{ "type": "genome", "identifier": "GCF_002000485.1", "organism": "Rodentibacter ratti", "title": "Rodentibacter ratti", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Copenhagen", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002000485.1", "bioproject": "PRJNA224116", "biosample": "SAMN05860832", "wgs_master": "MLAJ00000000.1", "refseq_category": "reference genome", "taxid": "1906745", "species_taxid": "1906745", "organism_name": "Rodentibacter ratti", "infraspecific_name": "strain=F75", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/02/15", "asm_name": "ASM200048v1", "asm_submitter": "University of Copenhagen", "gbrs_paired_asm": "GCA_002000485.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/000/485/GCF_002000485.1_ASM200048v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2033538", "genome_size_ungapped": "2033538", "gc_percent": "40.000000", "replicon_count": "0", "scaffold_count": "25", "contig_count": "25", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002000485.1-RS_2024_04_22", "annotation_date": "2024-04-22", "total_gene_count": "1970", "protein_coding_gene_count": "1899", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-02-15", "dateModified": "2017-02-15", "datePublished": "2017-02-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Rodentibacter ratti" ], "sample_taxid": [ "1906745" ], "sample_host_organism": [ "Chicken" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "unknown" ], "sample_host_location_id": [], "data_size": "0.575 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)": "2033538", "Number of Sequences": "25", "Longest Sequences (bp)": "448553", "N50 (bp)": "171630", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "40.2", "Number of CDSs": "1911", "Average Protein Length": "318.1", "Coding Ratio (%)": "89.7", "Number of rRNAs": "3", "Number of tRNAs": "48", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rodentibacter ratti", "strain": "strain=F75", "accession": "GCA_002000485.1", "taxid": 1906745, "species_taxid": 1906745, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 661, "total_fragments": 665, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rodentibacter mrazii", "strain": "strain=Ppn418", "accession": "GCA_001998825.1", "taxid": 1908257, "species_taxid": 1908257, "relation_to_type": "type", "validated": true, "ani": 90.4948, "matched_fragments": 551, "total_fragments": 665, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rodentibacter pneumotropicus", "strain": "strain=ATCC 35149", "accession": "GCA_000730685.1", "taxid": 758, "species_taxid": 758, "relation_to_type": "type", "validated": true, "ani": 89.8929, "matched_fragments": 583, "total_fragments": 665, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rodentibacter pneumotropicus", "strain": "strain=DSM 21403", "accession": "GCA_000379905.1", "taxid": 758, "species_taxid": 758, "relation_to_type": "type", "validated": true, "ani": 89.8787, "matched_fragments": 586, "total_fragments": 665, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rodentibacter rarus", "strain": "strain=CCUG 17206", "accession": "GCA_001998965.1", "taxid": 1908260, "species_taxid": 1908260, "relation_to_type": "type", "validated": true, "ani": 85.6891, "matched_fragments": 481, "total_fragments": 665, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rodentibacter trehalosifermentans", "strain": "strain=H1987082031", "accession": "GCA_002000545.1", "taxid": 1908263, "species_taxid": 1908263, "relation_to_type": "type", "validated": true, "ani": 84.7626, "matched_fragments": 494, "total_fragments": 665, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rodentibacter myodis", "strain": "strain=Ac151", "accession": "GCA_001999305.1", "taxid": 1907939, "species_taxid": 1907939, "relation_to_type": "type", "validated": true, "ani": 80.904, "matched_fragments": 440, "total_fragments": 665, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rodentibacter haemolyticus", "strain": "strain=DSM 111151", "accession": "GCA_015356115.1", "taxid": 2778911, "species_taxid": 2778911, "relation_to_type": "type", "validated": true, "ani": 80.3184, "matched_fragments": 445, "total_fragments": 665, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Haemophilus haemolyticus", "strain": "strain=CCUG 12834", "accession": "GCA_001679045.1", "taxid": 726, "species_taxid": 726, "relation_to_type": "type", "validated": true, "ani": 79.0296, "matched_fragments": 315, "total_fragments": 665, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aggregatibacter segnis", "strain": "strain=ATCC 33393", "accession": "GCA_000185305.1", "taxid": 739, "species_taxid": 739, "relation_to_type": "type", "validated": true, "ani": 78.3135, "matched_fragments": 216, "total_fragments": 665, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pasteurella multocida subsp. gallicida", "strain": "strain=NCTC10204", "accession": "GCA_900636625.1", "taxid": 123812, "species_taxid": 747, "relation_to_type": "type", "validated": true, "ani": 77.6488, "matched_fragments": 181, "total_fragments": 665, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pasteurella multocida subsp. septica", "strain": "strain=NCTC11995", "accession": "GCA_900454845.1", "taxid": 115545, "species_taxid": 747, "relation_to_type": "type", "validated": true, "ani": 77.5772, "matched_fragments": 191, "total_fragments": 665, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002000485.1", "gtdb_species": "s__Rodentibacter ratti", "ani": 100.0, "matched_fragments": 661, "total_fragments": 665, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.24", "min_intra_species_ani": "96.11", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.81", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_001998825.1", "gtdb_species": "s__Rodentibacter mrazii", "ani": 90.4948, "matched_fragments": 551, "total_fragments": 665, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.11", "min_intra_species_ani": "95.11", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000379905.1", "gtdb_species": "s__Rodentibacter pneumotropicus", "ani": 89.8787, "matched_fragments": 586, "total_fragments": 665, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.90", "min_intra_species_ani": "97.98", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.87", "num_clustered_genomes": 18, "status": "-" }, { "accession": "GCF_001999425.1", "gtdb_species": "s__Rodentibacter sp001999425", "ani": 86.7472, "matched_fragments": 571, "total_fragments": 665, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter", "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_001019715.1", "gtdb_species": "s__Rodentibacter heylii", "ani": 86.0919, "matched_fragments": 573, "total_fragments": 665, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.70", "min_intra_species_ani": "95.96", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.90", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_001999335.1", "gtdb_species": "s__Rodentibacter sp001999335", "ani": 85.9147, "matched_fragments": 563, "total_fragments": 665, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter", "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_001998965.1", "gtdb_species": "s__Rodentibacter rarus", "ani": 85.6833, "matched_fragments": 481, "total_fragments": 665, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.19", "min_intra_species_ani": "99.19", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001999285.1", "gtdb_species": "s__Rodentibacter sp001999285", "ani": 85.651, "matched_fragments": 530, "total_fragments": 665, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.96", "min_intra_species_ani": "97.96", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002000125.1", "gtdb_species": "s__Rodentibacter heidelbergensis", "ani": 84.5771, "matched_fragments": 481, "total_fragments": 665, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter", "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": null, "optimum_ph": null, "genome_size": 2478253.8, "gc_content": 39.995, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "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": [ "Rodentibacter", "ratti" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }