{ "type": "genome", "identifier": "GCF_900635455.1", "organism": "Yersinia intermedia", "title": "Yersinia intermedia", "description": "na", "data type": "Genome sequencing and assembly", "organization": "SC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900635455.1", "bioproject": "PRJNA224116", "biosample": "SAMEA2580313", "wgs_master": "na", "refseq_category": "na", "taxid": "631", "species_taxid": "631", "organism_name": "Yersinia intermedia", "infraspecific_name": "strain=NCTC11469", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/12/19", "asm_name": "28307_A01", "asm_submitter": "SC", "gbrs_paired_asm": "GCA_900635455.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/635/455/GCF_900635455.1_28307_A01", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4757282", "genome_size_ungapped": "4757282", "gc_percent": "47.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900635455.1-RS_2024_04_05", "annotation_date": "2024-04-05", "total_gene_count": "4281", "protein_coding_gene_count": "4066", "non_coding_gene_count": "119", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-12-19", "dateModified": "2018-12-19", "datePublished": "2018-12-19", "_annotation": { "sample_count": 1, "sample_organism": [ "Yersinia intermedia" ], "sample_taxid": [ "631" ], "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": "1.354 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)": "4757282", "Number of Sequences": "1", "Longest Sequences (bp)": "4757282", "N50 (bp)": "4757282", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "47.5", "Number of CDSs": "4141", "Average Protein Length": "321.6", "Coding Ratio (%)": "84.0", "Number of rRNAs": "22", "Number of tRNAs": "82", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Yersinia intermedia", "strain": "strain=NCTC11469", "accession": "GCA_900635455.1", "taxid": 631, "species_taxid": 631, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1585, "total_fragments": 1585, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Yersinia intermedia", "strain": "strain=ATCC 29909", "accession": "GCA_000168035.1", "taxid": 631, "species_taxid": 631, "relation_to_type": "type", "validated": true, "ani": 99.9607, "matched_fragments": 1520, "total_fragments": 1585, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Yersinia aleksiciae", "strain": "strain=159", "accession": "GCA_001047675.1", "taxid": 263819, "species_taxid": 263819, "relation_to_type": "type", "validated": true, "ani": 85.3268, "matched_fragments": 1016, "total_fragments": 1585, "ani_threshold": 95, "status": "below_threshold" }, { "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": 84.9693, "matched_fragments": 1116, "total_fragments": 1585, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yersinia aldovae", "strain": "strain=ATCC 35236", "accession": "GCA_000173735.1", "taxid": 29483, "species_taxid": 29483, "relation_to_type": "type", "validated": true, "ani": 84.8603, "matched_fragments": 1035, "total_fragments": 1585, "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": 84.8246, "matched_fragments": 1057, "total_fragments": 1585, "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": 84.8205, "matched_fragments": 1171, "total_fragments": 1585, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yersinia bercovieri", "strain": "strain=ATCC 43970", "accession": "GCA_000167975.1", "taxid": 634, "species_taxid": 634, "relation_to_type": "type", "validated": true, "ani": 84.8171, "matched_fragments": 1057, "total_fragments": 1585, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yersinia rochesterensis", "strain": "strain=ATCC BAA-2637", "accession": "GCA_003600645.1", "taxid": 1604335, "species_taxid": 1604335, "relation_to_type": "type", "validated": true, "ani": 84.7443, "matched_fragments": 1114, "total_fragments": 1585, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yersinia canariae", "strain": "strain=NCTC 14382", "accession": "GCA_009831415.1", "taxid": 2607663, "species_taxid": 2607663, "relation_to_type": "type", "validated": true, "ani": 84.5673, "matched_fragments": 1172, "total_fragments": 1585, "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": 84.524, "matched_fragments": 1134, "total_fragments": 1585, "ani_threshold": 95, "status": "below_threshold" }, { "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": 84.4959, "matched_fragments": 1136, "total_fragments": 1585, "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": 84.2288, "matched_fragments": 1087, "total_fragments": 1585, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yersinia hibernica", "strain": "strain=CFS1934", "accession": "GCA_004124235.1", "taxid": 2339259, "species_taxid": 2339259, "relation_to_type": "type", "validated": true, "ani": 84.1164, "matched_fragments": 1123, "total_fragments": 1585, "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": 79.6775, "matched_fragments": 402, "total_fragments": 1585, "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": 78.9629, "matched_fragments": 398, "total_fragments": 1585, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rahnella bonaserana", "strain": "strain=H11b", "accession": "GCA_019049675.1", "taxid": 2816248, "species_taxid": 2816248, "relation_to_type": "type", "validated": true, "ani": 78.8848, "matched_fragments": 355, "total_fragments": 1585, "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": 78.8663, "matched_fragments": 393, "total_fragments": 1585, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900635455.1", "gtdb_species": "s__Yersinia intermedia", "ani": 100.0, "matched_fragments": 1585, "total_fragments": 1585, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.02", "min_intra_species_ani": "97.82", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.88", "num_clustered_genomes": 29, "status": "conclusive" }, { "accession": "GCF_002082245.2", "gtdb_species": "s__Yersinia enterocolitica_E", "ani": 93.5884, "matched_fragments": 1383, "total_fragments": 1585, "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": 86.1222, "matched_fragments": 1076, "total_fragments": 1585, "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": "-" }, { "accession": "GCF_001047675.1", "gtdb_species": "s__Yersinia aleksiciae", "ani": 85.3281, "matched_fragments": 1018, "total_fragments": 1585, "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_901472495.1", "gtdb_species": "s__Yersinia enterocolitica", "ani": 84.9693, "matched_fragments": 1116, "total_fragments": 1585, "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_001098625.1", "gtdb_species": "s__Yersinia frederiksenii_C", "ani": 84.8452, "matched_fragments": 1153, 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"vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Yersinia", "intermedia" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }