{ "type": "genome", "identifier": "GCA_902787655.1", "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_902787655.1", "bioproject": "PRJEB31266", "biosample": "SAMEA6151440", "wgs_master": "CADAHP000000000.1", "refseq_category": "na", "taxid": "165186", "species_taxid": "165186", "organism_name": "uncultured Ruminococcus sp.", "infraspecific_name": "", "isolate": "RUG13303", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/02/14", "asm_name": "Rumen uncultured genome RUG13303", "submitter": "THE ROSLIN INSTITUTE", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/787/655/GCA_902787655.1_Rumen_uncultured_genome_RUG13303", "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": "2020-02-14", "dateModified": "2020-02-14", "datePublished": "2020-02-14", "_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": "0.460 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 66.67, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "1621502", "Number of Sequences": "198", "Longest Sequences (bp)": "42206", "N50 (bp)": "10665", "Gap Ratio (%)": "0.045698", "GCcontent (%)": "47.9", "Number of CDSs": "1357", "Average Protein Length": "304.4", "Coding Ratio (%)": "76.4", "Number of rRNAs": "1", "Number of tRNAs": "25", "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": 77.3168, "matched_fragments": 97, "total_fragments": 443, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 66.67, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_900319655.1", "gtdb_species": "s__Ruminococcus_E sp900319655", "ani": 96.3146, "matched_fragments": 311, "total_fragments": 443, "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": "97.18", "min_intra_species_ani": "96.05", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.70", "num_clustered_genomes": 33, "status": "conclusive" }, { "accession": "GCA_905235295.1", "gtdb_species": "s__Ruminococcus_E sp905235295", "ani": 81.5263, "matched_fragments": 292, "total_fragments": 443, "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_902798605.1", "gtdb_species": "s__Ruminococcus_E sp902798605", "ani": 81.2871, "matched_fragments": 290, "total_fragments": 443, "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": "97.91", "min_intra_species_ani": "97.91", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_902767845.1", "gtdb_species": "s__Ruminococcus_E sp902767845", "ani": 80.9085, "matched_fragments": 260, "total_fragments": 443, "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": "98.96", "min_intra_species_ani": "98.96", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900318495.1", "gtdb_species": "s__Ruminococcus_E sp900318495", "ani": 79.3742, "matched_fragments": 210, "total_fragments": 443, "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": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900316555.1", "gtdb_species": "s__Ruminococcus_E sp900316555", "ani": 79.0263, "matched_fragments": 191, "total_fragments": 443, "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": "-" }, { "accession": "GCA_900315085.1", "gtdb_species": "s__Ruminococcus_E sp900315085", "ani": 79.0197, "matched_fragments": 184, "total_fragments": 443, "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": "98.46", "min_intra_species_ani": "97.96", "mean_intra_species_af": "0.77", "min_intra_species_af": "0.69", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCA_902765625.1", "gtdb_species": "s__Ruminococcus_E sp902765625", "ani": 78.6193, "matched_fragments": 205, "total_fragments": 443, "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": "99.31", "min_intra_species_ani": "99.27", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.89", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_900316435.1", "gtdb_species": "s__Ruminococcus_E sp900316435", "ani": 78.5569, "matched_fragments": 172, "total_fragments": 443, "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": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900315195.1", "gtdb_species": "s__Ruminococcus_E sp900315195", "ani": 78.531, "matched_fragments": 167, "total_fragments": 443, "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_002491825.1", "gtdb_species": "s__Ruminococcus_E sp002491825", "ani": 78.2617, "matched_fragments": 114, "total_fragments": 443, "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_900315605.1", "gtdb_species": "s__Ruminococcus_E sp900315605", "ani": 78.1128, "matched_fragments": 154, "total_fragments": 443, "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": "97.58", "min_intra_species_ani": "96.04", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.75", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCA_900543095.1", "gtdb_species": "s__Ruminococcus_E sp900543095", "ani": 77.6699, "matched_fragments": 108, "total_fragments": 443, "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": "99.93", "min_intra_species_ani": "99.93", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_902797655.1", "gtdb_species": "s__Ruminococcus_E sp902797655", "ani": 77.6164, "matched_fragments": 109, "total_fragments": 443, "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": "98.42", "min_intra_species_ani": "98.42", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_902773035.1", "gtdb_species": "s__Ruminococcus_E sp902773035", "ani": 76.9956, "matched_fragments": 78, "total_fragments": 443, "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": "-" } ] }, "_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 sp900319655" ], "_genome_taxon": [ "uncultured", "Ruminococcus", "sp.", "d__Bacteria", "p__Bacillota_A", "c__Clostridia", "o__Oscillospirales", "f__Acutalibacteraceae", "g__Ruminococcus_E", "s__Ruminococcus_E sp900319655", "Bacteria", "Bacillota", "A", "Clostridia", "Oscillospirales", "Acutalibacteraceae", "Ruminococcus", "E", "Ruminococcus", "E", "sp900319655" ], "_meo": [ { "id": "MEO_0000046", "label": "rumen" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }