{ "type": "genome", "identifier": "GCA_902774965.1", "organism": "uncultured Lachnospiraceae bacterium", "title": "uncultured Lachnospiraceae bacterium", "description": "derived from environmental source; derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "THE ROSLIN INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCA_902774965.1", "bioproject": "PRJEB31266", "biosample": "SAMEA6150157", "wgs_master": "CACYKL000000000.1", "refseq_category": "na", "taxid": "297314", "species_taxid": "297314", "organism_name": "uncultured Lachnospiraceae bacterium", "infraspecific_name": "", "isolate": "RUG12022", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/02/17", "asm_name": "Rumen uncultured genome RUG12022", "submitter": "THE ROSLIN INSTITUTE", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/774/965/GCA_902774965.1_Rumen_uncultured_genome_RUG12022", "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": "2020-02-17", "dateModified": "2020-02-17", "datePublished": "2020-02-17", "_annotation": { "sample_count": 1, "sample_organism": [ "uncultured Lachnospiraceae bacterium" ], "sample_taxid": [ "297314" ], "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": "0.765 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 2.08, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2683355", "Number of Sequences": "174", "Longest Sequences (bp)": "77832", "N50 (bp)": "23195", "Gap Ratio (%)": "0.012783", "GCcontent (%)": "42.2", "Number of CDSs": "2446", "Average Protein Length": "309.4", "Coding Ratio (%)": "84.6", "Number of rRNAs": "0", "Number of tRNAs": "33", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Roseburia faecis", "strain": "strain=M72", "accession": "GCA_001406815.1", "taxid": 301302, "species_taxid": 301302, "relation_to_type": "type", "validated": true, "ani": 80.4468, "matched_fragments": 334, "total_fragments": 809, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseburia porci", "strain": "strain=MUC/MUC-530-WT-4D", "accession": "GCA_009695765.1", "taxid": 2605790, "species_taxid": 2605790, "relation_to_type": "type", "validated": true, "ani": 78.4529, "matched_fragments": 228, "total_fragments": 809, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseburia hominis", "strain": "strain=A2-183", "accession": "GCA_000225345.1", "taxid": 301301, "species_taxid": 301301, "relation_to_type": "type", "validated": true, "ani": 78.0274, "matched_fragments": 102, "total_fragments": 809, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseburia inulinivorans", "strain": "strain=DSM 16841", "accession": "GCA_000174195.1", "taxid": 360807, "species_taxid": 360807, "relation_to_type": "suspected-type", "validated": true, "ani": 77.9988, "matched_fragments": 149, "total_fragments": 809, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseburia intestinalis", "strain": "strain=L1-82", "accession": "GCA_900537995.1", "taxid": 166486, "species_taxid": 166486, "relation_to_type": "type", "validated": true, "ani": 77.8586, "matched_fragments": 164, "total_fragments": 809, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseburia intestinalis", "strain": "strain=L1 82", "accession": "GCA_025151715.1", "taxid": 166486, "species_taxid": 166486, "relation_to_type": "type", "validated": true, "ani": 77.8569, "matched_fragments": 161, "total_fragments": 809, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseburia intestinalis", "strain": "strain=L1-82", "accession": "GCA_000156535.1", "taxid": 166486, "species_taxid": 166486, "relation_to_type": "type", "validated": true, "ani": 77.8358, "matched_fragments": 162, "total_fragments": 809, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agathobacter ruminis", "strain": "strain=JK623", "accession": "GCA_002735305.1", "taxid": 1712665, "species_taxid": 1712665, "relation_to_type": "type", "validated": true, "ani": 77.8097, "matched_fragments": 99, "total_fragments": 809, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lachnobacterium bovis", "strain": "strain=DSM 14045", "accession": "GCA_900107245.1", "taxid": 140626, "species_taxid": 140626, "relation_to_type": "suspected-type", "validated": true, "ani": 77.6582, "matched_fragments": 51, "total_fragments": 809, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Ruminococcus] lactaris", "strain": "strain=ATCC 29176", "accession": "GCA_025152405.1", "taxid": 46228, "species_taxid": 46228, "relation_to_type": "type", "validated": true, "ani": 77.0003, "matched_fragments": 64, "total_fragments": 809, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Eubacterium ramulus", "strain": "strain=ATCC 29099", "accession": "GCA_000469345.1", "taxid": 39490, "species_taxid": 39490, "relation_to_type": "type", "validated": true, "ani": 76.8202, "matched_fragments": 97, "total_fragments": 809, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Coprococcus comes", "strain": "strain=ATCC 27758", "accession": "GCA_025149785.1", "taxid": 410072, "species_taxid": 410072, "relation_to_type": "type", "validated": true, "ani": 76.702, "matched_fragments": 66, "total_fragments": 809, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Blautia obeum", "strain": "strain=ATCC 29174", "accession": "GCA_025147765.1", "taxid": 40520, "species_taxid": 40520, "relation_to_type": "type", "validated": true, "ani": 76.6284, "matched_fragments": 73, "total_fragments": 809, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Ruminococcus] gnavus", "strain": "strain=ATCC 29149", "accession": "GCA_025152275.1", "taxid": 33038, "species_taxid": 33038, "relation_to_type": "type", "validated": true, "ani": 76.39, "matched_fragments": 55, "total_fragments": 809, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 2.08, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_900552085.1", "gtdb_species": "s__Agathobacter sp900552085", "ani": 98.206, "matched_fragments": 518, "total_fragments": 809, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.03", "min_intra_species_ani": "95.54", "mean_intra_species_af": "0.78", "min_intra_species_af": "0.69", "num_clustered_genomes": 7, "status": "conclusive" }, { "accession": "GCA_900550545.1", "gtdb_species": "s__Agathobacter sp900550545", "ani": 93.4477, "matched_fragments": 600, "total_fragments": 809, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter", "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_902363675.1", "gtdb_species": "s__Agathobacter sp000434275", "ani": 91.963, "matched_fragments": 638, "total_fragments": 809, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.18", "min_intra_species_ani": "99.14", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_001406815.1", "gtdb_species": "s__Agathobacter faecis", "ani": 80.477, "matched_fragments": 333, "total_fragments": 809, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.10", "min_intra_species_ani": "97.07", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.62", "num_clustered_genomes": 43, "status": "-" }, { "accession": "GCA_900543445.1", "gtdb_species": "s__Agathobacter sp900543445", "ani": 79.7619, "matched_fragments": 256, "total_fragments": 809, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.64", "min_intra_species_ani": "98.60", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.84", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_900549895.1", "gtdb_species": "s__Agathobacter sp900549895", "ani": 79.4635, "matched_fragments": 230, "total_fragments": 809, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter", "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_009695765.1", "gtdb_species": "s__VUNI01 sp009695765", "ani": 78.4462, "matched_fragments": 229, "total_fragments": 809, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__VUNI01", "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_017623935.1", "gtdb_species": "s__Agathobacter sp017623935", "ani": 78.1593, "matched_fragments": 119, "total_fragments": 809, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.03", "min_intra_species_ani": "99.03", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.82", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.239, "cell_length": 0.277, "doubling_h": 0.394, "growth_tmp": 37.0, "optimum_tmp": 36.16, "optimum_ph": 6.363, "genome_size": 3641163.5, "gc_content": 42.852, "coding_genes": 3283.347, "rRNA16S_genes": 6.0, "tRNA_genes": 63.727, "gram_stain": 0.885, "sporulation": 0.414, "motility": 0.448, "range_salinity": 0.0, "facultative_respiration": 0.0, "anaerobic_respiration": 0.988, "aerobic_respiration": 0.011, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.8, "coccus_cell_shape": 0.133, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.033, "vibrio_cell_shape": 0.033, "spiral_cell_shape": 0.0 }, "_gtdb_taxon": [ "d__Bacteria", "p__Bacillota_A", "c__Clostridia", "o__Lachnospirales", "f__Lachnospiraceae", "g__Agathobacter", "s__Agathobacter sp900552085" ], "_genome_taxon": [ "uncultured", "Lachnospiraceae", "bacterium", "d__Bacteria", "p__Bacillota_A", "c__Clostridia", "o__Lachnospirales", "f__Lachnospiraceae", "g__Agathobacter", "s__Agathobacter sp900552085", "Bacteria", "Bacillota", "A", "Clostridia", "Lachnospirales", "Lachnospiraceae", "Agathobacter", "Agathobacter", "sp900552085" ], "_meo": [ { "id": "MEO_0000046", "label": "rumen" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }