{ "type": "genome", "identifier": "GCF_015278125.1", "organism": "Vibrio fluminensis", "title": "Vibrio fluminensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "UFRJ", "publication": [ {} ], "properties": { "assembly_accession": "GCF_015278125.1", "bioproject": "PRJNA224116", "biosample": "SAMN16595172", "wgs_master": "JADILO000000000.1", "refseq_category": "reference genome", "taxid": "2783614", "species_taxid": "2783614", "organism_name": "Vibrio fluminensis", "infraspecific_name": "strain=A621", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/11/08", "asm_name": "ASM1527812v1", "asm_submitter": "UFRJ", "gbrs_paired_asm": "GCA_015278125.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/015/278/125/GCF_015278125.1_ASM1527812v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4854211", "genome_size_ungapped": "4854211", "gc_percent": "44.500000", "replicon_count": "0", "scaffold_count": "102", "contig_count": "102", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_015278125.1-RS_2024_06_03", "annotation_date": "2024-06-03", "total_gene_count": "4447", "protein_coding_gene_count": "4269", "non_coding_gene_count": "130", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-11-08", "dateModified": "2020-11-08", "datePublished": "2020-11-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Vibrio fluminensis" ], "sample_taxid": [ "2783614" ], "sample_host_organism": [ "Sphoeroides spengleri" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Brazil: Rio de Janeiro, Arraial do Cabo" ], "sample_host_location_id": [], "data_size": "1.390 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)": "4854211", "Number of Sequences": "102", "Longest Sequences (bp)": "603146", "N50 (bp)": "111428", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "44.5", "Number of CDSs": "4271", "Average Protein Length": "324.4", "Coding Ratio (%)": "85.6", "Number of rRNAs": "8", "Number of tRNAs": "111", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Vibrio ponticus", "strain": "strain=DSM 16217", "accession": "GCA_009938225.1", "taxid": 265668, "species_taxid": 265668, "relation_to_type": "type", "validated": true, "ani": 91.5607, "matched_fragments": 1250, "total_fragments": 1575, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio rhodolitus", "strain": "strain=G98", "accession": "GCA_003350325.1", "taxid": 2231649, "species_taxid": 2231649, "relation_to_type": "type", "validated": true, "ani": 86.9207, "matched_fragments": 1064, "total_fragments": 1575, "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": 83.4096, "matched_fragments": 906, "total_fragments": 1575, "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": 83.357, "matched_fragments": 898, "total_fragments": 1575, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio marinisediminis", "strain": "strain=404", "accession": "GCA_014050145.1", "taxid": 2758441, "species_taxid": 2758441, "relation_to_type": "type", "validated": true, "ani": 81.9933, "matched_fragments": 812, "total_fragments": 1575, "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": 81.2087, "matched_fragments": 625, "total_fragments": 1575, "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": 80.1976, "matched_fragments": 399, "total_fragments": 1575, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio chagasii", "strain": "strain=LMG 21353", "accession": "GCA_024347355.1", "taxid": 170679, "species_taxid": 170679, "relation_to_type": "suspected-type", "validated": true, "ani": 79.6395, "matched_fragments": 391, "total_fragments": 1575, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio cortegadensis", "strain": "strain=CECT 7227", "accession": "GCA_024347395.1", "taxid": 1328770, "species_taxid": 1328770, "relation_to_type": "type", "validated": true, "ani": 78.8606, "matched_fragments": 330, "total_fragments": 1575, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_015278125.1", "gtdb_species": "s__Vibrio sp015278125", "ani": 100.0, "matched_fragments": 1568, "total_fragments": 1575, "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_009938225.1", "gtdb_species": "s__Vibrio ponticus", "ani": 91.5471, "matched_fragments": 1251, "total_fragments": 1575, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.69", "min_intra_species_ani": "97.39", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.85", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003350325.1", "gtdb_species": "s__Vibrio rhodolitus", "ani": 86.9261, "matched_fragments": 1064, "total_fragments": 1575, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.24", "min_intra_species_ani": "97.24", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009938205.1", "gtdb_species": "s__Vibrio panuliri", "ani": 83.3515, "matched_fragments": 901, "total_fragments": 1575, "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": "98.57", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.94", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_009938165.1", "gtdb_species": "s__Vibrio taketomensis", "ani": 82.5755, "matched_fragments": 733, "total_fragments": 1575, "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_014050145.1", "gtdb_species": "s__Vibrio marinisediminis", "ani": 82.0087, "matched_fragments": 811, "total_fragments": 1575, "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_000222585.1", "gtdb_species": "s__Vibrio scophthalmi", "ani": 81.2019, "matched_fragments": 626, "total_fragments": 1575, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.31", "min_intra_species_ani": "96.70", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.84", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_002741985.1", "gtdb_species": "s__Vibrio rotiferianus", "ani": 80.5859, "matched_fragments": 436, "total_fragments": 1575, "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": "-" } ] }, "_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", "fluminensis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }