{ "type": "genome", "identifier": "GCA_902777075.1", "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_902777075.1", "bioproject": "PRJEB31266", "biosample": "SAMEA6150374", "wgs_master": "CACYSL000000000.1", "refseq_category": "na", "taxid": "297314", "species_taxid": "297314", "organism_name": "uncultured Lachnospiraceae bacterium", "infraspecific_name": "", "isolate": "RUG12239", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/02/17", "asm_name": "Rumen uncultured genome RUG12239", "submitter": "THE ROSLIN INSTITUTE", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/777/075/GCA_902777075.1_Rumen_uncultured_genome_RUG12239", "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": "0.861 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3060947", "Number of Sequences": "54", "Longest Sequences (bp)": "261642", "N50 (bp)": "132411", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "40.7", "Number of CDSs": "2875", "Average Protein Length": "317.7", "Coding Ratio (%)": "89.5", "Number of rRNAs": "0", "Number of tRNAs": "51", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "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": 78.5701, "matched_fragments": 191, "total_fragments": 994, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseburia faecis", "strain": "strain=M72", "accession": "GCA_001406815.1", "taxid": 301302, "species_taxid": 301302, "relation_to_type": "type", "validated": true, "ani": 78.321, "matched_fragments": 150, "total_fragments": 994, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Jutongia hominis", "strain": "strain=BX3", "accession": "GCA_014384965.1", "taxid": 2763664, "species_taxid": 2763664, "relation_to_type": "type", "validated": true, "ani": 78.2538, "matched_fragments": 67, "total_fragments": 994, "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": 78.1735, "matched_fragments": 179, "total_fragments": 994, "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": 78.0089, "matched_fragments": 198, "total_fragments": 994, "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": 77.9928, "matched_fragments": 134, "total_fragments": 994, "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": 77.9679, "matched_fragments": 200, "total_fragments": 994, "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": 77.912, "matched_fragments": 201, "total_fragments": 994, "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": 77.4909, "matched_fragments": 80, "total_fragments": 994, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseburia lenta", "strain": "strain=NSJ-9", "accession": "GCA_014287435.1", "taxid": 2763061, "species_taxid": 2763061, "relation_to_type": "type", "validated": true, "ani": 77.343, "matched_fragments": 102, "total_fragments": 994, "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": 77.1897, "matched_fragments": 112, "total_fragments": 994, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Ruminococcus] gnavus", "strain": "strain=JCM6515", "accession": "GCA_008121495.1", "taxid": 33038, "species_taxid": 33038, "relation_to_type": "suspected-type", "validated": true, "ani": 77.1634, "matched_fragments": 72, "total_fragments": 994, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Blautia coccoides", "strain": "strain=NCTC11035", "accession": "GCA_900461125.1", "taxid": 1532, "species_taxid": 1532, "relation_to_type": "type", "validated": true, "ani": 76.9427, "matched_fragments": 65, "total_fragments": 994, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hominisplanchenecus faecis", "strain": "strain=CLA-AA-H246", "accession": "GCA_020687205.1", "taxid": 2885351, "species_taxid": 2885351, "relation_to_type": "type", "validated": true, "ani": 76.9224, "matched_fragments": 87, "total_fragments": 994, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mediterraneibacter butyricigenes", "strain": "strain=KCTC 15684", "accession": "GCA_003574295.1", "taxid": 2316025, "species_taxid": 2316025, "relation_to_type": "type", "validated": true, "ani": 76.8852, "matched_fragments": 86, "total_fragments": 994, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Faecalimonas umbilicata", "strain": "strain=DSM 103426", "accession": "GCA_004346095.1", "taxid": 1912855, "species_taxid": 1912855, "relation_to_type": "type", "validated": true, "ani": 76.8445, "matched_fragments": 58, "total_fragments": 994, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Jingyaoa shaoxingensis", "strain": "strain=NSJ-46", "accession": "GCA_014385005.1", "taxid": 2763671, "species_taxid": 2763671, "relation_to_type": "type", "validated": true, "ani": 76.8122, "matched_fragments": 100, "total_fragments": 994, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Blautia coccoides", "strain": "strain=DSM 935", "accession": "GCA_004340925.1", "taxid": 1532, "species_taxid": 1532, "relation_to_type": "type", "validated": true, "ani": 76.8121, "matched_fragments": 64, "total_fragments": 994, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Faecalimonas umbilicata", "strain": "strain=EGH7", "accession": "GCA_003402615.1", "taxid": 1912855, "species_taxid": 1912855, "relation_to_type": "type", "validated": true, "ani": 76.7409, "matched_fragments": 54, "total_fragments": 994, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Blautia caecimuris", "strain": "strain=DSM 29492", "accession": "GCA_024622975.1", "taxid": 1796615, "species_taxid": 1796615, "relation_to_type": "type", "validated": true, "ani": 76.4911, "matched_fragments": 66, "total_fragments": 994, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Clostridium] polysaccharolyticum", "strain": "strain=DSM 1801", "accession": "GCA_900111595.1", "taxid": 29364, "species_taxid": 29364, "relation_to_type": "type", "validated": true, "ani": 76.373, "matched_fragments": 51, "total_fragments": 994, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Eisenbergiella tayi", "strain": "strain=DSM 26961", "accession": "GCA_001881565.1", "taxid": 1432052, "species_taxid": 1432052, "relation_to_type": "type", "validated": true, "ani": 76.0857, "matched_fragments": 60, "total_fragments": 994, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Anaerocolumna jejuensis", "strain": "strain=DSM 15929", "accession": "GCA_900142215.1", "taxid": 259063, "species_taxid": 259063, "relation_to_type": "type", "validated": true, "ani": 75.8341, "matched_fragments": 50, "total_fragments": 994, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_900315735.1", "gtdb_species": "s__RUG115 sp900315735", "ani": 99.3254, "matched_fragments": 850, "total_fragments": 994, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.35", "min_intra_species_ani": "98.93", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.85", "num_clustered_genomes": 5, "status": "conclusive" }, { "accession": "GCF_003479605.1", "gtdb_species": "s__RUG115 sp900066395", "ani": 93.8308, "matched_fragments": 743, "total_fragments": 994, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.27", "min_intra_species_ani": "97.78", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.83", "num_clustered_genomes": 29, "status": "-" }, { "accession": "GCF_001940225.1", "gtdb_species": "s__14-2 sp001940225", "ani": 78.6856, "matched_fragments": 179, "total_fragments": 994, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2", "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_001940165.1", "gtdb_species": "s__Roseburia sp001940165", "ani": 78.4785, "matched_fragments": 211, "total_fragments": 994, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia", "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_902782995.1", "gtdb_species": "s__RUG115 sp902782995", "ani": 78.4262, "matched_fragments": 201, "total_fragments": 994, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115", "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_000174195.1", "gtdb_species": "s__Roseburia inulinivorans", "ani": 78.1506, "matched_fragments": 182, "total_fragments": 994, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.45", "min_intra_species_ani": "95.90", "mean_intra_species_af": "0.77", "min_intra_species_af": "0.61", "num_clustered_genomes": 28, "status": "-" }, { "accession": "GCA_012519695.1", "gtdb_species": "s__14-2 sp012519695", "ani": 78.1243, "matched_fragments": 193, "total_fragments": 994, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.81", "min_intra_species_ani": "97.81", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_003507655.1", "gtdb_species": "s__UBA11774 sp003507655", "ani": 77.9739, "matched_fragments": 139, "total_fragments": 994, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA11774", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.49", "min_intra_species_ani": "98.09", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.83", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCA_902363825.1", "gtdb_species": "s__CAG-45 sp000438375", "ani": 77.9109, "matched_fragments": 157, "total_fragments": 994, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-45", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.60", "min_intra_species_ani": "98.28", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.87", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCA_002299665.1", "gtdb_species": "s__CAG-45 sp002299665", "ani": 77.8246, "matched_fragments": 153, "total_fragments": 994, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-45", "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_003483745.1", "gtdb_species": "s__Roseburia sp003483745", "ani": 77.7468, "matched_fragments": 178, "total_fragments": 994, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.45", "min_intra_species_ani": "97.41", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_900550935.1", "gtdb_species": "s__Roseburia sp900550935", "ani": 77.6374, "matched_fragments": 158, "total_fragments": 994, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.33", "min_intra_species_ani": "98.19", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.82", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_910578885.1", "gtdb_species": "s__RUG115 sp910578885", "ani": 77.6047, "matched_fragments": 162, "total_fragments": 994, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115", "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_017549185.1", "gtdb_species": "s__Roseburia sp017549185", "ani": 77.5452, "matched_fragments": 87, "total_fragments": 994, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia", "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_900753715.1", "gtdb_species": "s__Roseburia sp900753715", "ani": 77.3439, "matched_fragments": 163, "total_fragments": 994, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.04", "min_intra_species_ani": "99.04", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.83", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_017625255.1", "gtdb_species": "s__1XD42-69 sp017625255", "ani": 76.9984, "matched_fragments": 139, "total_fragments": 994, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD42-69", "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_017626625.1", "gtdb_species": "s__Roseburia sp017626625", "ani": 76.8777, "matched_fragments": 82, "total_fragments": 994, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia", "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": -0.239, "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__Roseburia_C", "s__Roseburia_C sp900315735" ], "_genome_taxon": [ "uncultured", "Lachnospiraceae", "bacterium", "d__Bacteria", "p__Bacillota_A", "c__Clostridia", "o__Lachnospirales", "f__Lachnospiraceae", "g__Roseburia_C", "s__Roseburia_C sp900315735", "Bacteria", "Bacillota", "A", "Clostridia", "Lachnospirales", "Lachnospiraceae", "Roseburia", "C", "Roseburia", "C", "sp900315735" ], "_meo": [ { "id": "MEO_0000046", "label": "rumen" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }