{ "type": "genome", "identifier": "GCF_000730475.1", "organism": "Photobacterium sanctipauli", "title": "Photobacterium sanctipauli", "description": "na", "data type": "Genome sequencing and assembly", "organization": "UFRJ", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000730475.1", "bioproject": "PRJNA224116", "biosample": "SAMN02689500", "wgs_master": "JGVO00000000.1", "refseq_category": "na", "taxid": "1342794", "species_taxid": "1342794", "organism_name": "Photobacterium sanctipauli", "infraspecific_name": "strain=A-394", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/07/17", "asm_name": "Psan_v.1", "asm_submitter": "UFRJ", "gbrs_paired_asm": "GCA_000730475.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/730/475/GCF_000730475.1_Psan_v.1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5689593", "genome_size_ungapped": "5689593", "gc_percent": "48.000000", "replicon_count": "0", "scaffold_count": "1636", "contig_count": "1636", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000730475.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "5857", "protein_coding_gene_count": "5458", "non_coding_gene_count": "71", "pubmed_id": "25024905" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-07-17", "dateModified": "2014-07-17", "datePublished": "2014-07-17", "_annotation": { "sample_count": 1, "sample_organism": [ "Photobacterium sanctipauli" ], "sample_taxid": [ "1342794" ], "sample_host_organism": [ "Madracis decactis" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Atlantic Ocean: Brazil, St Paul's rocks" ], "sample_host_location_id": [], "data_size": "1.649 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)": "5689593", "Number of Sequences": "1636", "Longest Sequences (bp)": "24391", "N50 (bp)": "5900", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "48.1", "Number of CDSs": "4084", "Average Protein Length": "302.5", "Coding Ratio (%)": "65.1", "Number of rRNAs": "5", "Number of tRNAs": "57", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Photobacterium sanctipauli", "strain": "strain=A-394", "accession": "GCA_000730475.1", "taxid": 1342794, "species_taxid": 1342794, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1159, "total_fragments": 1194, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Photobacterium sanctipauli", "strain": "strain=DSM 100436", "accession": "GCA_003026495.1", "taxid": 1342794, "species_taxid": 1342794, "relation_to_type": "type", "validated": true, "ani": 99.9913, "matched_fragments": 1167, "total_fragments": 1194, "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": 81.2837, "matched_fragments": 514, "total_fragments": 1194, "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": 81.2513, "matched_fragments": 514, "total_fragments": 1194, "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": 81.0583, "matched_fragments": 556, "total_fragments": 1194, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium lutimaris", "strain": "strain=JCM 13586", "accession": "GCA_003025555.1", "taxid": 388278, "species_taxid": 388278, "relation_to_type": "type", "validated": true, "ani": 80.8924, "matched_fragments": 512, "total_fragments": 1194, "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": 80.535, "matched_fragments": 408, "total_fragments": 1194, "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": 80.5014, "matched_fragments": 432, "total_fragments": 1194, "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": 80.2771, "matched_fragments": 387, "total_fragments": 1194, "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": 80.2532, "matched_fragments": 447, "total_fragments": 1194, "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": 79.5496, "matched_fragments": 298, "total_fragments": 1194, "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": 79.5441, "matched_fragments": 312, "total_fragments": 1194, "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": 79.5361, "matched_fragments": 312, "total_fragments": 1194, "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": 79.4738, "matched_fragments": 309, "total_fragments": 1194, "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": 78.6355, "matched_fragments": 203, "total_fragments": 1194, "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": 78.484, "matched_fragments": 204, "total_fragments": 1194, "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": 78.0058, "matched_fragments": 131, "total_fragments": 1194, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 2.08, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003026495.1", "gtdb_species": "s__Photobacterium sanctipauli", "ani": 99.9913, "matched_fragments": 1167, "total_fragments": 1194, "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_000940995.1", "gtdb_species": "s__Photobacterium gaetbulicola", "ani": 81.2973, "matched_fragments": 513, "total_fragments": 1194, "gtdb_taxonomy": 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