{ "type": "genome", "identifier": "GCF_013074385.2", "organism": "Vibrio ostreicida", "title": "Vibrio ostreicida", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Southern Oregon Univeristy", "publication": [ {} ], "properties": { "assembly_accession": "GCF_013074385.2", "bioproject": "PRJNA224116", "biosample": "SAMN14842399", "wgs_master": "JABEYA000000000.2", "refseq_category": "reference genome", "taxid": "526588", "species_taxid": "526588", "organism_name": "Vibrio ostreicida", "infraspecific_name": "strain=PP-203", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/05/26", "asm_name": "ASM1307438v2", "asm_submitter": "Southern Oregon Univeristy", "gbrs_paired_asm": "GCA_013074385.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/074/385/GCF_013074385.2_ASM1307438v2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4371716", "genome_size_ungapped": "4371330", "gc_percent": "45.500000", "replicon_count": "0", "scaffold_count": "33", "contig_count": "33", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_013074385.2-RS_2024_07_26", "annotation_date": "2024-07-26", "total_gene_count": "4026", "protein_coding_gene_count": "3869", "non_coding_gene_count": "87", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-05-26", "dateModified": "2020-05-26", "datePublished": "2020-05-26", "_annotation": { "sample_count": 1, "sample_organism": [ "Vibrio ostreicida" ], "sample_taxid": [ "526588" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Spain: Galicia" ], "sample_host_location_id": [], "data_size": "1.254 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)": "4371716", "Number of Sequences": "33", "Longest Sequences (bp)": "878417", "N50 (bp)": "216287", "Gap Ratio (%)": "0.008829", "GCcontent (%)": "45.6", "Number of CDSs": "3908", "Average Protein Length": "322.0", "Coding Ratio (%)": "86.4", "Number of rRNAs": "4", "Number of tRNAs": "76", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Vibrio ostreicida", "strain": "strain=PP-203", "accession": "GCA_013074385.2", "taxid": 526588, "species_taxid": 526588, "relation_to_type": "type", "validated": true, "ani": 99.9822, "matched_fragments": 1441, "total_fragments": 1442, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Vibrio coralliilyticus", "strain": "strain=ATCC BAA-450", "accession": "GCA_000176135.1", "taxid": 190893, "species_taxid": 190893, "relation_to_type": "type", "validated": true, "ani": 79.8388, "matched_fragments": 467, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio europaeus", "strain": "strain=PP-638", "accession": "GCA_001695575.1", "taxid": 300876, "species_taxid": 300876, "relation_to_type": "type", "validated": true, "ani": 79.4295, "matched_fragments": 350, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio tubiashii", "strain": "strain=ATCC 19109", "accession": "GCA_000222665.2", "taxid": 29498, "species_taxid": 29498, "relation_to_type": "suspected-type", "validated": true, "ani": 79.356, "matched_fragments": 350, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio orientalis", "strain": "strain=CIP 102891", "accession": "GCA_000176235.1", "taxid": 28175, "species_taxid": 28175, "relation_to_type": "type", "validated": true, "ani": 79.3182, "matched_fragments": 348, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio aquaticus", "strain": "strain=BEI207", "accession": "GCA_003970385.1", "taxid": 2496559, "species_taxid": 2496559, "relation_to_type": "type", "validated": true, "ani": 79.3182, "matched_fragments": 326, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio salilacus", "strain": "strain=DSG-S6", "accession": "GCA_002811245.1", "taxid": 1323749, "species_taxid": 1323749, "relation_to_type": "type", "validated": true, "ani": 79.3161, "matched_fragments": 311, "total_fragments": 1442, "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": 79.1495, "matched_fragments": 337, "total_fragments": 1442, "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": 79.1133, "matched_fragments": 251, "total_fragments": 1442, "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": 79.0884, "matched_fragments": 238, "total_fragments": 1442, "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": 79.057, "matched_fragments": 256, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio antiquarius", "strain": "strain=EX25", "accession": "GCA_000024825.1", "taxid": 150340, "species_taxid": 150340, "relation_to_type": "suspected-type", "validated": true, "ani": 79.0279, "matched_fragments": 248, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio alginolyticus", "strain": "strain=NCTC12160", "accession": "GCA_900460285.1", "taxid": 663, "species_taxid": 663, "relation_to_type": "type", "validated": true, "ani": 78.9497, "matched_fragments": 249, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio sagamiensis", "strain": "strain=NBRC 104589", "accession": "GCA_007990935.1", "taxid": 512650, "species_taxid": 512650, "relation_to_type": "type", "validated": true, "ani": 78.8924, "matched_fragments": 207, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio tasmaniensis", "strain": "strain=LMG 20012", "accession": "GCA_024347635.1", "taxid": 212663, "species_taxid": 212663, "relation_to_type": "suspected-type", "validated": true, "ani": 78.875, "matched_fragments": 213, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio alginolyticus", "strain": "strain=FDAARGOS_97", "accession": "GCA_001471275.2", "taxid": 663, "species_taxid": 663, "relation_to_type": "type", "validated": true, "ani": 78.875, "matched_fragments": 247, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio hyugaensis", "strain": "strain=090810a", "accession": "GCA_000818435.1", "taxid": 1534743, "species_taxid": 1534743, "relation_to_type": "type", "validated": true, "ani": 78.8203, "matched_fragments": 247, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio sagamiensis", "strain": "strain=NBRC 104589", "accession": "GCA_000400425.1", "taxid": 512650, "species_taxid": 512650, "relation_to_type": "type", "validated": true, "ani": 78.8115, "matched_fragments": 206, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio marinisediminis", "strain": "strain=404", "accession": "GCA_014050145.1", "taxid": 2758441, "species_taxid": 2758441, "relation_to_type": "type", "validated": true, "ani": 78.6948, "matched_fragments": 259, "total_fragments": 1442, "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": 78.6845, "matched_fragments": 226, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio vulnificus", "strain": "strain=ATCC 27562", "accession": "GCA_002224265.1", "taxid": 672, "species_taxid": 672, "relation_to_type": "type", "validated": true, "ani": 78.6398, "matched_fragments": 242, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio ziniensis", "strain": "strain=ZWAL4003", "accession": "GCA_011064285.1", "taxid": 2711221, "species_taxid": 2711221, "relation_to_type": "type", "validated": true, "ani": 78.4333, "matched_fragments": 204, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio vulnificus", "strain": "strain=ATCC 27562", "accession": "GCA_000299635.1", "taxid": 672, "species_taxid": 672, "relation_to_type": "suspected-type", "validated": true, "ani": 78.4, "matched_fragments": 197, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio antiquarius", "strain": "strain=EX25", "accession": "GCA_000152485.1", "taxid": 150340, "species_taxid": 150340, "relation_to_type": "suspected-type", "validated": true, "ani": 78.1475, "matched_fragments": 218, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_013074385.2", "gtdb_species": "s__Vibrio ostreicida", "ani": 99.9822, "matched_fragments": 1441, "total_fragments": 1442, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.53", "min_intra_species_ani": "99.53", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_000176135.1", "gtdb_species": "s__Vibrio coralliilyticus", "ani": 79.848, "matched_fragments": 465, "total_fragments": 1442, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.33", "min_intra_species_ani": "96.21", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.87", "num_clustered_genomes": 36, "status": "-" }, { "accession": "GCF_013113835.1", "gtdb_species": "s__Vibrio sp013113835", "ani": 79.6398, "matched_fragments": 486, "total_fragments": 1442, "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_000967495.1", "gtdb_species": "s__Vibrio neptunius", "ani": 79.6174, "matched_fragments": 492, "total_fragments": 1442, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.83", "min_intra_species_ani": "96.84", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_009811315.1", "gtdb_species": "s__Vibrio atypicus", "ani": 79.604, "matched_fragments": 324, "total_fragments": 1442, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.15", "min_intra_species_ani": "97.15", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004551525.1", "gtdb_species": "s__Vibrio ouci", "ani": 79.4881, "matched_fragments": 321, "total_fragments": 1442, "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_003970385.1", "gtdb_species": "s__Vibrio aquaticus", "ani": 79.3422, "matched_fragments": 324, "total_fragments": 1442, "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": 79.3326, "matched_fragments": 346, "total_fragments": 1442, "gtdb_taxonomy": 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