{ "type": "genome", "identifier": "GCA_902793735.1", "organism": "uncultured Methanobrevibacter sp.", "title": "uncultured Methanobrevibacter sp.", "description": "derived from environmental source; derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "THE ROSLIN INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCA_902793735.1", "bioproject": "PRJEB31266", "biosample": "SAMEA6152030", "wgs_master": "CADBEP000000000.1", "refseq_category": "na", "taxid": "253161", "species_taxid": "253161", "organism_name": "uncultured Methanobrevibacter sp.", "infraspecific_name": "", "isolate": "RUG13892", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/02/14", "asm_name": "Rumen uncultured genome RUG13892", "submitter": "THE ROSLIN INSTITUTE", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/793/735/GCA_902793735.1_Rumen_uncultured_genome_RUG13892", "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 Methanobrevibacter sp." ], "sample_taxid": [ "253161" ], "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": "0.500 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 70.45, "contamination": 8.33, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "1797112", "Number of Sequences": "68", "Longest Sequences (bp)": "123105", "N50 (bp)": "49369", "Gap Ratio (%)": "0.009515", "GCcontent (%)": "32.2", "Number of CDSs": "1726", "Average Protein Length": "298.0", "Coding Ratio (%)": "85.9", "Number of rRNAs": "0", "Number of tRNAs": "25", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Methanobrevibacter millerae", "strain": "strain=DSM 16643", "accession": "GCA_900103415.1", "taxid": 230361, "species_taxid": 230361, "relation_to_type": "type", "validated": true, "ani": 80.363, "matched_fragments": 276, "total_fragments": 564, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanobrevibacter thaueri", "strain": "strain=DSM 11995", "accession": "GCA_003111625.1", "taxid": 190975, "species_taxid": 190975, "relation_to_type": "type", "validated": true, "ani": 79.9411, "matched_fragments": 197, "total_fragments": 564, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanobrevibacter woesei", "strain": "strain=DSM 11979", "accession": "GCA_003111605.1", "taxid": 190976, "species_taxid": 190976, "relation_to_type": "type", "validated": true, "ani": 79.2551, "matched_fragments": 145, "total_fragments": 564, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanobrevibacter smithii", "strain": "strain=ATCC 35061; PS; DSMZ 861", "accession": "GCA_000016525.1", "taxid": 2173, "species_taxid": 2173, "relation_to_type": "type", "validated": true, "ani": 79.0474, "matched_fragments": 202, "total_fragments": 564, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanobrevibacter olleyae", "strain": "strain=DSM 16632", "accession": "GCA_900114585.1", "taxid": 294671, "species_taxid": 294671, "relation_to_type": "type", "validated": true, "ani": 77.1175, "matched_fragments": 101, "total_fragments": 564, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 70.45, "contamination": 8.33, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001477655.1", "gtdb_species": "s__Methanobrevibacter_A millerae_A", "ani": 97.9957, "matched_fragments": 497, "total_fragments": 564, "gtdb_taxonomy": "d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A", "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": "conclusive" }, { "accession": "GCA_015063005.1", "gtdb_species": "s__Methanobrevibacter_A millerae_B", "ani": 84.3169, "matched_fragments": 364, "total_fragments": 564, "gtdb_taxonomy": "d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.89", "min_intra_species_ani": "97.89", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_017434555.1", "gtdb_species": "s__Methanobrevibacter_A sp017434555", "ani": 83.2915, "matched_fragments": 364, "total_fragments": 564, "gtdb_taxonomy": "d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.09", "min_intra_species_ani": "97.80", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.83", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_902771225.1", "gtdb_species": "s__Methanobrevibacter_A sp900319535", "ani": 83.1026, "matched_fragments": 335, "total_fragments": 564, "gtdb_taxonomy": 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79.0888, "matched_fragments": 189, "total_fragments": 564, "gtdb_taxonomy": "d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A", "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": -0.345, "cell_length": -0.04, "doubling_h": 1.37, "growth_tmp": 35.769, "optimum_tmp": 35.515, "optimum_ph": 7.107, "genome_size": 2226869.989, "gc_content": 30.616, "coding_genes": 1977.708, "rRNA16S_genes": 2.0, "tRNA_genes": 39.916, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "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": 0.538, "coccus_cell_shape": 0.23, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.23, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_gtdb_taxon": [ "d__Archaea", "p__Methanobacteriota", "c__Methanobacteria", "o__Methanobacteriales", "f__Methanobacteriaceae", "g__Methanobrevibacter_A", "s__Methanobrevibacter_A millerae_A" ], "_genome_taxon": [ "uncultured", "Methanobrevibacter", "sp.", "d__Archaea", "p__Methanobacteriota", "c__Methanobacteria", "o__Methanobacteriales", "f__Methanobacteriaceae", "g__Methanobrevibacter_A", "s__Methanobrevibacter_A millerae_A", "Archaea", "Methanobacteriota", "Methanobacteria", "Methanobacteriales", "Methanobacteriaceae", "Methanobrevibacter", "A", "Methanobrevibacter", "A", "millerae", "A" ], "_meo": [ { "id": "MEO_0000046", "label": "rumen" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }