{ "type": "genome", "identifier": "GCF_900460425.1", "organism": "Yersinia frederiksenii", "title": "Yersinia frederiksenii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "SC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900460425.1", "bioproject": "PRJNA224116", "biosample": "SAMEA2580314", "wgs_master": "UHJA00000000.1", "refseq_category": "na", "taxid": "29484", "species_taxid": "29484", "organism_name": "Yersinia frederiksenii", "infraspecific_name": "strain=NCTC11470", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/08/01", "asm_name": "28307_B01", "asm_submitter": "SC", "gbrs_paired_asm": "GCA_900460425.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/460/425/GCF_900460425.1_28307_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": "5004305", "genome_size_ungapped": "5004305", "gc_percent": "47.000000", "replicon_count": "0", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900460425.1-RS_2024_08_15", "annotation_date": "2024-08-15", "total_gene_count": "4560", "protein_coding_gene_count": "4368", "non_coding_gene_count": "113", "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": [ "Yersinia frederiksenii" ], "sample_taxid": [ "29484" ], "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": "1.419 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)": "5004305", "Number of Sequences": "2", "Longest Sequences (bp)": "4992991", "N50 (bp)": "4992991", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "47.0", "Number of CDSs": "4427", "Average Protein Length": "322.1", "Coding Ratio (%)": "85.5", "Number of rRNAs": "22", "Number of tRNAs": "82", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Yersinia frederiksenii", "strain": "strain=NCTC11470", "accession": "GCA_900460425.1", "taxid": 29484, "species_taxid": 29484, "relation_to_type": "suspected-type", "validated": true, "ani": 100.0, "matched_fragments": 1664, "total_fragments": 1667, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Yersinia frederiksenii", "strain": "strain=ATCC 33641", "accession": "GCA_000754805.1", "taxid": 29484, "species_taxid": 29484, "relation_to_type": "suspected-type", "validated": true, "ani": 99.9927, "matched_fragments": 1638, "total_fragments": 1667, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Yersinia frederiksenii", "strain": "strain=ATCC 33641", "accession": "GCA_000168015.1", "taxid": 29484, "species_taxid": 29484, "relation_to_type": "suspected-type", "validated": true, "ani": 99.9594, "matched_fragments": 1575, "total_fragments": 1667, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Yersinia alsatica", "strain": "strain=IP38850", "accession": "GCA_902170305.1", "taxid": 2890317, "species_taxid": 2890317, "relation_to_type": "type", "validated": true, "ani": 92.1451, "matched_fragments": 1388, "total_fragments": 1667, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yersinia vastinensis", "strain": "strain=IP38594", "accession": "GCA_902726565.1", "taxid": 2890318, "species_taxid": 2890318, "relation_to_type": "type", "validated": true, "ani": 87.1653, "matched_fragments": 1229, "total_fragments": 1667, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yersinia proxima", "strain": "strain=IP37424", "accession": "GCA_902170785.1", "taxid": 2890316, "species_taxid": 2890316, "relation_to_type": "type", "validated": true, "ani": 85.4397, "matched_fragments": 1176, "total_fragments": 1667, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yersinia aldovae", "strain": "strain=IP06005", "accession": "GCA_001091225.1", "taxid": 29483, "species_taxid": 29483, "relation_to_type": "type", "validated": true, "ani": 83.8262, "matched_fragments": 1046, "total_fragments": 1667, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia entomophila", "strain": "strain=A1", "accession": "GCA_021462285.1", "taxid": 42906, "species_taxid": 42906, "relation_to_type": "type", "validated": true, "ani": 79.7248, "matched_fragments": 383, "total_fragments": 1667, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia nevei", "strain": "strain=S15", "accession": "GCA_008364245.1", "taxid": 2703794, "species_taxid": 2703794, "relation_to_type": "type", "validated": true, "ani": 79.2313, "matched_fragments": 373, "total_fragments": 1667, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia bockelmannii", "strain": "strain=S3", "accession": "GCA_008011855.1", "taxid": 2703793, "species_taxid": 2703793, "relation_to_type": "type", "validated": true, "ani": 79.0756, "matched_fragments": 371, "total_fragments": 1667, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Buttiauxella massiliensis", "strain": "strain=Marseille-P9829", "accession": "GCA_902500225.1", "taxid": 2831590, "species_taxid": 2831590, "relation_to_type": "type", "validated": true, "ani": 78.4497, "matched_fragments": 269, "total_fragments": 1667, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000754805.1", "gtdb_species": "s__Yersinia frederiksenii", "ani": 99.9927, "matched_fragments": 1638, "total_fragments": 1667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.36", "min_intra_species_ani": "98.91", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.85", "num_clustered_genomes": 11, "status": "conclusive" }, { "accession": "GCF_001098625.1", "gtdb_species": "s__Yersinia frederiksenii_C", "ani": 92.1764, "matched_fragments": 1409, "total_fragments": 1667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.63", "min_intra_species_ani": "97.69", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 21, "status": "-" }, { "accession": "GCF_001155565.1", "gtdb_species": "s__Yersinia frederiksenii_A", "ani": 86.9757, "matched_fragments": 1276, "total_fragments": 1667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.53", "min_intra_species_ani": "99.44", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_000173775.1", "gtdb_species": "s__Yersinia rohdei", "ani": 85.8947, "matched_fragments": 1149, "total_fragments": 1667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.41", "min_intra_species_ani": "99.12", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.89", "num_clustered_genomes": 12, "status": "-" }, { "accession": "GCF_009831415.1", "gtdb_species": "s__Yersinia canariae", "ani": 85.7646, "matched_fragments": 1258, "total_fragments": 1667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.93", "min_intra_species_ani": "98.81", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_004124235.1", "gtdb_species": "s__Yersinia hibernica", "ani": 85.6643, "matched_fragments": 1220, "total_fragments": 1667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.98", "min_intra_species_ani": "98.46", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.87", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_901472495.1", "gtdb_species": "s__Yersinia enterocolitica", "ani": 85.5061, "matched_fragments": 1173, "total_fragments": 1667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.11", "min_intra_species_ani": "96.22", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.83", "num_clustered_genomes": 185, "status": "-" }, { "accession": "GCF_001123825.1", "gtdb_species": "s__Yersinia kristensenii_C", "ani": 85.4686, "matched_fragments": 1133, "total_fragments": 1667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.60", "min_intra_species_ani": "99.58", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.93", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_902726525.1", "gtdb_species": "s__Yersinia enterocolitica_H", "ani": 85.4533, "matched_fragments": 1169, "total_fragments": 1667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900460525.1", "gtdb_species": "s__Yersinia kristensenii", "ani": 85.4285, "matched_fragments": 1198, "total_fragments": 1667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.20", "min_intra_species_ani": "97.89", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.89", "num_clustered_genomes": 22, "status": "-" }, { "accession": "GCF_003600645.1", "gtdb_species": "s__Yersinia rochesterensis", "ani": 85.3986, "matched_fragments": 1182, "total_fragments": 1667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.46", "min_intra_species_ani": "98.81", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.91", "num_clustered_genomes": 13, "status": "-" }, { "accession": "GCF_001995075.1", "gtdb_species": "s__Yersinia enterocolitica_F", "ani": 85.2997, "matched_fragments": 1186, "total_fragments": 1667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.25", "min_intra_species_ani": "99.14", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001047675.1", "gtdb_species": "s__Yersinia aleksiciae", "ani": 85.0338, "matched_fragments": 1037, "total_fragments": 1667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.22", "min_intra_species_ani": "98.37", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.82", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_002858675.1", "gtdb_species": "s__Chimaeribacter californicus", "ani": 79.1124, "matched_fragments": 305, "total_fragments": 1667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chimaeribacter", "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_018141005.1", "gtdb_species": "s__Erwinia sp001422605", "ani": 78.8733, "matched_fragments": 222, "total_fragments": 1667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.39", "min_intra_species_ani": "98.36", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900068835.1", "gtdb_species": "s__Pantoea ludwigii_B", "ani": 78.321, "matched_fragments": 227, "total_fragments": 1667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.17", "min_intra_species_ani": "96.60", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 10, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.078, "cell_length": 0.265, "doubling_h": 0.264, "growth_tmp": 30.0, "optimum_tmp": 29.644, "optimum_ph": 7.6, "genome_size": 4857116.3, "gc_content": 45.822, "coding_genes": 4193.75, "rRNA16S_genes": 7.0, "tRNA_genes": 79.667, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.0, "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": 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": [ "Yersinia", "frederiksenii" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }