{ "type": "genome", "identifier": "GCF_001656035.1", "organism": "Yersinia entomophaga", "title": "Yersinia entomophaga", "description": "na", "data type": "Genome sequencing and assembly", "organization": "AgResearch", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001656035.1", "bioproject": "PRJNA224116", "biosample": "SAMN03177402", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "935293", "species_taxid": "935293", "organism_name": "Yersinia entomophaga", "infraspecific_name": "strain=MH96", "isolate": "na", "version_status": "latest", "assembly_level": "Chromosome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/06/03", "asm_name": "ASM165603v1", "asm_submitter": "AgResearch", "gbrs_paired_asm": "GCA_001656035.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/656/035/GCF_001656035.1_ASM165603v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4275406", "genome_size_ungapped": "4274770", "gc_percent": "48.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001656035.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "3927", "protein_coding_gene_count": "3722", "non_coding_gene_count": "119", "pubmed_id": "27187466" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-06-03", "dateModified": "2016-06-03", "datePublished": "2016-06-03", "_annotation": { "sample_count": 1, "sample_organism": [ "Yersinia entomophaga" ], "sample_taxid": [ "935293" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "New Zealand: Canterbury" ], "sample_host_location_id": [], "data_size": "1.216 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)": "4275406", "Number of Sequences": "1", "Longest Sequences (bp)": "4275406", "N50 (bp)": "4275406", "Gap Ratio (%)": "0.014993", "GCcontent (%)": "48.6", "Number of CDSs": "3791", "Average Protein Length": "314.7", "Coding Ratio (%)": "83.7", "Number of rRNAs": "23", "Number of tRNAs": "86", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Yersinia entomophaga", "strain": "strain=MH96", "accession": "GCA_001656035.1", "taxid": 935293, "species_taxid": 935293, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1424, "total_fragments": 1425, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Yersinia ruckeri", "strain": "strain=NCTC12986", "accession": "GCA_900460715.1", "taxid": 29486, "species_taxid": 29486, "relation_to_type": "type", "validated": true, "ani": 84.1248, "matched_fragments": 860, "total_fragments": 1425, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yersinia ruckeri", "strain": "strain=ATCC 29473", "accession": "GCA_000173755.1", "taxid": 29486, "species_taxid": 29486, "relation_to_type": "type", "validated": true, "ani": 84.0162, "matched_fragments": 827, "total_fragments": 1425, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yersinia ruckeri", "strain": "strain=ATCC 29473", "accession": "GCA_000754815.1", "taxid": 29486, "species_taxid": 29486, "relation_to_type": "type", "validated": true, "ani": 83.9788, "matched_fragments": 864, "total_fragments": 1425, "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": 81.5794, "matched_fragments": 659, "total_fragments": 1425, "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": 81.4544, "matched_fragments": 684, "total_fragments": 1425, "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": 81.4247, "matched_fragments": 659, "total_fragments": 1425, "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": 81.3634, "matched_fragments": 664, "total_fragments": 1425, "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": 81.2287, "matched_fragments": 682, "total_fragments": 1425, "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": 80.9707, "matched_fragments": 620, "total_fragments": 1425, "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": 79.6569, "matched_fragments": 517, "total_fragments": 1425, "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": 79.3523, "matched_fragments": 496, "total_fragments": 1425, "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": 79.2854, "matched_fragments": 486, "total_fragments": 1425, "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": 79.174, "matched_fragments": 415, "total_fragments": 1425, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001656035.1", "gtdb_species": "s__Yersinia entomophaga", "ani": 100.0, "matched_fragments": 1424, "total_fragments": 1425, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.84", "min_intra_species_ani": "99.69", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_001112925.1", "gtdb_species": "s__Yersinia nurmii", "ani": 94.7, "matched_fragments": 1298, "total_fragments": 1425, "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_000754815.1", "gtdb_species": "s__Yersinia ruckeri", "ani": 83.9788, "matched_fragments": 864, "total_fragments": 1425, "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": "-" }, { "accession": "GCF_900635455.1", "gtdb_species": "s__Yersinia intermedia", "ani": 81.5669, "matched_fragments": 658, "total_fragments": 1425, "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": "-" }, { "accession": "GCF_001047675.1", "gtdb_species": "s__Yersinia aleksiciae", "ani": 81.4718, "matched_fragments": 636, "total_fragments": 1425, "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": 81.4564, "matched_fragments": 685, "total_fragments": 1425, "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_002082245.2", "gtdb_species": "s__Yersinia enterocolitica_E", "ani": 81.4276, "matched_fragments": 670, "total_fragments": 1425, "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_003600645.1", "gtdb_species": "s__Yersinia rochesterensis", "ani": 81.4193, "matched_fragments": 661, "total_fragments": 1425, "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_902726525.1", "gtdb_species": "s__Yersinia enterocolitica_H", "ani": 81.2501, "matched_fragments": 652, "total_fragments": 1425, "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_001995075.1", "gtdb_species": "s__Yersinia enterocolitica_F", "ani": 81.2056, "matched_fragments": 681, "total_fragments": 1425, "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_001098625.1", "gtdb_species": "s__Yersinia frederiksenii_C", "ani": 81.197, "matched_fragments": 677, "total_fragments": 1425, "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_900460465.1", "gtdb_species": "s__Yersinia pestis", "ani": 80.9685, "matched_fragments": 606, "total_fragments": 1425, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.78", "min_intra_species_ani": "97.10", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.85", "num_clustered_genomes": 655, "status": "-" }, { "accession": "GCF_001053095.1", "gtdb_species": "s__Yersinia similis", "ani": 80.8982, "matched_fragments": 582, "total_fragments": 1425, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.47", "min_intra_species_ani": "99.21", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_001152565.1", "gtdb_species": "s__Yersinia pekkanenii", "ani": 80.8478, "matched_fragments": 652, "total_fragments": 1425, "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_001902635.1", "gtdb_species": "s__Serratia marcescens_F", "ani": 79.3886, "matched_fragments": 487, "total_fragments": 1425, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia", "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_006438725.1", "gtdb_species": "s__Ewingella americana_A", "ani": 79.2185, "matched_fragments": 393, "total_fragments": 1425, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Ewingella", "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": -0.155, "cell_length": 0.23, "doubling_h": 0.264, "growth_tmp": 29.0, "optimum_tmp": 33.5, "optimum_ph": 7.6, "genome_size": 4575854.635, "gc_content": 47.407, "coding_genes": 4010.575, "rRNA16S_genes": 6.998, "tRNA_genes": 78.744, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.0, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "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", "entomophaga" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }