{ "type": "genome", "identifier": "GCF_900088415.1", "organism": "Vibrio mediterranei", "title": "Vibrio mediterranei", "description": "na", "data type": "Genome sequencing and assembly", "organization": "UVEG", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900088415.1", "bioproject": "PRJNA224116", "biosample": "SAMEA2343670", "wgs_master": "FLLQ00000000.1", "refseq_category": "na", "taxid": "689", "species_taxid": "689", "organism_name": "Vibrio mediterranei", "infraspecific_name": "na", "isolate": "50", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/06/24", "asm_name": "VmediterraneiCECT0621_SPAdes_Prokka", "asm_submitter": "UVEG", "gbrs_paired_asm": "GCA_900088415.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/088/415/GCF_900088415.1_VmediterraneiCECT0621_SPAdes_Prokka", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5668610", "genome_size_ungapped": "5668610", "gc_percent": "44.000000", "replicon_count": "0", "scaffold_count": "43", "contig_count": "43", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900088415.1-RS_2024_08_20", "annotation_date": "2024-08-20", "total_gene_count": "5272", "protein_coding_gene_count": "5109", "non_coding_gene_count": "122", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-06-24", "dateModified": "2016-06-24", "datePublished": "2016-06-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Vibrio mediterranei" ], "sample_taxid": [ "689" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Mediterranean Sea" ], "sample_host_location_id": [], "data_size": "1.620 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)": "5668610", "Number of Sequences": "43", "Longest Sequences (bp)": "1374341", "N50 (bp)": "523683", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "44.1", "Number of CDSs": "5138", "Average Protein Length": "321.3", "Coding Ratio (%)": "87.4", "Number of rRNAs": "7", "Number of tRNAs": "98", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Vibrio mediterranei", "strain": "", "accession": "GCA_900088415.1", "taxid": 689, "species_taxid": 689, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1869, "total_fragments": 1871, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Vibrio mediterranei", "strain": "strain=NBRC 15635", "accession": "GCA_001591125.1", "taxid": 689, "species_taxid": 689, "relation_to_type": "type", "validated": true, "ani": 99.9845, "matched_fragments": 1837, "total_fragments": 1871, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Vibrio barjaei", "strain": "strain=3062", "accession": "GCA_001639065.2", "taxid": 1676683, "species_taxid": 1676683, "relation_to_type": "type", "validated": true, "ani": 95.1694, "matched_fragments": 1628, "total_fragments": 1871, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Vibrio thalassae", "strain": "strain=CECT8203", "accession": "GCA_900089835.1", "taxid": 1243014, "species_taxid": 1243014, "relation_to_type": "type", "validated": true, "ani": 88.1522, "matched_fragments": 1203, "total_fragments": 1871, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio hangzhouensis", "strain": "strain=CGMCC 1.7062", "accession": "GCA_900107935.1", "taxid": 462991, "species_taxid": 462991, "relation_to_type": "type", "validated": true, "ani": 82.3586, "matched_fragments": 824, "total_fragments": 1871, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio pelagius", "strain": "strain=ATCC 25916", "accession": "GCA_024347575.1", "taxid": 28169, "species_taxid": 28169, "relation_to_type": "type", "validated": true, "ani": 79.8698, "matched_fragments": 355, "total_fragments": 1871, "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": 79.514, "matched_fragments": 299, "total_fragments": 1871, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio crassostreae", "strain": "strain=LMG 22240", "accession": "GCA_024347415.1", "taxid": 246167, "species_taxid": 246167, "relation_to_type": "type", "validated": true, "ani": 79.4747, "matched_fragments": 367, "total_fragments": 1871, "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": 79.4745, "matched_fragments": 303, "total_fragments": 1871, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio orientalis", "strain": "strain=CIP 102891", "accession": "GCA_000222645.2", "taxid": 28175, "species_taxid": 28175, "relation_to_type": "type", "validated": true, "ani": 79.4627, "matched_fragments": 349, "total_fragments": 1871, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio pomeroyi", "strain": "strain=LMG 20537", "accession": "GCA_024347595.1", "taxid": 198832, "species_taxid": 198832, "relation_to_type": "type", "validated": true, "ani": 79.2622, "matched_fragments": 360, "total_fragments": 1871, "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": 78.8531, "matched_fragments": 311, "total_fragments": 1871, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900088415.1", "gtdb_species": "s__Vibrio mediterranei", "ani": 100.0, "matched_fragments": 1869, "total_fragments": 1871, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.1582, "mean_intra_species_ani": "98.19", "min_intra_species_ani": "97.23", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.86", "num_clustered_genomes": 13, "status": "conclusive" }, { "accession": "GCF_001639065.2", "gtdb_species": "s__Vibrio barjaei", "ani": 95.1582, "matched_fragments": 1629, "total_fragments": 1871, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.1582, "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_900089835.1", "gtdb_species": "s__Vibrio thalassae", "ani": 88.1387, "matched_fragments": 1204, "total_fragments": 1871, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.8081, "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_000695745.1", "gtdb_species": "s__Vibrio madracius", "ani": 87.4248, "matched_fragments": 560, "total_fragments": 1871, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.8081, "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_900107935.1", "gtdb_species": "s__Vibrio hangzhouensis", "ani": 82.3573, "matched_fragments": 825, "total_fragments": 1871, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "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_000755385.1", "gtdb_species": "s__Vibrio maritimus_B", "ani": 82.03, "matched_fragments": 777, "total_fragments": 1871, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.88", "min_intra_species_ani": "95.88", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_000755425.1", "gtdb_species": "s__Vibrio maritimus_A", "ani": 81.9683, "matched_fragments": 762, "total_fragments": 1871, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "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_003263775.1", "gtdb_species": "s__Vibrio maritimus", "ani": 81.9319, "matched_fragments": 768, "total_fragments": 1871, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "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_003263785.1", "gtdb_species": "s__Vibrio variabilis", "ani": 81.6897, "matched_fragments": 720, "total_fragments": 1871, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "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_000176235.1", "gtdb_species": "s__Vibrio orientalis", "ani": 79.5101, "matched_fragments": 354, "total_fragments": 1871, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "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_001695575.1", "gtdb_species": "s__Vibrio europaeus", "ani": 79.4842, "matched_fragments": 364, "total_fragments": 1871, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.44", "min_intra_species_ani": "98.30", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.91", "num_clustered_genomes": 4, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.18, "cell_length": 0.215, "doubling_h": -0.527, "growth_tmp": 28.0, "optimum_tmp": 26.0, "optimum_ph": 7.4, "genome_size": 5687913.333, "gc_content": 44.046, "coding_genes": 5133.0, "rRNA16S_genes": 10.063, "tRNA_genes": 114.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.923, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 1.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Vibrio", "mediterranei" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }