": "s__Photobacterium indicum", "ani": 79.5798, "matched_fragments": 492, "total_fragments": 1896, "gtdb_taxonomy": 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"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_001029435.1", "gtdb_species": "s__Photobacterium aphoticum", "ani": 79.4612, "matched_fragments": 469, "total_fragments": 1896, "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_003026285.1", "gtdb_species": "s__Photobacterium profundum", "ani": 79.4121, "matched_fragments": 496, "total_fragments": 1896, "gtdb_taxonomy": 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"coccobacillus_cell_shape": 0.333, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Photobacterium", "chitinilyticum" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }