{ "type": "genome", "identifier": "GCA_017084005.1", "organism": "Ornithobacterium rhinotracheale", "title": "Ornithobacterium rhinotracheale", "description": "derived from metagenome; fragmented assembly", "data type": "Genome sequencing and assembly", "organization": "USDA", "publication": [ {} ], "properties": { "assembly_accession": "GCA_017084005.1", "bioproject": "PRJNA557334", "biosample": "SAMN12395191", "wgs_master": "VWRM00000000.1", "refseq_category": "na", "taxid": "28251", "species_taxid": "28251", "organism_name": "Ornithobacterium rhinotracheale", "infraspecific_name": "", "isolate": "ORT3331-2017", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/03/01", "asm_name": "ASM1708400v1", "submitter": "USDA", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/017/084/005/GCA_017084005.1_ASM1708400v1", "excluded_from_refseq": "derived from metagenome; fragmented assembly", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-03-01", "dateModified": "2021-03-01", "datePublished": "2021-03-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Ornithobacterium rhinotracheale" ], "sample_taxid": [ "28251" ], "sample_host_organism": [ "chicken" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: GA" ], "sample_host_location_id": [], "data_size": "0.595 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 87.5, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2299446", "Number of Sequences": "13", "Longest Sequences (bp)": "418907", "N50 (bp)": "248962", "Gap Ratio (%)": "9.731561", "GCcontent (%)": "38.0", "Number of CDSs": "1724", "Average Protein Length": "321.6", "Coding Ratio (%)": "72.3", "Number of rRNAs": "3", "Number of tRNAs": "26", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Ornithobacterium rhinotracheale", "strain": "strain=DSM 15997", "accession": "GCA_000265465.1", "taxid": 28251, "species_taxid": 28251, "relation_to_type": "type", "validated": true, "ani": 99.4499, "matched_fragments": 728, "total_fragments": 760, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Polaribacter cellanae", "strain": "strain=SM13", "accession": "GCA_017569185.1", "taxid": 2818493, "species_taxid": 2818493, "relation_to_type": "type", "validated": true, "ani": 76.1549, "matched_fragments": 55, "total_fragments": 760, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Empedobacter tilapiae", "strain": "strain=MRS2", "accession": "GCA_004785645.1", "taxid": 2491114, "species_taxid": 2491114, "relation_to_type": "type", "validated": true, "ani": 75.9005, "matched_fragments": 69, "total_fragments": 760, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Empedobacter brevis", "strain": "strain=NBRC 14943", "accession": "GCA_007990795.1", "taxid": 247, "species_taxid": 247, "relation_to_type": "type", "validated": true, "ani": 75.7583, "matched_fragments": 54, "total_fragments": 760, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Empedobacter brevis", "strain": "strain=ATCC 43319", "accession": "GCA_000382425.1", "taxid": 247, "species_taxid": 247, "relation_to_type": "type", "validated": true, "ani": 75.6841, "matched_fragments": 54, "total_fragments": 760, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 87.5, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000265465.1", "gtdb_species": "s__Ornithobacterium rhinotracheale", "ani": 99.4321, "matched_fragments": 730, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Ornithobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.94", "min_intra_species_ani": "99.94", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.96", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_009659645.1", "gtdb_species": "s__Ornithobacterium rhinotracheale_B", "ani": 91.4285, "matched_fragments": 574, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Ornithobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.88", "min_intra_species_ani": "95.75", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_004088395.1", "gtdb_species": "s__Ornithobacterium rhinotracheale_A", "ani": 90.64, "matched_fragments": 577, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Ornithobacterium", "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_900538215.1", "gtdb_species": "s__Ornithobacterium hominis", "ani": 77.1867, "matched_fragments": 76, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Ornithobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.52", "min_intra_species_ani": "98.52", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_019218445.1", "gtdb_species": "s__Ornithobacterium sp019218445", "ani": 76.9008, "matched_fragments": 160, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Ornithobacterium", "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_013488205.1", "gtdb_species": "s__Empedobacter falsenii_A", "ani": 76.2183, "matched_fragments": 60, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.19", "min_intra_species_ani": "95.74", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.86", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_000745775.1", "gtdb_species": "s__Flavobacterium sp000745775", "ani": 75.712, "matched_fragments": 50, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "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": "GCA_002378465.1", "gtdb_species": "s__Empedobacter sp002378465", "ani": 75.6159, "matched_fragments": 52, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.64", "min_intra_species_ani": "95.90", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.86", "num_clustered_genomes": 24, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": 36.0, "optimum_tmp": 37.0, "optimum_ph": null, "genome_size": 2389835.333, "gc_content": 37.467, "coding_genes": 2240.8, "rRNA16S_genes": 3.0, "tRNA_genes": 43.0, "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": 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 }, "_gtdb_taxon": [ "d__Bacteria", "p__Bacteroidota", "c__Bacteroidia", "o__Flavobacteriales", "f__Weeksellaceae", "g__Ornithobacterium", "s__Ornithobacterium rhinotracheale" ], "_genome_taxon": [ "Ornithobacterium", "rhinotracheale", "d__Bacteria", "p__Bacteroidota", "c__Bacteroidia", "o__Flavobacteriales", "f__Weeksellaceae", "g__Ornithobacterium", "s__Ornithobacterium rhinotracheale", "Bacteria", "Bacteroidota", "Bacteroidia", "Flavobacteriales", "Weeksellaceae", "Ornithobacterium", "Ornithobacterium", "rhinotracheale" ], "_meo": [ { "id": "MEO_0000495", "label": "respiratory tract" } ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }