{ "type": "genome", "identifier": "GCF_900114245.1", "organism": "Pseudovibrio ascidiaceicola", "title": "Pseudovibrio ascidiaceicola", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900114245.1", "bioproject": "PRJNA224116", "biosample": "SAMN04488518", "wgs_master": "FOSK00000000.1", "refseq_category": "na", "taxid": "285279", "species_taxid": "285279", "organism_name": "Pseudovibrio ascidiaceicola", "infraspecific_name": "strain=DSM 16392", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/11/05", "asm_name": "IMG-taxon 2615840717 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900114245.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/114/245/GCF_900114245.1_IMG-taxon_2615840717_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5845495", "genome_size_ungapped": "5844600", "gc_percent": "51.000000", "replicon_count": "0", "scaffold_count": "45", "contig_count": "45", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900114245.1-RS_2024_04_24", "annotation_date": "2024-04-24", "total_gene_count": "5321", "protein_coding_gene_count": "5214", "non_coding_gene_count": "71", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-11-05", "dateModified": "2016-11-05", "datePublished": "2016-11-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudovibrio ascidiaceicola" ], "sample_taxid": [ "285279" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.668 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)": "5845495", "Number of Sequences": "45", "Longest Sequences (bp)": "874353", "N50 (bp)": "353031", "Gap Ratio (%)": "0.015311", "GCcontent (%)": "51.2", "Number of CDSs": "5273", "Average Protein Length": "313.2", "Coding Ratio (%)": "84.8", "Number of rRNAs": "5", "Number of tRNAs": "61", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudovibrio ascidiaceicola", "strain": "strain=DSM 16392", "accession": "GCA_900114245.1", "taxid": 285279, "species_taxid": 285279, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1918, "total_fragments": 1923, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudovibrio brasiliensis", "strain": "strain=Ab134", "accession": "GCA_018282095.1", "taxid": 1898042, "species_taxid": 1898042, "relation_to_type": "type", "validated": true, "ani": 86.2784, "matched_fragments": 1566, "total_fragments": 1923, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudovibrio brasiliensis", "strain": "strain=Ab134", "accession": "GCA_001941685.1", "taxid": 1898042, "species_taxid": 1898042, "relation_to_type": "type", "validated": true, "ani": 86.2399, "matched_fragments": 1552, "total_fragments": 1923, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudovibrio denitrificans", "strain": "strain=DSM 17465", "accession": "GCA_900116575.1", "taxid": 258256, "species_taxid": 258256, "relation_to_type": "type", "validated": true, "ani": 86.0354, "matched_fragments": 1565, "total_fragments": 1923, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudovibrio denitrificans", "strain": "strain=JCM 12308", "accession": "GCA_001310815.1", "taxid": 258256, "species_taxid": 258256, "relation_to_type": "type", "validated": true, "ani": 85.9955, "matched_fragments": 1542, "total_fragments": 1923, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudovibrio japonicus", "strain": "strain=KCTC 12861", "accession": "GCA_014651595.1", "taxid": 366534, "species_taxid": 366534, "relation_to_type": "type", "validated": true, "ani": 83.1805, "matched_fragments": 1164, "total_fragments": 1923, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudovibrio flavus", "strain": "strain=RKSG542", "accession": "GCA_009711345.1", "taxid": 2529854, "species_taxid": 2529854, "relation_to_type": "type", "validated": true, "ani": 77.6228, "matched_fragments": 261, "total_fragments": 1923, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseibium limicola", "strain": "strain=CAU 1637", "accession": "GCA_017313085.1", "taxid": 2816037, "species_taxid": 2816037, "relation_to_type": "type", "validated": true, "ani": 76.7328, "matched_fragments": 90, "total_fragments": 1923, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900114245.1", "gtdb_species": "s__Pseudovibrio ascidiaceicola", "ani": 100.0, "matched_fragments": 1917, "total_fragments": 1923, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.13", "min_intra_species_ani": "95.42", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_001623075.1", "gtdb_species": "s__Pseudovibrio sp001623075", "ani": 93.2283, "matched_fragments": 1621, "total_fragments": 1923, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.77", "min_intra_species_ani": "96.77", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900143565.1", "gtdb_species": "s__Pseudovibrio sp900143565", "ani": 92.1503, "matched_fragments": 1705, "total_fragments": 1923, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.56", "min_intra_species_ani": "96.48", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_018282095.1", "gtdb_species": "s__Pseudovibrio brasiliensis", "ani": 86.2785, "matched_fragments": 1566, "total_fragments": 1923, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001310815.1", "gtdb_species": "s__Pseudovibrio denitrificans", "ani": 85.9919, "matched_fragments": 1543, "total_fragments": 1923, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.81", "min_intra_species_ani": "95.18", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.91", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_001310715.1", "gtdb_species": "s__Pseudovibrio sp001310715", "ani": 83.4565, "matched_fragments": 1009, "total_fragments": 1923, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio", "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_014651595.1", "gtdb_species": "s__Pseudovibrio japonicus", "ani": 83.1821, "matched_fragments": 1162, "total_fragments": 1923, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pseudovibrio", "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": -0.097, "cell_length": 0.079, "doubling_h": null, "growth_tmp": 25.0, "optimum_tmp": 26.944, "optimum_ph": 7.0, "genome_size": 5845495.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pseudovibrio", "ascidiaceicola" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }