{ "type": "genome", "identifier": "GCA_018435745.1", "organism": "Methanoregulaceae archaeon", "title": "Methanoregulaceae archaeon", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "University of California, Berkeley", "publication": [ {} ], "properties": { "assembly_accession": "GCA_018435745.1", "bioproject": "PRJNA655520", "biosample": "SAMN16056059", "wgs_master": "JAHDMZ000000000.1", "refseq_category": "na", "taxid": "2485498", "species_taxid": "2485498", "organism_name": "Methanoregulaceae archaeon", "infraspecific_name": "", "isolate": "R3-B32", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/05/21", "asm_name": "R3", "submitter": "University of California, Berkeley", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/018/435/745/GCA_018435745.1_R3", "excluded_from_refseq": "derived from metagenome; genus undefined", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-05-21", "dateModified": "2021-05-21", "datePublished": "2021-05-21", "_annotation": { "sample_count": 1, "sample_organism": [ "Methanoregulaceae archaeon" ], "sample_taxid": [ "2485498" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Richmond, CA" ], "sample_host_location_id": [], "data_size": "0.734 MB", "sample_ph_range": { "min": 7.0, "max": 7.0 }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2557466", "Number of Sequences": "500", "Longest Sequences (bp)": "58468", "N50 (bp)": "7568", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "54.4", "Number of CDSs": "2158", "Average Protein Length": "262.0", "Coding Ratio (%)": "66.3", "Number of rRNAs": "3", "Number of tRNAs": "45", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Methanoculleus sediminis", "strain": "strain=S3Fa", "accession": "GCA_001017125.1", "taxid": 1550566, "species_taxid": 1550566, "relation_to_type": "type", "validated": true, "ani": 76.5364, "matched_fragments": 56, "total_fragments": 580, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_018432765.1", "gtdb_species": "s__SD8 sp018432765", "ani": 98.9004, "matched_fragments": 399, "total_fragments": 580, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoregulaceae;g__SD8", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.01", "min_intra_species_ani": "99.01", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.81", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCA_002509485.1", "gtdb_species": "s__SD8 sp002509485", "ani": 94.0736, "matched_fragments": 359, "total_fragments": 580, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoregulaceae;g__SD8", "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_001412335.1", "gtdb_species": "s__SD8 sp001412335", "ani": 92.4228, "matched_fragments": 348, "total_fragments": 580, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoregulaceae;g__SD8", "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_002503825.1", "gtdb_species": "s__UBA467 sp002503825", "ani": 77.2899, "matched_fragments": 74, "total_fragments": 580, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoregulaceae;g__UBA467", "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_018263335.1", "gtdb_species": "s__Methanolinea_A sp002067155", "ani": 76.9789, "matched_fragments": 81, "total_fragments": 580, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoregulaceae;g__Methanolinea_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.35", "min_intra_species_ani": "99.35", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.348, "cell_length": 0.099, "doubling_h": 1.593, "growth_tmp": 35.75, "optimum_tmp": 38.333, "optimum_ph": 6.15, "genome_size": 2506240.0, "gc_content": 54.95, "coding_genes": 2580.333, "rRNA16S_genes": 2.0, "tRNA_genes": 51.5, "gram_stain": 0.333, "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": 0.75, "coccus_cell_shape": 0.25, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_gtdb_taxon": [ "d__Archaea", "p__Halobacteriota", "c__Methanomicrobia", "o__Methanomicrobiales", "f__Methanospirillaceae", "g__SD8", "s__SD8 sp018432765" ], "_genome_taxon": [ "Methanoregulaceae", "archaeon", "d__Archaea", "p__Halobacteriota", "c__Methanomicrobia", "o__Methanomicrobiales", "f__Methanospirillaceae", "g__SD8", "s__SD8 sp018432765", "Archaea", "Halobacteriota", "Methanomicrobia", "Methanomicrobiales", "Methanospirillaceae", "SD8", "SD8", "sp018432765" ], "_meo": [ { "id": "MEO_0000035", "label": "waste water" }, { "id": "MEO_0000014", "label": "activated sludge" } ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }