{ "type": "genome", "identifier": "GCF_011064285.1", "organism": "Vibrio ziniensis", "title": "Vibrio ziniensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Third Institute of Oceanography", "publication": [ {} ], "properties": { "assembly_accession": "GCF_011064285.1", "bioproject": "PRJNA224116", "biosample": "SAMN14142770", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2711221", "species_taxid": "2711221", "organism_name": "Vibrio ziniensis", "infraspecific_name": "strain=ZWAL4003", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/03/04", "asm_name": "ASM1106428v1", "asm_submitter": "Third Institute of Oceanography", "gbrs_paired_asm": "GCA_011064285.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/011/064/285/GCF_011064285.1_ASM1106428v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4650556", "genome_size_ungapped": "4650556", "gc_percent": "43.000000", "replicon_count": "2", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_011064285.1-RS_2024_05_05", "annotation_date": "2024-05-05", "total_gene_count": "4299", "protein_coding_gene_count": "4129", "non_coding_gene_count": "145", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-03-04", "dateModified": "2020-03-04", "datePublished": "2020-03-04", "_annotation": { "sample_count": 1, "sample_organism": [ "Vibrio ziniensis" ], "sample_taxid": [ "2711221" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Zhangzhou" ], "sample_host_location_id": [], "data_size": "1.322 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)": "4650556", "Number of Sequences": "2", "Longest Sequences (bp)": "3207372", "N50 (bp)": "3207372", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "42.8", "Number of CDSs": "4188", "Average Protein Length": "318.4", "Coding Ratio (%)": "86.0", "Number of rRNAs": "31", "Number of tRNAs": "109", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Vibrio ziniensis", "strain": "strain=ZWAL4003", "accession": "GCA_011064285.1", "taxid": 2711221, "species_taxid": 2711221, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1550, "total_fragments": 1550, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Vibrio plantisponsor", "strain": "strain=LMG 24470", "accession": "GCA_013041605.1", "taxid": 664643, "species_taxid": 664643, "relation_to_type": "type", "validated": true, "ani": 86.3337, "matched_fragments": 1070, "total_fragments": 1550, "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": 85.4259, "matched_fragments": 1076, "total_fragments": 1550, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio fluvialis", "strain": "strain=ATCC 33809", "accession": "GCA_001558415.2", "taxid": 676, "species_taxid": 676, "relation_to_type": "type", "validated": true, "ani": 80.0813, "matched_fragments": 500, "total_fragments": 1550, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio fluvialis", "strain": "strain=NCTC11327", "accession": "GCA_900460245.1", "taxid": 676, "species_taxid": 676, "relation_to_type": "type", "validated": true, "ani": 79.9334, "matched_fragments": 505, "total_fragments": 1550, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio parahaemolyticus", "strain": "strain=NCTC10903", "accession": "GCA_900460535.1", "taxid": 670, "species_taxid": 670, "relation_to_type": "type", "validated": true, "ani": 79.9216, "matched_fragments": 395, "total_fragments": 1550, "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": 79.8485, "matched_fragments": 335, "total_fragments": 1550, "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": 79.7792, "matched_fragments": 310, "total_fragments": 1550, "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": 79.7752, "matched_fragments": 394, "total_fragments": 1550, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio fortis", "strain": "strain=LMG 21557", "accession": "GCA_024347475.1", "taxid": 212667, "species_taxid": 212667, "relation_to_type": "type", "validated": true, "ani": 79.7606, "matched_fragments": 352, "total_fragments": 1550, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio furnissii", "strain": "strain=FDAARGOS_777", "accession": "GCA_006364355.1", "taxid": 29494, "species_taxid": 29494, "relation_to_type": "type", "validated": true, "ani": 79.7098, "matched_fragments": 492, "total_fragments": 1550, "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": 79.4806, "matched_fragments": 367, "total_fragments": 1550, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio furnissii", "strain": "strain=CIP 102972", "accession": "GCA_000176175.1", "taxid": 29494, "species_taxid": 29494, "relation_to_type": "type", "validated": true, "ani": 79.4471, "matched_fragments": 472, "total_fragments": 1550, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio rotiferianus", "strain": "strain=CAIM 577", "accession": "GCA_002741985.1", "taxid": 190895, "species_taxid": 190895, "relation_to_type": "type", "validated": true, "ani": 79.3827, "matched_fragments": 364, "total_fragments": 1550, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio parahaemolyticus", "strain": "strain=ATCC 17802", "accession": "GCA_001011015.1", "taxid": 670, "species_taxid": 670, "relation_to_type": "type", "validated": true, "ani": 79.2109, "matched_fragments": 388, "total_fragments": 1550, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio tarriae", "strain": "strain=2521-89", "accession": "GCA_002216685.1", "taxid": 2014742, "species_taxid": 2014742, "relation_to_type": "type", "validated": true, "ani": 79.1951, "matched_fragments": 384, "total_fragments": 1550, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio owensii", "strain": "strain=DY05", "accession": "GCA_000817815.1", "taxid": 696485, "species_taxid": 696485, "relation_to_type": "type", "validated": true, "ani": 79.1359, "matched_fragments": 390, "total_fragments": 1550, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio scophthalmi", "strain": "strain=LMG 19158", "accession": "GCA_000222585.2", "taxid": 45658, "species_taxid": 45658, "relation_to_type": "type", "validated": true, "ani": 78.9833, "matched_fragments": 323, "total_fragments": 1550, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_011064285.1", "gtdb_species": "s__Vibrio ziniensis", "ani": 100.0, "matched_fragments": 1550, "total_fragments": 1550, "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_013041605.1", "gtdb_species": "s__Vibrio plantisponsor", "ani": 86.3422, "matched_fragments": 1069, "total_fragments": 1550, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.35", "min_intra_species_ani": "98.35", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000740015.1", "gtdb_species": "s__Vibrio diazotrophicus", "ani": 85.417, "matched_fragments": 1077, "total_fragments": 1550, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.42", "min_intra_species_ani": "96.82", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.85", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_014596725.1", "gtdb_species": "s__Vibrio sp014596725", "ani": 84.687, "matched_fragments": 1058, "total_fragments": 1550, "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": "98.52", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900460245.1", "gtdb_species": "s__Vibrio fluvialis", "ani": 79.997, "matched_fragments": 505, "total_fragments": 1550, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.04", "min_intra_species_ani": "97.07", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.86", "num_clustered_genomes": 63, "status": "-" }, { "accession": "GCF_009938165.1", "gtdb_species": "s__Vibrio taketomensis", "ani": 79.8414, "matched_fragments": 342, "total_fragments": 1550, "gtdb_taxonomy": "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_001274785.1", "gtdb_species": "s__Vibrio hepatarius", "ani": 79.4651, "matched_fragments": 356, "total_fragments": 1550, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.05", "min_intra_species_ani": "98.05", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000176175.1", "gtdb_species": "s__Vibrio furnissii", "ani": 79.422, "matched_fragments": 474, "total_fragments": 1550, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.58", "min_intra_species_ani": "97.97", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 12, "status": "-" }, { "accession": "GCF_000817815.1", "gtdb_species": "s__Vibrio owensii", "ani": 79.1474, "matched_fragments": 389, "total_fragments": 1550, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.72", "min_intra_species_ani": "96.06", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.79", "num_clustered_genomes": 29, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.18, "cell_length": 0.215, "doubling_h": -0.527, "growth_tmp": 27.81, "optimum_tmp": 26.308, "optimum_ph": 7.4, "genome_size": 4870437.62, "gc_content": 44.906, "coding_genes": 4624.827, "rRNA16S_genes": 10.063, "tRNA_genes": 116.411, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.864, "range_salinity": 0.923, "facultative_respiration": 0.602, "anaerobic_respiration": 0.011, "aerobic_respiration": 0.386, "mesophilic_range_tmp": 0.976, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.023, "bacillus_cell_shape": 0.637, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.034, "vibrio_cell_shape": 0.327, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Vibrio", "ziniensis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }