{ "type": "genome", "identifier": "GCA_902797935.1", "organism": "Oscillospiraceae bacterium", "title": "Oscillospiraceae bacterium", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "THE ROSLIN INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCA_902797935.1", "bioproject": "PRJEB31266", "biosample": "SAMEA6152459", "wgs_master": "CADBUQ000000000.1", "refseq_category": "na", "taxid": "2485925", "species_taxid": "2485925", "organism_name": "Oscillospiraceae bacterium", "infraspecific_name": "", "isolate": "RUG14321", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/02/15", "asm_name": "Rumen uncultured genome RUG14321", "submitter": "THE ROSLIN INSTITUTE", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/797/935/GCA_902797935.1_Rumen_uncultured_genome_RUG14321", "excluded_from_refseq": "derived from metagenome; genus undefined", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-02-15", "dateModified": "2020-02-15", "datePublished": "2020-02-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Oscillospiraceae bacterium" ], "sample_taxid": [ "2485925" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "United Kingdom" ], "sample_host_location_id": [], "data_size": "0.656 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 69.68, "contamination": 4.17, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2340675", "Number of Sequences": "235", "Longest Sequences (bp)": "68849", "N50 (bp)": "13759", "Gap Ratio (%)": "0.054087", "GCcontent (%)": "61.1", "Number of CDSs": "1966", "Average Protein Length": "309.1", "Coding Ratio (%)": "77.9", "Number of rRNAs": "0", "Number of tRNAs": "31", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudoflavonifractor gallinarum", "strain": "strain=DSM 107456", "accession": "GCA_014982855.1", "taxid": 2779352, "species_taxid": 2779352, "relation_to_type": "type", "validated": true, "ani": 77.4659, "matched_fragments": 99, "total_fragments": 662, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dysosmobacter welbionis", "strain": "strain=J115", "accession": "GCA_005121165.3", "taxid": 2093857, "species_taxid": 2093857, "relation_to_type": "type", "validated": true, "ani": 77.3379, "matched_fragments": 109, "total_fragments": 662, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium phoceensis", "strain": "strain=GD3", "accession": "GCA_001244495.1", "taxid": 1650661, "species_taxid": 1650661, "relation_to_type": "type", "validated": true, "ani": 77.2433, "matched_fragments": 81, "total_fragments": 662, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vescimonas fastidiosa", "strain": "strain=MM35", "accession": "GCA_018326305.1", "taxid": 2714353, "species_taxid": 2714353, "relation_to_type": "type", "validated": true, "ani": 77.2426, "matched_fragments": 75, "total_fragments": 662, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavonifractor plautii", "strain": "strain=JCM 32125", "accession": "GCA_010508875.1", "taxid": 292800, "species_taxid": 292800, "relation_to_type": "suspected-type", "validated": true, "ani": 77.2154, "matched_fragments": 112, "total_fragments": 662, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavonifractor plautii", "strain": "strain=ATCC 29863", "accession": "GCA_000239295.1", "taxid": 292800, "species_taxid": 292800, "relation_to_type": "suspected-type", "validated": true, "ani": 77.177, "matched_fragments": 109, "total_fragments": 662, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dysosmobacter acutus", "strain": "strain=MSJ-2", "accession": "GCA_018919205.1", "taxid": 2841504, "species_taxid": 2841504, "relation_to_type": "type", "validated": true, "ani": 77.1213, "matched_fragments": 87, "total_fragments": 662, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vescimonas coprocola", "strain": "strain=MM50", "accession": "GCA_018408575.1", "taxid": 2714355, "species_taxid": 2714355, "relation_to_type": "type", "validated": true, "ani": 76.8956, "matched_fragments": 94, "total_fragments": 662, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Intestinimonas butyriciproducens", "strain": "strain=DSM 26588", "accession": "GCA_003096335.1", "taxid": 1297617, "species_taxid": 1297617, "relation_to_type": "type", "validated": true, "ani": 76.6891, "matched_fragments": 72, "total_fragments": 662, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bittarella massiliensis", "strain": "strain=GD6", "accession": "GCA_001486165.1", "taxid": 1720313, "species_taxid": 1720313, "relation_to_type": "type", "validated": true, "ani": 76.4408, "matched_fragments": 62, "total_fragments": 662, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pusillibacter faecalis", "strain": "strain=MM59", "accession": "GCA_018408705.1", "taxid": 2714358, "species_taxid": 2714358, "relation_to_type": "type", "validated": true, "ani": 76.3443, "matched_fragments": 57, "total_fragments": 662, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 69.68, "contamination": 4.17, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCA_900319635.1", "gtdb_species": "s__Limivicinus sp900319635", "ani": 96.6944, "matched_fragments": 506, "total_fragments": 662, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.84", "min_intra_species_ani": "96.83", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.76", "num_clustered_genomes": 6, "status": "conclusive" }, { "accession": "GCA_017428565.1", "gtdb_species": "s__Limivicinus sp017428565", "ani": 87.2853, "matched_fragments": 483, "total_fragments": 662, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "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_902775355.1", "gtdb_species": "s__Limivicinus sp902775355", "ani": 84.0824, "matched_fragments": 451, "total_fragments": 662, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "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_017545165.1", "gtdb_species": "s__Limivicinus sp017545165", "ani": 83.8223, "matched_fragments": 346, "total_fragments": 662, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "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_900316255.1", "gtdb_species": "s__Limivicinus sp900316255", "ani": 83.7864, "matched_fragments": 397, "total_fragments": 662, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.92", "min_intra_species_ani": "95.41", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.79", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_902765595.1", "gtdb_species": "s__Limivicinus sp002350825", "ani": 83.661, "matched_fragments": 382, "total_fragments": 662, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.80", "min_intra_species_ani": "99.80", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900316205.1", "gtdb_species": "s__Limivicinus sp900316205", "ani": 83.4744, "matched_fragments": 424, "total_fragments": 662, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.11", "min_intra_species_ani": "98.31", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.81", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_902775985.1", "gtdb_species": "s__Limivicinus sp902775985", "ani": 82.0326, "matched_fragments": 274, "total_fragments": 662, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.70", "min_intra_species_ani": "98.45", "mean_intra_species_af": "0.76", "min_intra_species_af": "0.73", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_902778275.1", "gtdb_species": "s__Limivicinus sp902778275", "ani": 80.5762, "matched_fragments": 269, "total_fragments": 662, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "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_902774015.1", "gtdb_species": "s__Limivicinus sp902774015", "ani": 80.3915, "matched_fragments": 284, "total_fragments": 662, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "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_902795045.1", "gtdb_species": "s__Limivicinus sp902795045", "ani": 79.2146, "matched_fragments": 219, "total_fragments": 662, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.71", "min_intra_species_ani": "97.45", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.77", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_902791215.1", "gtdb_species": "s__Limivicinus sp902791215", "ani": 79.0877, "matched_fragments": 236, "total_fragments": 662, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "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": -0.302, "cell_length": 0.397, "doubling_h": null, "growth_tmp": 30.0, "optimum_tmp": 30.0, "optimum_ph": 6.25, "genome_size": 4470621.5, "gc_content": 49.895, "coding_genes": 4347.333, "rRNA16S_genes": 3.0, "tRNA_genes": 61.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": null, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "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__Bacillota_A", "c__Clostridia", "o__Oscillospirales", "f__Oscillospiraceae", "g__Limivicinus", "s__Limivicinus sp900319635" ], "_genome_taxon": [ "Oscillospiraceae", "bacterium", "d__Bacteria", "p__Bacillota_A", "c__Clostridia", "o__Oscillospirales", "f__Oscillospiraceae", "g__Limivicinus", "s__Limivicinus sp900319635", "Bacteria", "Bacillota", "A", "Clostridia", "Oscillospirales", "Oscillospiraceae", "Limivicinus", "Limivicinus", "sp900319635" ], "_meo": [ { "id": "MEO_0000046", "label": "rumen" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }