{ "type": "genome", "identifier": "GCF_900460535.1", "organism": "Vibrio parahaemolyticus", "title": "Vibrio parahaemolyticus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "SC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900460535.1", "bioproject": "PRJNA224116", "biosample": "SAMEA3649022", "wgs_master": "UHIL00000000.1", "refseq_category": "na", "taxid": "670", "species_taxid": "670", "organism_name": "Vibrio parahaemolyticus", "infraspecific_name": "strain=NCTC10903", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/08/01", "asm_name": "42650_C02", "asm_submitter": "SC", "gbrs_paired_asm": "GCA_900460535.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/460/535/GCF_900460535.1_42650_C02", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5168732", "genome_size_ungapped": "5168732", "gc_percent": "45.500000", "replicon_count": "0", "scaffold_count": "5", "contig_count": "5", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900460535.1-RS_2024_08_15", "annotation_date": "2024-08-15", "total_gene_count": "4721", "protein_coding_gene_count": "4481", "non_coding_gene_count": "192", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-08-01", "dateModified": "2018-08-01", "datePublished": "2018-08-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Vibrio parahaemolyticus" ], "sample_taxid": [ "670" ], "sample_host_organism": [ "not available" ], "sample_host_organism_id": [], "sample_host_disease": [ "not available: to be reported later" ], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.462 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)": "5168732", "Number of Sequences": "5", "Longest Sequences (bp)": "3297116", "N50 (bp)": "3297116", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "45.3", "Number of CDSs": "4519", "Average Protein Length": "323.5", "Coding Ratio (%)": "84.9", "Number of rRNAs": "48", "Number of tRNAs": "139", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Vibrio parahaemolyticus", "strain": "strain=NCTC10903", "accession": "GCA_900460535.1", "taxid": 670, "species_taxid": 670, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1715, "total_fragments": 1720, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Vibrio parahaemolyticus", "strain": "", "accession": "GCA_001558495.2", "taxid": 670, "species_taxid": 670, "relation_to_type": "type", "validated": true, "ani": 99.9997, "matched_fragments": 1709, "total_fragments": 1720, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Vibrio parahaemolyticus", "strain": "strain=ATCC 17802", "accession": "GCA_001011015.1", "taxid": 670, "species_taxid": 670, "relation_to_type": "type", "validated": true, "ani": 99.9778, "matched_fragments": 1658, "total_fragments": 1720, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Vibrio parahaemolyticus", "strain": "strain=ATCC 17802", "accession": "GCA_001998785.1", "taxid": 670, "species_taxid": 670, "relation_to_type": "type", "validated": true, "ani": 99.9775, "matched_fragments": 1657, "total_fragments": 1720, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Vibrio parahaemolyticus", "strain": "strain=NBRC 12711", "accession": "GCA_000813305.1", "taxid": 670, "species_taxid": 670, "relation_to_type": "type", "validated": true, "ani": 99.9545, "matched_fragments": 1643, "total_fragments": 1720, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Vibrio natriegens", "strain": "strain=14048", "accession": "GCA_024508015.1", "taxid": 691, "species_taxid": 691, "relation_to_type": "type", "validated": true, "ani": 83.5454, "matched_fragments": 927, "total_fragments": 1720, "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": 80.7282, "matched_fragments": 407, "total_fragments": 1720, "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": 80.5669, "matched_fragments": 411, "total_fragments": 1720, "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": 80.4597, "matched_fragments": 489, "total_fragments": 1720, "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": 80.3351, "matched_fragments": 512, "total_fragments": 1720, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900460535.1", "gtdb_species": "s__Vibrio parahaemolyticus", "ani": 100.0, "matched_fragments": 1717, "total_fragments": 1720, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.33", "min_intra_species_ani": "97.74", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.76", "num_clustered_genomes": 1553, "status": "conclusive" }, { "accession": "GCA_001048675.1", "gtdb_species": "s__Vibrio diabolicus", "ani": 86.7551, "matched_fragments": 1314, "total_fragments": 1720, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.98", "min_intra_species_ani": "97.44", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 43, "status": "-" }, { "accession": "GCF_000354175.2", "gtdb_species": "s__Vibrio alginolyticus", "ani": 86.1826, "matched_fragments": 1255, "total_fragments": 1720, "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_002163755.1", "gtdb_species": "s__Vibrio campbellii", "ani": 84.1338, "matched_fragments": 1020, "total_fragments": 1720, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.60", "min_intra_species_ani": "95.95", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.77", "num_clustered_genomes": 78, "status": "-" }, { "accession": "GCF_000817815.1", "gtdb_species": "s__Vibrio owensii", "ani": 83.8861, "matched_fragments": 1067, "total_fragments": 1720, "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": "-" }, { "accession": "GCF_002906655.1", "gtdb_species": "s__Vibrio hyugaensis", "ani": 83.7804, "matched_fragments": 1126, "total_fragments": 1720, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.28", "min_intra_species_ani": "97.73", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.90", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_001591145.1", "gtdb_species": "s__Vibrio harveyi", "ani": 83.7246, "matched_fragments": 1061, "total_fragments": 1720, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.80", "min_intra_species_ani": "98.53", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.89", "num_clustered_genomes": 41, "status": "-" }, { "accession": "GCF_002741985.1", "gtdb_species": "s__Vibrio rotiferianus", "ani": 83.5458, "matched_fragments": 973, "total_fragments": 1720, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.35", "min_intra_species_ani": "95.73", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.85", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_000400365.1", "gtdb_species": "s__Vibrio jasicida", "ani": 83.4247, "matched_fragments": 1067, "total_fragments": 1720, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.91", "min_intra_species_ani": "97.51", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 25, "status": "-" }, { "accession": "GCF_000417905.1", "gtdb_species": "s__Vibrio natriegens", "ani": 83.3144, "matched_fragments": 933, "total_fragments": 1720, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.60", "min_intra_species_ani": "95.57", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.90", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCF_905175385.1", "gtdb_species": "s__Vibrio sp903986855", "ani": 83.0896, "matched_fragments": 883, "total_fragments": 1720, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.64", "min_intra_species_ani": "97.95", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_018223135.1", "gtdb_species": "s__Vibrio sp018223135", "ani": 82.9484, "matched_fragments": 859, "total_fragments": 1720, "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_018222805.1", "gtdb_species": "s__Vibrio sp018222805", "ani": 82.9157, "matched_fragments": 838, "total_fragments": 1720, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.18, "cell_length": 0.215, "doubling_h": -0.639, "growth_tmp": 31.667, "optimum_tmp": 30.6, "optimum_ph": 7.4, "genome_size": 5108288.795, "gc_content": 45.159, "coding_genes": 4796.31, "rRNA16S_genes": 11.091, "tRNA_genes": 129.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 1.0, "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", "parahaemolyticus" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }