{ "type": "genome", "identifier": "GCF_900460255.1", "organism": "Vibrio cincinnatiensis", "title": "Vibrio cincinnatiensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "SC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900460255.1", "bioproject": "PRJNA224116", "biosample": "SAMEA3121335", "wgs_master": "UHIE00000000.1", "refseq_category": "reference genome", "taxid": "675", "species_taxid": "675", "organism_name": "Vibrio cincinnatiensis", "infraspecific_name": "strain=NCTC12012", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/08/01", "asm_name": "34500_B01", "asm_submitter": "SC", "gbrs_paired_asm": "GCA_900460255.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/460/255/GCF_900460255.1_34500_B01", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3800816", "genome_size_ungapped": "3800816", "gc_percent": "44.000000", "replicon_count": "0", "scaffold_count": "3", "contig_count": "3", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900460255.1-RS_2024_04_27", "annotation_date": "2024-04-27", "total_gene_count": "3490", "protein_coding_gene_count": "3299", "non_coding_gene_count": "140", "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 cincinnatiensis" ], "sample_taxid": [ "675" ], "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": "1.072 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)": "3800816", "Number of Sequences": "3", "Longest Sequences (bp)": "2772819", "N50 (bp)": "2772819", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "43.8", "Number of CDSs": "3365", "Average Protein Length": "323.7", "Coding Ratio (%)": "86.0", "Number of rRNAs": "31", "Number of tRNAs": "103", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Vibrio cincinnatiensis", "strain": "strain=NCTC12012", "accession": "GCA_900460255.1", "taxid": 675, "species_taxid": 675, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1263, "total_fragments": 1265, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Vibrio cincinnatiensis", "strain": "strain=DSM 19608", "accession": "GCA_900167345.1", "taxid": 675, "species_taxid": 675, "relation_to_type": "type", "validated": true, "ani": 99.9573, "matched_fragments": 1189, "total_fragments": 1265, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Vibrio fujianensis", "strain": "strain=FJ201301", "accession": "GCA_002749895.1", "taxid": 1974215, "species_taxid": 1974215, "relation_to_type": "type", "validated": true, "ani": 84.5818, "matched_fragments": 848, "total_fragments": 1265, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio metschnikovii", "strain": "strain=NCTC8443", "accession": "GCA_900460295.1", "taxid": 28172, "species_taxid": 28172, "relation_to_type": "type", "validated": true, "ani": 80.9587, "matched_fragments": 535, "total_fragments": 1265, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio metschnikovii", "strain": "strain=CIP 69.14", "accession": "GCA_000176155.1", "taxid": 28172, "species_taxid": 28172, "relation_to_type": "type", "validated": true, "ani": 80.8456, "matched_fragments": 534, "total_fragments": 1265, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio injensis", "strain": "strain=M12-1144", "accession": "GCA_001895205.1", "taxid": 1307414, "species_taxid": 1307414, "relation_to_type": "type", "validated": true, "ani": 80.3578, "matched_fragments": 502, "total_fragments": 1265, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio furnissii", "strain": "strain=PartQ-Vfurnissii-RM8376", "accession": "GCA_022869905.1", "taxid": 29494, "species_taxid": 29494, "relation_to_type": "type", "validated": true, "ani": 80.1782, "matched_fragments": 416, "total_fragments": 1265, "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": 80.1565, "matched_fragments": 416, "total_fragments": 1265, "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": 80.0422, "matched_fragments": 418, "total_fragments": 1265, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio fluvialis", "strain": "strain=NBRC 103150", "accession": "GCA_001598835.1", "taxid": 676, "species_taxid": 676, "relation_to_type": "type", "validated": true, "ani": 79.5816, "matched_fragments": 406, "total_fragments": 1265, "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": 79.3342, "matched_fragments": 328, "total_fragments": 1265, "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": 79.1605, "matched_fragments": 383, "total_fragments": 1265, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio paracholerae", "strain": "strain=EDC-792", "accession": "GCA_017169525.1", "taxid": 650003, "species_taxid": 650003, "relation_to_type": "type", "validated": true, "ani": 79.1423, "matched_fragments": 334, "total_fragments": 1265, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio porteresiae", "strain": "strain=MSSRF30", "accession": "GCA_024347055.1", "taxid": 435912, "species_taxid": 435912, "relation_to_type": "type", "validated": true, "ani": 78.9424, "matched_fragments": 292, "total_fragments": 1265, "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": 78.9363, "matched_fragments": 262, "total_fragments": 1265, "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": 78.7941, "matched_fragments": 360, "total_fragments": 1265, "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": 78.6657, "matched_fragments": 257, "total_fragments": 1265, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900167345.1", "gtdb_species": "s__Vibrio cincinnatiensis", "ani": 99.9573, "matched_fragments": 1189, "total_fragments": 1265, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.52", "min_intra_species_ani": "99.06", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.94", "num_clustered_genomes": 6, "status": "conclusive" }, { "accession": "GCF_002749895.1", "gtdb_species": "s__Vibrio fujianensis", "ani": 84.5921, "matched_fragments": 846, "total_fragments": 1265, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.21", "min_intra_species_ani": "99.14", "mean_intra_species_af": "0.95", 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"num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900460245.1", "gtdb_species": "s__Vibrio fluvialis", "ani": 80.0069, "matched_fragments": 418, "total_fragments": 1265, "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_000176175.1", "gtdb_species": "s__Vibrio furnissii", "ani": 79.775, "matched_fragments": 399, "total_fragments": 1265, "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": "-" }, { 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"matched_fragments": 297, "total_fragments": 1265, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.98", "min_intra_species_ani": "98.98", "mean_intra_species_af": "0.80", "min_intra_species_af": "0.80", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014596725.1", "gtdb_species": "s__Vibrio sp014596725", "ani": 78.8571, "matched_fragments": 307, "total_fragments": 1265, "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_012395185.1", "gtdb_species": "s__Vibrio aestuarianus", "ani": 78.6725, "matched_fragments": 362, "total_fragments": 1265, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.70", "min_intra_species_ani": "96.75", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.80", "num_clustered_genomes": 14, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.155, "cell_length": 0.215, "doubling_h": -0.527, "growth_tmp": 30.0, "optimum_tmp": 26.308, "optimum_ph": 7.4, "genome_size": 3665830.0, "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": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "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", "cincinnatiensis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }