{ "type": "genome", "identifier": "GCF_000253175.1", "organism": "Yersinia enterocolitica subsp. palearctica Y11", "title": "Yersinia enterocolitica subsp. palearctica Y11", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Max von Pettenkofer-Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000253175.1", "bioproject": "PRJNA224116", "biosample": "SAMEA2271938", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "930944", "species_taxid": "630", "organism_name": "Yersinia enterocolitica subsp. palearctica Y11", "infraspecific_name": "strain=Y11", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2011/01/20", "asm_name": "ASM25317v1", "asm_submitter": "Max von Pettenkofer-Institute", "gbrs_paired_asm": "GCA_000253175.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/253/175/GCF_000253175.1_ASM25317v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4625880", "genome_size_ungapped": "4625880", "gc_percent": "47.000000", "replicon_count": "2", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000253175.1-RS_2024_12_11", "annotation_date": "2024-12-11", "total_gene_count": "4238", "protein_coding_gene_count": "3903", "non_coding_gene_count": "100", "pubmed_id": "21296963" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2011-01-20", "dateModified": "2011-01-20", "datePublished": "2011-01-20", "_annotation": { "sample_count": 1, "sample_organism": [ "Yersinia enterocolitica subsp. palearctica Y11" ], "sample_taxid": [ "930944" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.314 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)": "4625880", "Number of Sequences": "2", "Longest Sequences (bp)": "4553420", "N50 (bp)": "4553420", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "47.0", "Number of CDSs": "4204", "Average Protein Length": "307.8", "Coding Ratio (%)": "83.9", "Number of rRNAs": "22", "Number of tRNAs": "70", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Yersinia enterocolitica subsp. palearctica", "strain": "strain=Y11", "accession": "GCA_000253175.1", "taxid": 150053, "species_taxid": 630, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1539, "total_fragments": 1541, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Yersinia enterocolitica subsp. palearctica", "strain": "strain=NCTC13769", "accession": "GCA_900637005.1", "taxid": 150053, "species_taxid": 630, "relation_to_type": "type", "validated": true, "ani": 99.9927, "matched_fragments": 1509, "total_fragments": 1541, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Yersinia enterocolitica", "strain": "strain=ATCC 9610", "accession": "GCA_000755055.1", "taxid": 630, "species_taxid": 630, "relation_to_type": "type", "validated": true, "ani": 96.8821, "matched_fragments": 1302, "total_fragments": 1541, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Yersinia enterocolitica subsp. enterocolitica", "strain": "strain=NBRC 105693", "accession": "GCA_001598735.1", "taxid": 150052, "species_taxid": 630, "relation_to_type": "type", "validated": true, "ani": 96.876, "matched_fragments": 1293, "total_fragments": 1541, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Yersinia enterocolitica subsp. enterocolitica", "strain": "strain=NCTC12982", "accession": "GCA_901472495.1", "taxid": 150052, "species_taxid": 630, "relation_to_type": "type", "validated": true, "ani": 96.8602, "matched_fragments": 1311, "total_fragments": 1541, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Yersinia proxima", "strain": "strain=IP37424", "accession": "GCA_902170785.1", "taxid": 2890316, "species_taxid": 2890316, "relation_to_type": "type", "validated": true, "ani": 93.6535, "matched_fragments": 1277, "total_fragments": 1541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yersinia artesiana", "strain": "strain=IP42281", "accession": "GCA_902726545.1", "taxid": 2890315, "species_taxid": 2890315, "relation_to_type": "type", "validated": true, "ani": 93.5571, "matched_fragments": 1211, "total_fragments": 1541, "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": 85.6606, "matched_fragments": 1059, "total_fragments": 1541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yersinia alsatica", "strain": "strain=IP38850", "accession": "GCA_902170305.1", "taxid": 2890317, "species_taxid": 2890317, "relation_to_type": "type", "validated": true, "ani": 85.5831, "matched_fragments": 1185, "total_fragments": 1541, "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": 79.5726, "matched_fragments": 406, "total_fragments": 1541, "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": 79.0422, "matched_fragments": 384, "total_fragments": 1541, "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": 79.0162, "matched_fragments": 388, "total_fragments": 1541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hafnia paralvei", "strain": "strain=ATCC 29927", "accession": "GCA_023698525.1", "taxid": 546367, "species_taxid": 546367, "relation_to_type": "type", "validated": true, "ani": 78.9833, "matched_fragments": 308, "total_fragments": 1541, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_901472495.1", "gtdb_species": "s__Yersinia enterocolitica", "ani": 96.9023, "matched_fragments": 1309, "total_fragments": 1541, "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": "conclusive" }, { "accession": "GCF_001995075.1", "gtdb_species": "s__Yersinia enterocolitica_F", "ani": 93.7183, "matched_fragments": 1256, "total_fragments": 1541, "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_902726525.1", "gtdb_species": "s__Yersinia enterocolitica_H", "ani": 93.5185, "matched_fragments": 1240, "total_fragments": 1541, "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_003600645.1", "gtdb_species": "s__Yersinia rochesterensis", "ani": 88.1192, "matched_fragments": 1208, "total_fragments": 1541, "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_001123825.1", "gtdb_species": "s__Yersinia kristensenii_C", "ani": 88.0549, "matched_fragments": 1205, "total_fragments": 1541, "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_900460525.1", "gtdb_species": "s__Yersinia kristensenii", "ani": 88.0022, "matched_fragments": 1235, "total_fragments": 1541, "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_009831415.1", "gtdb_species": "s__Yersinia canariae", "ani": 87.7803, "matched_fragments": 1228, "total_fragments": 1541, "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": 86.369, "matched_fragments": 1216, "total_fragments": 1541, "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_000173735.1", "gtdb_species": "s__Yersinia aldovae", "ani": 85.7234, "matched_fragments": 1036, "total_fragments": 1541, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.00", "min_intra_species_ani": "96.65", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.91", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCF_001098625.1", "gtdb_species": "s__Yersinia frederiksenii_C", "ani": 85.601, "matched_fragments": 1190, "total_fragments": 1541, "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_000754805.1", "gtdb_species": "s__Yersinia frederiksenii", "ani": 85.2615, "matched_fragments": 1178, "total_fragments": 1541, "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": "-" }, { "accession": "GCF_002082245.2", "gtdb_species": "s__Yersinia enterocolitica_E", "ani": 84.6964, "matched_fragments": 1144, "total_fragments": 1541, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "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_001152565.1", "gtdb_species": "s__Yersinia pekkanenii", "ani": 84.5229, "matched_fragments": 1052, "total_fragments": 1541, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.90", "min_intra_species_ani": "99.90", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.078, "cell_length": 0.265, "doubling_h": 0.264, "growth_tmp": 30.5, "optimum_tmp": 28.929, "optimum_ph": 7.6, "genome_size": 4603445.82, "gc_content": 45.099, "coding_genes": 4211.04, "rRNA16S_genes": 7.286, "tRNA_genes": 73.941, "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", "enterocolitica", "subsp.", "palearctica", "Y11" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }