{ "type": "genome", "identifier": "GCF_008933155.1", "organism": "Aliivibrio finisterrensis", "title": "Aliivibrio finisterrensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Tasmania", "publication": [ {} ], "properties": { "assembly_accession": "GCF_008933155.1", "bioproject": "PRJNA224116", "biosample": "SAMN12877490", "wgs_master": "WBVP00000000.1", "refseq_category": "na", "taxid": "511998", "species_taxid": "511998", "organism_name": "Aliivibrio finisterrensis", "infraspecific_name": "strain=LMG 23869", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/10/09", "asm_name": "ASM893315v1", "asm_submitter": "University of Tasmania", "gbrs_paired_asm": "GCA_008933155.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/008/933/155/GCF_008933155.1_ASM893315v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3916971", "genome_size_ungapped": "3916971", "gc_percent": "39.500000", "replicon_count": "0", "scaffold_count": "143", "contig_count": "143", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_008933155.1-RS_2024_04_23", "annotation_date": "2024-04-23", "total_gene_count": "3505", "protein_coding_gene_count": "3353", "non_coding_gene_count": "80", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-10-09", "dateModified": "2019-10-09", "datePublished": "2019-10-09", "_annotation": { "sample_count": 1, "sample_organism": [ "Aliivibrio finisterrensis" ], "sample_taxid": [ "511998" ], "sample_host_organism": [ "Ruditapes philippinarum" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Spain:north-western coast" ], "sample_host_location_id": [], "data_size": "1.111 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)": "3916971", "Number of Sequences": "143", "Longest Sequences (bp)": "405803", "N50 (bp)": "168183", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "39.5", "Number of CDSs": "3347", "Average Protein Length": "323.0", "Coding Ratio (%)": "82.8", "Number of rRNAs": "1", "Number of tRNAs": "69", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Aliivibrio finisterrensis", "strain": "strain=LMG 23869", "accession": "GCA_008933155.1", "taxid": 511998, "species_taxid": 511998, "relation_to_type": "suspected-type", "validated": true, "ani": 100.0, "matched_fragments": 1256, "total_fragments": 1260, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Aliivibrio sifiae", "strain": "strain=NBRC 105001", "accession": "GCA_002954715.1", "taxid": 566293, "species_taxid": 566293, "relation_to_type": "type", "validated": true, "ani": 85.4116, "matched_fragments": 973, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aliivibrio fischeri", "strain": "strain=ATCC 7744", "accession": "GCA_016464335.1", "taxid": 668, "species_taxid": 668, "relation_to_type": "suspected-type", "validated": true, "ani": 84.5903, "matched_fragments": 850, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aliivibrio fischeri", "strain": "strain=DSM 507", "accession": "GCA_023983475.1", "taxid": 668, "species_taxid": 668, "relation_to_type": "suspected-type", "validated": true, "ani": 84.5181, "matched_fragments": 876, "total_fragments": 1260, "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": 79.4979, "matched_fragments": 277, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio celticus", "strain": "strain=CECT 7224", "accession": "GCA_024347335.1", "taxid": 446372, "species_taxid": 446372, "relation_to_type": "type", "validated": true, "ani": 79.1517, "matched_fragments": 279, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio cortegadensis", "strain": "strain=CECT 7227", "accession": "GCA_024347395.1", "taxid": 1328770, "species_taxid": 1328770, "relation_to_type": "type", "validated": true, "ani": 79.0494, "matched_fragments": 278, "total_fragments": 1260, "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": 78.393, "matched_fragments": 194, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio gangliei", "strain": "strain=SZDIS-1", "accession": "GCA_002934045.1", "taxid": 2077090, "species_taxid": 2077090, "relation_to_type": "type", "validated": true, "ani": 78.2235, "matched_fragments": 184, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio penaeicida", "strain": "strain=IFO 15640", "accession": "GCA_019977755.1", "taxid": 104609, "species_taxid": 104609, "relation_to_type": "type", "validated": true, "ani": 78.1379, "matched_fragments": 184, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio diazotrophicus", "strain": "strain=NBRC 103148", "accession": "GCA_000740015.1", "taxid": 685, "species_taxid": 685, "relation_to_type": "type", "validated": true, "ani": 78.1208, "matched_fragments": 199, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium toruni", "strain": "strain=CECT 9189", "accession": "GCA_024529955.1", "taxid": 1935446, "species_taxid": 1935446, "relation_to_type": "type", "validated": true, "ani": 78.1164, "matched_fragments": 212, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium phosphoreum", "strain": "strain=ATCC 11040", "accession": "GCA_000949955.1", "taxid": 659, "species_taxid": 659, "relation_to_type": "type", "validated": true, "ani": 77.952, "matched_fragments": 206, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_008933155.1", "gtdb_species": "s__Aliivibrio finisterrensis", "ani": 100.0, "matched_fragments": 1256, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.53", "min_intra_species_ani": "95.03", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.80", "num_clustered_genomes": 11, "status": "conclusive" }, { "accession": "GCF_900312675.1", "gtdb_species": "s__Aliivibrio sp900312675", "ani": 88.8915, "matched_fragments": 1019, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio", "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": "GCA_000953695.1", "gtdb_species": "s__Aliivibrio wodanis", "ani": 86.5831, "matched_fragments": 924, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio", "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_002954705.1", "gtdb_species": "s__Aliivibrio sifiae_A", "ani": 86.2409, "matched_fragments": 938, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio", "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_002954715.1", "gtdb_species": "s__Aliivibrio sifiae", "ani": 85.4397, "matched_fragments": 969, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.51", "min_intra_species_ani": "98.40", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.91", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_001690985.1", "gtdb_species": "s__Aliivibrio sp001690985", "ani": 85.2046, "matched_fragments": 912, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.59", "min_intra_species_ani": "99.19", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_016464335.1", "gtdb_species": "s__Aliivibrio fischeri", "ani": 84.5935, "matched_fragments": 850, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio", "ani_circumscription_radius": 95.1568, "mean_intra_species_ani": "96.45", "min_intra_species_ani": "95.48", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.84", "num_clustered_genomes": 60, "status": "-" }, { "accession": "GCF_009727955.1", "gtdb_species": "s__Aliivibrio fischeri_A", "ani": 84.3731, "matched_fragments": 889, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio", "ani_circumscription_radius": 95.1568, "mean_intra_species_ani": "98.75", "min_intra_species_ani": "97.87", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.92", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_000196495.1", "gtdb_species": "s__Aliivibrio salmonicida_A", "ani": 83.1099, "matched_fragments": 814, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.90", "min_intra_species_ani": "97.13", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.80", "num_clustered_genomes": 5, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": -0.302, "growth_tmp": 28.0, "optimum_tmp": 17.714, "optimum_ph": null, "genome_size": 4559432.969, "gc_content": 38.373, "coding_genes": 3950.111, "rRNA16S_genes": 10.333, "tRNA_genes": 103.666, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.5, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 0.666, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.333, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Aliivibrio", "finisterrensis" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }