{ "type": "genome", "identifier": "GCA_902784945.1", "organism": "uncultured Ruminococcus sp.", "title": "uncultured Ruminococcus sp.", "description": "derived from environmental source; derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "THE ROSLIN INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCA_902784945.1", "bioproject": "PRJEB31266", "biosample": "SAMEA6151156", "wgs_master": "CACZWW000000000.1", "refseq_category": "na", "taxid": "165186", "species_taxid": "165186", "organism_name": "uncultured Ruminococcus sp.", "infraspecific_name": "", "isolate": "RUG13020", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/02/15", "asm_name": "Rumen uncultured genome RUG13020", "submitter": "THE ROSLIN INSTITUTE", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/784/945/GCA_902784945.1_Rumen_uncultured_genome_RUG13020", "excluded_from_refseq": "derived from environmental source; derived from metagenome", "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": [ "uncultured Ruminococcus sp." ], "sample_taxid": [ "165186" ], "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": "0.558 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 92.19, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "1979013", "Number of Sequences": "185", "Longest Sequences (bp)": "59043", "N50 (bp)": "15905", "Gap Ratio (%)": "0.012986", "GCcontent (%)": "54.6", "Number of CDSs": "1739", "Average Protein Length": "298.9", "Coding Ratio (%)": "78.8", "Number of rRNAs": "3", "Number of tRNAs": "27", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Ruminococcus bromii", "strain": "strain=ATCC 27255", "accession": "GCA_002834225.1", "taxid": 40518, "species_taxid": 40518, "relation_to_type": "suspected-type", "validated": true, "ani": 76.9418, "matched_fragments": 52, "total_fragments": 567, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 92.19, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_900317315.1", "gtdb_species": "s__Ruminococcus_E sp900317315", "ani": 98.8567, "matched_fragments": 470, "total_fragments": 567, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.84", "min_intra_species_ani": "97.27", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.80", "num_clustered_genomes": 119, "status": "conclusive" }, { "accession": "GCA_902784855.1", "gtdb_species": "s__Ruminococcus_E sp902784855", "ani": 81.9695, "matched_fragments": 360, "total_fragments": 567, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E", "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_902799325.1", "gtdb_species": "s__Ruminococcus_E sp902799325", "ani": 81.832, "matched_fragments": 315, "total_fragments": 567, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E", "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_900316815.1", "gtdb_species": "s__Ruminococcus_E sp900316815", "ani": 81.8046, "matched_fragments": 318, "total_fragments": 567, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.08", "min_intra_species_ani": "98.49", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.78", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCA_902794395.1", "gtdb_species": "s__Ruminococcus_E sp902794395", "ani": 80.4937, "matched_fragments": 333, "total_fragments": 567, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E", "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_900317595.1", "gtdb_species": "s__Ruminococcus_E sp900317595", "ani": 80.3008, "matched_fragments": 285, "total_fragments": 567, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.55", "min_intra_species_ani": "99.10", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.83", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_902776375.1", "gtdb_species": "s__Ruminococcus_E sp902776375", "ani": 80.2522, "matched_fragments": 336, "total_fragments": 567, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E", "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_902797525.1", "gtdb_species": "s__Ruminococcus_E sp902797525", "ani": 80.0555, "matched_fragments": 241, "total_fragments": 567, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E", "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_902761375.1", "gtdb_species": "s__Ruminococcus_E sp902761375", "ani": 79.5022, "matched_fragments": 224, "total_fragments": 567, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E", "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_900320415.1", "gtdb_species": "s__Ruminococcus_E sp900320415", "ani": 79.1618, "matched_fragments": 178, "total_fragments": 567, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.69", "min_intra_species_ani": "99.69", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900315195.1", "gtdb_species": "s__Ruminococcus_E sp900315195", "ani": 79.1382, "matched_fragments": 228, "total_fragments": 567, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.59", "min_intra_species_ani": "99.19", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_900316555.1", "gtdb_species": "s__Ruminococcus_E sp900316555", "ani": 78.8288, "matched_fragments": 219, "total_fragments": 567, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.80", "min_intra_species_ani": "96.62", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.77", "num_clustered_genomes": 62, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.18, "cell_length": -0.18, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 37.7, "optimum_ph": 7.0, "genome_size": 3334855.36, "gc_content": 43.875, "coding_genes": 2772.666, "rRNA16S_genes": 4.0, "tRNA_genes": 64.0, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 0.0, "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": 0.0, "coccus_cell_shape": 1.0, "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__Acutalibacteraceae", "g__Ruminococcus_E", "s__Ruminococcus_E sp900317315" ], "_genome_taxon": [ "uncultured", "Ruminococcus", "sp.", "d__Bacteria", "p__Bacillota_A", "c__Clostridia", "o__Oscillospirales", "f__Acutalibacteraceae", "g__Ruminococcus_E", "s__Ruminococcus_E sp900317315", "Bacteria", "Bacillota", "A", "Clostridia", "Oscillospirales", "Acutalibacteraceae", "Ruminococcus", "E", "Ruminococcus", "E", "sp900317315" ], "_meo": [ { "id": "MEO_0000046", "label": "rumen" } ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }