{ "type": "genome", "identifier": "GCF_004363665.1", "organism": "Photobacterium lutimaris", "title": "Photobacterium lutimaris", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004363665.1", "bioproject": "PRJNA224116", "biosample": "SAMN09074956", "wgs_master": "SNZO00000000.1", "refseq_category": "na", "taxid": "388278", "species_taxid": "388278", "organism_name": "Photobacterium lutimaris", "infraspecific_name": "strain=CECT 7642", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/22", "asm_name": "ASM436366v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_004363665.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/363/665/GCF_004363665.1_ASM436366v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5952688", "genome_size_ungapped": "5951814", "gc_percent": "47.500000", "replicon_count": "0", "scaffold_count": "50", "contig_count": "50", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004363665.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "5325", "protein_coding_gene_count": "5145", "non_coding_gene_count": "128", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-22", "dateModified": "2019-03-22", "datePublished": "2019-03-22", "_annotation": { "sample_count": 1, "sample_organism": [ "Photobacterium lutimaris" ], "sample_taxid": [ "388278" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.702 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)": "5952688", "Number of Sequences": "50", "Longest Sequences (bp)": "907738", "N50 (bp)": "407134", "Gap Ratio (%)": "0.014817", "GCcontent (%)": "47.6", "Number of CDSs": "5193", "Average Protein Length": "324.5", "Coding Ratio (%)": "84.9", "Number of rRNAs": "5", "Number of tRNAs": "115", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Photobacterium lutimaris", "strain": "strain=JCM 13586", "accession": "GCA_003025555.1", "taxid": 388278, "species_taxid": 388278, "relation_to_type": "type", "validated": true, "ani": 99.9959, "matched_fragments": 1956, "total_fragments": 1962, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Photobacterium gaetbulicola", "strain": "strain=Gung47", "accession": "GCA_000940995.1", "taxid": 1295392, "species_taxid": 1295392, "relation_to_type": "type", "validated": true, "ani": 83.7412, "matched_fragments": 1390, "total_fragments": 1962, "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": 83.7256, "matched_fragments": 1376, "total_fragments": 1962, "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": 83.4125, "matched_fragments": 1219, "total_fragments": 1962, "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": 80.9638, "matched_fragments": 522, "total_fragments": 1962, "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": 80.6277, "matched_fragments": 747, "total_fragments": 1962, "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": 80.3496, "matched_fragments": 602, "total_fragments": 1962, "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": 80.3292, "matched_fragments": 557, "total_fragments": 1962, "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": 80.2317, "matched_fragments": 607, "total_fragments": 1962, "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": 79.8768, "matched_fragments": 504, "total_fragments": 1962, "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": 78.5162, "matched_fragments": 167, "total_fragments": 1962, "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": 78.4617, "matched_fragments": 162, "total_fragments": 1962, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio stylophorae", "strain": "strain=CECT 7929", "accession": "GCA_921293875.1", "taxid": 659351, "species_taxid": 659351, "relation_to_type": "type", "validated": true, "ani": 78.249, "matched_fragments": 128, "total_fragments": 1962, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003025555.1", "gtdb_species": "s__Photobacterium lutimaris", "ani": 99.9959, "matched_fragments": 1956, "total_fragments": 1962, "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": "conclusive" }, { "accession": "GCF_000940995.1", "gtdb_species": "s__Photobacterium gaetbulicola", "ani": 83.7345, "matched_fragments": 1391, "total_fragments": 1962, "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", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003026455.1", "gtdb_species": "s__Photobacterium rosenbergii", "ani": 83.4125, "matched_fragments": 1219, "total_fragments": 1962, "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_003026495.1", "gtdb_species": "s__Photobacterium sanctipauli", "ani": 80.6453, "matched_fragments": 746, "total_fragments": 1962, "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_001029435.1", 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"s__Photobacterium aquae", "ani": 80.0509, "matched_fragments": 559, "total_fragments": 1962, "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": 79.8629, "matched_fragments": 505, "total_fragments": 1962, "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": 0.041, "cell_length": 0.255, "doubling_h": 0.223, "growth_tmp": 28.0, "optimum_tmp": 27.5, "optimum_ph": 8.0, "genome_size": 5044823.821, "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": 0.0, "anaerobic_respiration": 1.0, "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", "lutimaris" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }