{ "type": "genome", "identifier": "GCF_000222685.1", "organism": "Vibrio nigripulchritudo ATCC 27043", "title": "Vibrio nigripulchritudo ATCC 27043", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Food and Drug Administration", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000222685.1", "bioproject": "PRJNA224116", "biosample": "SAMN02951906", "wgs_master": "AFWJ00000000.1", "refseq_category": "na", "taxid": "1051649", "species_taxid": "28173", "organism_name": "Vibrio nigripulchritudo ATCC 27043", "infraspecific_name": "strain=ATCC 27043", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2011/08/04", "asm_name": "ASM22268v1", "asm_submitter": "Food and Drug Administration", "gbrs_paired_asm": "GCA_000222685.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/222/685/GCF_000222685.1_ASM22268v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6113582", "genome_size_ungapped": "6113582", "gc_percent": "46.000000", "replicon_count": "0", "scaffold_count": "332", "contig_count": "332", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2023-04-24", "total_gene_count": "5736", "protein_coding_gene_count": "5502", "non_coding_gene_count": "91", "pubmed_id": "21930677" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2011-08-04", "dateModified": "2011-08-04", "datePublished": "2011-08-04", "_annotation": { "sample_count": 1, "sample_organism": [ "Vibrio nigripulchritudo ATCC 27043" ], "sample_taxid": [ "1051649" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.758 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)": "6113582", "Number of Sequences": "332", "Longest Sequences (bp)": "226863", "N50 (bp)": "35691", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "45.8", "Number of CDSs": "5336", "Average Protein Length": "317.7", "Coding Ratio (%)": "83.2", "Number of rRNAs": "4", "Number of tRNAs": "77", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Vibrio nigripulchritudo", "strain": "strain=ATCC 27043", "accession": "GCA_000222685.2", "taxid": 28173, "species_taxid": 28173, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1871, "total_fragments": 1883, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Vibrio penaeicida", "strain": "strain=IFO 15640", "accession": "GCA_019977755.1", "taxid": 104609, "species_taxid": 104609, "relation_to_type": "type", "validated": true, "ani": 81.7325, "matched_fragments": 951, "total_fragments": 1883, "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": 81.6952, "matched_fragments": 847, "total_fragments": 1883, "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": 79.5472, "matched_fragments": 321, "total_fragments": 1883, "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": 79.5142, "matched_fragments": 284, "total_fragments": 1883, "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": 79.4196, "matched_fragments": 304, "total_fragments": 1883, "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": 79.4138, "matched_fragments": 301, "total_fragments": 1883, "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": 79.3805, "matched_fragments": 305, "total_fragments": 1883, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio tubiashii", "strain": "strain=ATCC 19109", "accession": "GCA_000772105.1", "taxid": 29498, "species_taxid": 29498, "relation_to_type": "suspected-type", "validated": true, "ani": 79.3804, "matched_fragments": 315, "total_fragments": 1883, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio campbellii", "strain": "strain=CAIM 519", "accession": "GCA_000334195.1", "taxid": 680, "species_taxid": 680, "relation_to_type": "type", "validated": true, "ani": 79.3717, "matched_fragments": 304, "total_fragments": 1883, "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": 79.3261, "matched_fragments": 297, "total_fragments": 1883, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio mediterranei", "strain": "strain=NBRC 15635", "accession": "GCA_001591125.1", "taxid": 689, "species_taxid": 689, "relation_to_type": "type", "validated": true, "ani": 79.325, "matched_fragments": 237, "total_fragments": 1883, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio hangzhouensis", "strain": "strain=CGMCC 1.7062", "accession": "GCA_900107935.1", "taxid": 462991, "species_taxid": 462991, "relation_to_type": "type", "validated": true, "ani": 79.2987, "matched_fragments": 240, "total_fragments": 1883, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio nereis", "strain": "strain=NBRC 15637", "accession": "GCA_001591105.1", "taxid": 693, "species_taxid": 693, "relation_to_type": "type", "validated": true, "ani": 79.2589, "matched_fragments": 284, "total_fragments": 1883, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio harveyi", "strain": "strain=NBRC 15634", "accession": "GCA_001591145.1", "taxid": 669, "species_taxid": 669, "relation_to_type": "type", "validated": true, "ani": 79.2433, "matched_fragments": 331, "total_fragments": 1883, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio nereis", "strain": "strain=DSM 19584", "accession": "GCA_001274805.1", "taxid": 693, "species_taxid": 693, "relation_to_type": "type", "validated": true, "ani": 79.2432, "matched_fragments": 291, "total_fragments": 1883, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio albus", "strain": "strain=E4404", "accession": "GCA_003144035.1", "taxid": 2200953, "species_taxid": 2200953, "relation_to_type": "type", "validated": true, "ani": 79.237, "matched_fragments": 193, "total_fragments": 1883, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio parahaemolyticus", "strain": "strain=NBRC 12711", "accession": "GCA_000813305.1", "taxid": 670, "species_taxid": 670, "relation_to_type": "type", "validated": true, "ani": 79.1983, "matched_fragments": 312, "total_fragments": 1883, "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": 79.1955, "matched_fragments": 309, "total_fragments": 1883, "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": 79.1922, "matched_fragments": 312, "total_fragments": 1883, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio harveyi", "strain": "strain=ATCC 14126", "accession": "GCA_001263135.1", "taxid": 669, "species_taxid": 669, "relation_to_type": "type", "validated": true, "ani": 79.1346, "matched_fragments": 333, "total_fragments": 1883, "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": 79.1244, "matched_fragments": 321, "total_fragments": 1883, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio crassostreae", "strain": "strain=LMG 22240", "accession": "GCA_024347415.1", "taxid": 246167, "species_taxid": 246167, "relation_to_type": "type", "validated": true, "ani": 79.0872, "matched_fragments": 301, "total_fragments": 1883, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio atlanticus", "strain": "strain=CECT 7223", "accession": "GCA_024347315.1", "taxid": 693153, "species_taxid": 693153, "relation_to_type": "type", "validated": true, "ani": 78.8227, "matched_fragments": 287, "total_fragments": 1883, "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": 78.6841, "matched_fragments": 247, "total_fragments": 1883, "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": 78.4178, "matched_fragments": 230, "total_fragments": 1883, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000222685.1", "gtdb_species": "s__Vibrio nigripulchritudo", "ani": 100.0, "matched_fragments": 1871, "total_fragments": 1883, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.90", "min_intra_species_ani": "96.77", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.87", "num_clustered_genomes": 18, "status": "conclusive" }, { "accession": "GCF_002933855.1", "gtdb_species": "s__Vibrio penaeicida_A", "ani": 81.7911, "matched_fragments": 996, "total_fragments": 1883, "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_003970425.1", "gtdb_species": "s__Vibrio penaeicida", "ani": 81.6711, "matched_fragments": 851, "total_fragments": 1883, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.14", "min_intra_species_ani": "96.14", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014694455.1", "gtdb_species": "s__Vibrio sp014694455", "ani": 80.6579, "matched_fragments": 813, "total_fragments": 1883, "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_002741985.1", "gtdb_species": "s__Vibrio rotiferianus", "ani": 79.5924, "matched_fragments": 318, "total_fragments": 1883, "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_000695685.1", "gtdb_species": "s__Vibrio fortis", "ani": 79.5649, "matched_fragments": 293, "total_fragments": 1883, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.41", "min_intra_species_ani": "96.21", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.88", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_002163755.1", "gtdb_species": "s__Vibrio campbellii", "ani": 79.483, "matched_fragments": 317, "total_fragments": 1883, "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_000354175.2", "gtdb_species": "s__Vibrio alginolyticus", "ani": 79.4208, "matched_fragments": 303, "total_fragments": 1883, "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_011806575.1", "gtdb_species": "s__Vibrio hepatarius_A", "ani": 79.397, "matched_fragments": 307, "total_fragments": 1883, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.94", "min_intra_species_ani": "98.94", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000772105.1", "gtdb_species": "s__Vibrio tubiashii", "ani": 79.3773, "matched_fragments": 314, "total_fragments": 1883, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.61", "min_intra_species_ani": "95.85", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.87", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_900107935.1", "gtdb_species": "s__Vibrio hangzhouensis", "ani": 79.3108, "matched_fragments": 241, "total_fragments": 1883, "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_001591105.1", "gtdb_species": "s__Vibrio nereis", "ani": 79.2673, "matched_fragments": 284, "total_fragments": 1883, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "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": 79.2636, "matched_fragments": 302, "total_fragments": 1883, "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_001591145.1", "gtdb_species": "s__Vibrio harveyi", "ani": 79.2159, "matched_fragments": 332, "total_fragments": 1883, "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_900460535.1", "gtdb_species": "s__Vibrio parahaemolyticus", "ani": 79.1476, "matched_fragments": 319, "total_fragments": 1883, "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": "-" }, { "accession": "GCF_000189255.1", "gtdb_species": "s__Vibrio brasiliensis", "ani": 79.0939, "matched_fragments": 298, "total_fragments": 1883, "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_005281825.1", "gtdb_species": "s__Vibrio gallaecicus", "ani": 78.7841, "matched_fragments": 259, "total_fragments": 1883, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_013114625.1", "gtdb_species": "s__Vibrio sp013114625", "ani": 78.7805, "matched_fragments": 258, "total_fragments": 1883, "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_009763805.1", "gtdb_species": "s__Vibrio cidicii", "ani": 78.6001, "matched_fragments": 253, "total_fragments": 1883, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.3805, "mean_intra_species_ani": "98.20", "min_intra_species_ani": "97.77", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.87", "num_clustered_genomes": 8, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.18, "cell_length": 0.215, "doubling_h": -0.527, "growth_tmp": 27.0, "optimum_tmp": 26.308, "optimum_ph": 7.4, "genome_size": 6359683.176, "gc_content": 45.76, "coding_genes": 7404.667, "rRNA16S_genes": 8.0, "tRNA_genes": 154.5, "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", "nigripulchritudo", "ATCC", "27043" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }