{ "type": "genome", "identifier": "GCA_934503795.1", "organism": "uncultured Ruminococcus sp.", "title": "uncultured Ruminococcus sp.", "description": "derived from environmental source; derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "stanford university school of medicine", "publication": [ {} ], "properties": { "assembly_accession": "GCA_934503795.1", "bioproject": "PRJEB49206", "biosample": "SAMEA13493772", "wgs_master": "CAKSVP000000000.1", "refseq_category": "na", "taxid": "165186", "species_taxid": "165186", "organism_name": "uncultured Ruminococcus sp.", "infraspecific_name": "", "isolate": "REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-I-L_C_22_2578.51", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/04/15", "asm_name": "ERR7737967_bin.51", "submitter": "stanford university school of medicine", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/934/503/795/GCA_934503795.1_ERR7737967_bin.51", "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": "2022-04-15", "dateModified": "2022-04-15", "datePublished": "2022-04-15", "_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": [ "Tanzania" ], "sample_host_location_id": [], "data_size": "0.621 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2186502", "Number of Sequences": "72", "Longest Sequences (bp)": "121579", "N50 (bp)": "56761", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "39.4", "Number of CDSs": "2011", "Average Protein Length": "308.3", "Coding Ratio (%)": "85.1", "Number of rRNAs": "2", "Number of tRNAs": "34", "Number of CRISPRs": "1" }, "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": 79.7835, "matched_fragments": 249, "total_fragments": 693, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ruminococcus bovis", "strain": "strain=JE7A12", "accession": "GCA_005601135.1", "taxid": 2564099, "species_taxid": 2564099, "relation_to_type": "type", "validated": true, "ani": 76.968, "matched_fragments": 79, "total_fragments": 693, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003438075.1", "gtdb_species": "s__Ruminococcus_E sp003438075", "ani": 96.9305, "matched_fragments": 602, "total_fragments": 693, "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": "98.49", "min_intra_species_ani": "97.62", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.88", "num_clustered_genomes": 5, "status": "conclusive" }, { "accession": "GCF_014288065.1", "gtdb_species": "s__Ruminococcus_E sp003526955", "ani": 91.3491, "matched_fragments": 547, "total_fragments": 693, "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": "97.97", "min_intra_species_ani": "97.37", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.74", "num_clustered_genomes": 16, "status": "-" }, { "accession": "GCA_900755995.1", "gtdb_species": "s__Ruminococcus_E sp900755995", "ani": 82.0987, "matched_fragments": 372, "total_fragments": 693, "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": "GCF_002834235.1", "gtdb_species": "s__Ruminococcus_E bromii_B", "ani": 79.948, "matched_fragments": 268, "total_fragments": 693, "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": "97.64", "min_intra_species_ani": "96.93", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.80", "num_clustered_genomes": 74, "status": "-" }, { "accession": "GCF_002834225.1", "gtdb_species": "s__Ruminococcus_E bromii", "ani": 79.7614, "matched_fragments": 250, "total_fragments": 693, "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": "98.59", "min_intra_species_ani": "98.08", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.90", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCA_905215855.1", "gtdb_species": "s__Ruminococcus_E sp905215855", "ani": 79.5125, "matched_fragments": 271, "total_fragments": 693, "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": "97.72", "min_intra_species_ani": "97.72", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.84", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_902771755.1", "gtdb_species": "s__Ruminococcus_E sp902771755", "ani": 79.4085, "matched_fragments": 219, "total_fragments": 693, "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_902766775.1", "gtdb_species": "s__Ruminococcus_E sp902766775", "ani": 78.9472, "matched_fragments": 214, "total_fragments": 693, "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_003521625.1", "gtdb_species": "s__Ruminococcus_E sp003521625", "ani": 78.7165, "matched_fragments": 208, "total_fragments": 693, "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_902766885.1", "gtdb_species": "s__Ruminococcus_E sp902766885", "ani": 78.5031, "matched_fragments": 209, "total_fragments": 693, "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_002493005.1", "gtdb_species": "s__Ruminococcus_E sp002493005", "ani": 78.384, "matched_fragments": 162, "total_fragments": 693, "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 sp003438075" ], "_genome_taxon": [ "uncultured", "Ruminococcus", "sp.", "d__Bacteria", "p__Bacillota_A", "c__Clostridia", "o__Oscillospirales", "f__Acutalibacteraceae", "g__Ruminococcus_E", "s__Ruminococcus_E sp003438075", "Bacteria", "Bacillota", "A", "Clostridia", "Oscillospirales", "Acutalibacteraceae", "Ruminococcus", "E", "Ruminococcus", "E", "sp003438075" ], "_meo": [ { "id": "MEO_0000054", "label": "feces" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }