{ "type": "genome", "identifier": "GCA_024697705.1", "organism": "Ruminococcus sp.", "title": "Ruminococcus sp.", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "Baqiyatallah University of Medical Sciences", "publication": [ {} ], "properties": { "assembly_accession": "GCA_024697705.1", "bioproject": "PRJNA746430", "biosample": "SAMN20246799", "wgs_master": "JAILFF000000000.1", "refseq_category": "na", "taxid": "41978", "species_taxid": "41978", "organism_name": "Ruminococcus sp.", "infraspecific_name": "", "isolate": "RUI065", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/08/15", "asm_name": "ASM2469770v1", "submitter": "Baqiyatallah University of Medical Sciences", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/024/697/705/GCA_024697705.1_ASM2469770v1", "excluded_from_refseq": "derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-08-15", "dateModified": "2022-08-15", "datePublished": "2022-08-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Ruminococcus sp." ], "sample_taxid": [ "41978" ], "sample_host_organism": [ "camel" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Iran: Karaj" ], "sample_host_location_id": [], "data_size": "0.895 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 79.17, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3142306", "Number of Sequences": "343", "Longest Sequences (bp)": "44282", "N50 (bp)": "12133", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "51.2", "Number of CDSs": "2568", "Average Protein Length": "314.5", "Coding Ratio (%)": "77.1", "Number of rRNAs": "0", "Number of tRNAs": "45", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Ruminococcus albus", "strain": "strain=DSM 20455", "accession": "GCA_000621285.1", "taxid": 1264, "species_taxid": 1264, "relation_to_type": "suspected-type", "validated": true, "ani": 77.7444, "matched_fragments": 93, "total_fragments": 882, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ruminococcus albus", "strain": "strain=7", "accession": "GCA_000179635.2", "taxid": 1264, "species_taxid": 1264, "relation_to_type": "suspected-type", "validated": true, "ani": 77.6952, "matched_fragments": 93, "total_fragments": 882, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ruminococcus flavefaciens", "strain": "strain=ATCC 19208", "accession": "GCA_000518765.1", "taxid": 1265, "species_taxid": 1265, "relation_to_type": "suspected-type", "validated": true, "ani": 76.3214, "matched_fragments": 52, "total_fragments": 882, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 79.17, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_902776945.1", "gtdb_species": "s__Ruminococcus_D sp902776945", "ani": 87.4128, "matched_fragments": 687, "total_fragments": 882, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D", "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_902781565.1", "gtdb_species": "s__Ruminococcus_D sp902781565", "ani": 79.3031, "matched_fragments": 321, "total_fragments": 882, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D", "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_900119155.1", "gtdb_species": "s__Ruminococcus_D sp900119155", "ani": 78.5518, "matched_fragments": 292, "total_fragments": 882, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_902766335.1", "gtdb_species": "s__Ruminococcus_D sp902766335", "ani": 77.9284, "matched_fragments": 193, "total_fragments": 882, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D", "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_000434695.1", "gtdb_species": "s__Ruminococcus_D sp000434695", "ani": 77.5784, "matched_fragments": 143, "total_fragments": 882, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.00", "min_intra_species_ani": "97.86", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.86", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_902797535.1", "gtdb_species": "s__Ruminococcus_D sp902797535", "ani": 77.2034, "matched_fragments": 115, "total_fragments": 882, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.84", "min_intra_species_ani": "97.84", "mean_intra_species_af": "0.78", "min_intra_species_af": "0.78", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900104495.1", "gtdb_species": "s__Ruminococcus_D sp900104495", "ani": 77.1942, "matched_fragments": 118, "total_fragments": 882, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D", "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_017450925.1", "gtdb_species": "s__Ruminococcus_D sp017450925", "ani": 76.927, "matched_fragments": 64, "total_fragments": 882, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D", "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_017478965.1", "gtdb_species": "s__Ruminococcus_D sp017478965", "ani": 76.8734, "matched_fragments": 58, "total_fragments": 882, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D", "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_902786965.1", "gtdb_species": "s__Ruminococcus_D sp902786965", "ani": 76.2607, "matched_fragments": 78, "total_fragments": 882, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.48", "min_intra_species_ani": "97.28", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.79", "num_clustered_genomes": 5, "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__Ruminococcaceae", "g__YE71", "s__YE71 sp024697705" ], "_genome_taxon": [ "Ruminococcus", "sp.", "d__Bacteria", "p__Bacillota_A", "c__Clostridia", "o__Oscillospirales", "f__Ruminococcaceae", "g__YE71", "s__YE71 sp024697705", "Bacteria", "Bacillota", "A", "Clostridia", "Oscillospirales", "Ruminococcaceae", "YE71", "YE71", "sp024697705" ], "_meo": [ { "id": "MEO_0000046", "label": "rumen" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }