{ "type": "genome", "identifier": "GCF_003856525.1", "organism": "Vibrio viridaestus", "title": "Vibrio viridaestus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Ocean University of China", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003856525.1", "bioproject": "PRJNA224116", "biosample": "SAMN10372278", "wgs_master": "RJVQ00000000.1", "refseq_category": "reference genome", "taxid": "2487322", "species_taxid": "2487322", "organism_name": "Vibrio viridaestus", "infraspecific_name": "strain=LJC006", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/12/03", "asm_name": "ASM385652v1", "asm_submitter": "Ocean University of China", "gbrs_paired_asm": "GCA_003856525.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/856/525/GCF_003856525.1_ASM385652v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4713072", "genome_size_ungapped": "4713072", "gc_percent": "42.000000", "replicon_count": "0", "scaffold_count": "191", "contig_count": "191", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003856525.1-RS_2024_08_07", "annotation_date": "2024-08-07", "total_gene_count": "4417", "protein_coding_gene_count": "4255", "non_coding_gene_count": "114", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-12-03", "dateModified": "2018-12-03", "datePublished": "2018-12-03", "_annotation": { "sample_count": 1, "sample_organism": [ "Vibrio viridaestus" ], "sample_taxid": [ "2487322" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Qingdao" ], "sample_host_location_id": [], "data_size": "1.354 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 1.88, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4713072", "Number of Sequences": "191", "Longest Sequences (bp)": "849228", "N50 (bp)": "355290", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "41.9", "Number of CDSs": "4251", "Average Protein Length": "319.4", "Coding Ratio (%)": "86.4", "Number of rRNAs": "10", "Number of tRNAs": "95", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Vibrio viridaestus", "strain": "strain=LJC006", "accession": "GCA_003856525.1", "taxid": 2487322, "species_taxid": 2487322, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1523, "total_fragments": 1525, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Vibrio salinus", "strain": "strain=DNF-1", "accession": "GCA_021272385.1", "taxid": 2899784, "species_taxid": 2899784, "relation_to_type": "type", "validated": true, "ani": 79.986, "matched_fragments": 412, "total_fragments": 1525, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio qinghaiensis", "strain": "strain=Q67", "accession": "GCA_002257545.1", "taxid": 2025808, "species_taxid": 2025808, "relation_to_type": "type", "validated": true, "ani": 79.0927, "matched_fragments": 188, "total_fragments": 1525, "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": 79.0807, "matched_fragments": 136, "total_fragments": 1525, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio aestuarianus subsp. cardii", "strain": "strain=12/122 3T3", "accession": "GCA_011090275.1", "taxid": 2807650, "species_taxid": 28171, "relation_to_type": "type", "validated": true, "ani": 79.0489, "matched_fragments": 198, "total_fragments": 1525, "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": 79.0118, "matched_fragments": 184, "total_fragments": 1525, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio alginolyticus", "strain": "strain=ATCC 17749", "accession": "GCA_000354175.2", "taxid": 663, "species_taxid": 663, "relation_to_type": "type", "validated": true, "ani": 78.9783, "matched_fragments": 186, "total_fragments": 1525, "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": 78.9422, "matched_fragments": 184, "total_fragments": 1525, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio anguillarum", "strain": "strain=NCTC12159", "accession": "GCA_900452855.1", "taxid": 55601, "species_taxid": 55601, "relation_to_type": "type", "validated": true, "ani": 78.9212, "matched_fragments": 200, "total_fragments": 1525, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio aestuarianus", "strain": "strain=LMG 7909", "accession": "GCA_012395185.1", "taxid": 28171, "species_taxid": 28171, "relation_to_type": "type", "validated": true, "ani": 78.9091, "matched_fragments": 191, "total_fragments": 1525, "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": 78.8651, "matched_fragments": 150, "total_fragments": 1525, "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": 78.8534, "matched_fragments": 180, "total_fragments": 1525, "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": 78.8359, "matched_fragments": 176, "total_fragments": 1525, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio penaeicida", "strain": "strain=CAIM 285", "accession": "GCA_003970425.1", "taxid": 104609, "species_taxid": 104609, "relation_to_type": "type", "validated": true, "ani": 78.833, "matched_fragments": 137, "total_fragments": 1525, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio alginolyticus", "strain": "strain=NBRC 15630", "accession": "GCA_000467145.1", "taxid": 663, "species_taxid": 663, "relation_to_type": "type", "validated": true, "ani": 78.7908, "matched_fragments": 179, "total_fragments": 1525, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio nitrifigilis", "strain": "strain=NFV-1", "accession": "GCA_015686695.1", "taxid": 2789781, "species_taxid": 2789781, "relation_to_type": "type", "validated": true, "ani": 78.7892, "matched_fragments": 231, "total_fragments": 1525, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio cholerae", "strain": "strain=ATCC 14035", "accession": "GCA_000621645.1", "taxid": 666, "species_taxid": 666, "relation_to_type": "type", "validated": true, "ani": 78.7091, "matched_fragments": 159, "total_fragments": 1525, "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": 78.6932, "matched_fragments": 182, "total_fragments": 1525, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio ponticus", "strain": "strain=DSM 16217", "accession": "GCA_009938225.1", "taxid": 265668, "species_taxid": 265668, "relation_to_type": "type", "validated": true, "ani": 78.655, "matched_fragments": 183, "total_fragments": 1525, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio pectenicida", "strain": "strain=LMG 19642", "accession": "GCA_024347015.1", "taxid": 62763, "species_taxid": 62763, "relation_to_type": "type", "validated": true, "ani": 78.4501, "matched_fragments": 144, "total_fragments": 1525, "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": 78.4042, "matched_fragments": 158, "total_fragments": 1525, "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": 78.3666, "matched_fragments": 156, "total_fragments": 1525, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio palustris", "strain": "strain=CECT 9027", "accession": "GCA_024346995.1", "taxid": 1918946, "species_taxid": 1918946, "relation_to_type": "type", "validated": true, "ani": 78.302, "matched_fragments": 180, "total_fragments": 1525, "ani_threshold": 95, "status": "below_threshold" }, { "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": 77.615, "matched_fragments": 123, "total_fragments": 1525, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 1.88, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003856525.1", "gtdb_species": "s__Vibrio viridaestus", "ani": 100.0, "matched_fragments": 1523, "total_fragments": 1525, "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": "conclusive" }, { "accession": "GCF_003605645.1", "gtdb_species": "s__Vibrio sinensis", "ani": 79.1588, "matched_fragments": 166, "total_fragments": 1525, "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_000257205.1", "gtdb_species": "s__Vibrio ordalii", "ani": 79.1375, "matched_fragments": 166, "total_fragments": 1525, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 96.3484, "mean_intra_species_ani": "98.90", "min_intra_species_ani": "98.90", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000354175.2", "gtdb_species": "s__Vibrio alginolyticus", "ani": 78.9768, "matched_fragments": 185, "total_fragments": 1525, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.52", "min_intra_species_ani": "98.30", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 169, "status": "-" }, { "accession": "GCF_002933855.1", "gtdb_species": "s__Vibrio penaeicida_A", "ani": 78.9696, "matched_fragments": 148, "total_fragments": 1525, "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_900088415.1", "gtdb_species": "s__Vibrio mediterranei", "ani": 78.9515, "matched_fragments": 166, "total_fragments": 1525, "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": "-" }, { "accession": "GCF_003544875.1", "gtdb_species": "s__Vibrio alfacsensis", "ani": 78.9488, "matched_fragments": 178, "total_fragments": 1525, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.49", "min_intra_species_ani": "96.49", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_012395185.1", "gtdb_species": "s__Vibrio aestuarianus", "ani": 78.9091, "matched_fragments": 191, "total_fragments": 1525, "gtdb_taxonomy": 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"d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.31", "min_intra_species_ani": "98.31", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003970385.1", "gtdb_species": "s__Vibrio aquaticus", "ani": 78.6773, "matched_fragments": 181, "total_fragments": 1525, "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_012641465.1", "gtdb_species": "s__Vibrio agarilyticus", "ani": 78.6695, "matched_fragments": 134, "total_fragments": 1525, "gtdb_taxonomy": 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