{ "type": "genome", "identifier": "GCF_900460715.1", "organism": "Yersinia ruckeri", "title": "Yersinia ruckeri", "description": "na", "data type": "Genome sequencing and assembly", "organization": "SC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900460715.1", "bioproject": "PRJNA224116", "biosample": "SAMEA3282972", "wgs_master": "UHJF00000000.1", "refseq_category": "na", "taxid": "29486", "species_taxid": "29486", "organism_name": "Yersinia ruckeri", "infraspecific_name": "strain=NCTC12986", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/08/01", "asm_name": "36725_G02", "asm_submitter": "SC", "gbrs_paired_asm": "GCA_900460715.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/460/715/GCF_900460715.1_36725_G02", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3840207", "genome_size_ungapped": "3840207", "gc_percent": "47.500000", "replicon_count": "0", "scaffold_count": "4", "contig_count": "4", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900460715.1-RS_2024_08_15", "annotation_date": "2024-08-15", "total_gene_count": "3506", "protein_coding_gene_count": "3291", "non_coding_gene_count": "116", "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 ruckeri" ], "sample_taxid": [ "29486" ], "sample_host_organism": [ "Rainbow Trout" ], "sample_host_organism_id": [], "sample_host_disease": [ "not available: to be reported later" ], "sample_host_disease_id": [], "sample_host_location": [ "USA: Idaho State" ], "sample_host_location_id": [], "data_size": "1.090 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)": "3840207", "Number of Sequences": "4", "Longest Sequences (bp)": "3698808", "N50 (bp)": "3698808", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "47.5", "Number of CDSs": "3393", "Average Protein Length": "314.7", "Coding Ratio (%)": "83.4", "Number of rRNAs": "21", "Number of tRNAs": "81", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Yersinia ruckeri", "strain": "strain=NCTC12986", "accession": "GCA_900460715.1", "taxid": 29486, "species_taxid": 29486, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1274, "total_fragments": 1278, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Yersinia ruckeri", "strain": "strain=ATCC 29473", "accession": "GCA_000754815.1", "taxid": 29486, "species_taxid": 29486, "relation_to_type": "type", "validated": true, "ani": 99.9788, "matched_fragments": 1252, "total_fragments": 1278, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Yersinia ruckeri", "strain": "strain=ATCC 29473", "accession": "GCA_000173755.1", "taxid": 29486, "species_taxid": 29486, "relation_to_type": "type", "validated": true, "ani": 99.9286, "matched_fragments": 1186, "total_fragments": 1278, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Yersinia entomophaga", "strain": "strain=MH96", "accession": "GCA_001656035.1", "taxid": 935293, "species_taxid": 935293, "relation_to_type": "type", "validated": true, "ani": 84.144, "matched_fragments": 878, "total_fragments": 1278, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yersinia intermedia", "strain": "strain=NCTC11469", "accession": "GCA_900635455.1", "taxid": 631, "species_taxid": 631, "relation_to_type": "type", "validated": true, "ani": 81.5407, "matched_fragments": 634, "total_fragments": 1278, "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": 81.1586, "matched_fragments": 611, "total_fragments": 1278, "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": 81.1376, "matched_fragments": 631, "total_fragments": 1278, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yersinia pseudotuberculosis", "strain": "strain=NCTC10275", "accession": "GCA_900637475.1", "taxid": 633, "species_taxid": 633, "relation_to_type": "suspected-type", "validated": true, "ani": 81.0726, "matched_fragments": 585, "total_fragments": 1278, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yersinia similis", "strain": "strain=Y228", "accession": "GCA_001053095.1", "taxid": 367190, "species_taxid": 367190, "relation_to_type": "type", "validated": true, "ani": 80.9652, "matched_fragments": 587, "total_fragments": 1278, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yersinia mollaretii", "strain": "strain=ATCC 43969", "accession": "GCA_013282725.1", "taxid": 33060, "species_taxid": 33060, "relation_to_type": "type", "validated": true, "ani": 80.9648, "matched_fragments": 644, "total_fragments": 1278, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yersinia kristensenii", "strain": "strain=ATCC 33638", "accession": "GCA_000173715.1", "taxid": 28152, "species_taxid": 28152, "relation_to_type": "type", "validated": true, "ani": 80.8973, "matched_fragments": 588, "total_fragments": 1278, "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": 79.6397, "matched_fragments": 404, "total_fragments": 1278, "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": 79.1226, "matched_fragments": 383, "total_fragments": 1278, "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": 78.945, "matched_fragments": 391, "total_fragments": 1278, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rahnella ecdela", "strain": "strain=FRB 231", "accession": "GCA_019049625.1", "taxid": 2816250, "species_taxid": 2816250, "relation_to_type": "type", "validated": true, "ani": 78.8114, "matched_fragments": 362, "total_fragments": 1278, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000754815.1", "gtdb_species": "s__Yersinia ruckeri", "ani": 99.9788, "matched_fragments": 1252, "total_fragments": 1278, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.70", "min_intra_species_ani": "97.63", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.91", "num_clustered_genomes": 69, "status": "conclusive" }, { "accession": "GCF_001656035.1", "gtdb_species": "s__Yersinia 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