{ "type": "genome", "identifier": "GCA_004332335.1", "organism": "Methanoregulaceae archaeon UXB-2016", "title": "Methanoregulaceae archaeon UXB-2016", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "Georgetown University", "publication": [ {} ], "properties": { "assembly_accession": "GCA_004332335.1", "bioproject": "PRJNA521775", "biosample": "SAMN10910799", "wgs_master": "SISS00000000.1", "refseq_category": "na", "taxid": "2576309", "species_taxid": "2576309", "organism_name": "Methanoregulaceae archaeon UXB-2016", "infraspecific_name": "", "isolate": "UXB-2016", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/07", "asm_name": "ASM433233v1", "submitter": "Georgetown University", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/004/332/335/GCA_004332335.1_ASM433233v1", "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": "2019-03-07", "dateModified": "2019-03-07", "datePublished": "2019-03-07", "_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": [ "Antarctica: East Antarctica, Lake Untersee" ], "sample_host_location_id": [], "data_size": "0.654 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2367119", "Number of Sequences": "45", "Longest Sequences (bp)": "311423", "N50 (bp)": "69553", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "66.4", "Number of CDSs": "2392", "Average Protein Length": "287.0", "Coding Ratio (%)": "87.0", "Number of rRNAs": "3", "Number of tRNAs": "47", "Number of CRISPRs": "2" }, "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": 77.6154, "matched_fragments": 118, "total_fragments": 768, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanoculleus horonobensis", "strain": "strain=T10", "accession": "GCA_001602375.1", "taxid": 528314, "species_taxid": 528314, "relation_to_type": "type", "validated": true, "ani": 77.391, "matched_fragments": 119, "total_fragments": 768, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanoculleus marisnigri", "strain": "strain=JR1", "accession": "GCA_000015825.1", "taxid": 2198, "species_taxid": 2198, "relation_to_type": "type", "validated": true, "ani": 77.2046, "matched_fragments": 120, "total_fragments": 768, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanofollis liminatans", "strain": "strain=DSM 4140", "accession": "GCA_000275865.1", "taxid": 2201, "species_taxid": 2201, "relation_to_type": "type", "validated": true, "ani": 76.9406, "matched_fragments": 113, "total_fragments": 768, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanosphaerula palustris", "strain": "strain=E1-9c", "accession": "GCA_000021965.1", "taxid": 475088, "species_taxid": 475088, "relation_to_type": "type", "validated": true, "ani": 76.8388, "matched_fragments": 146, "total_fragments": 768, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanolinea mesophila", "strain": "strain=DSM 23604", "accession": "GCA_017873855.1", "taxid": 547055, "species_taxid": 547055, "relation_to_type": "type", "validated": true, "ani": 76.7287, "matched_fragments": 66, "total_fragments": 768, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_004332335.1", "gtdb_species": "s__UBA288 sp004332335", "ani": 100.0, "matched_fragments": 765, "total_fragments": 768, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanosphaerulaceae;g__UBA288", "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_017883495.1", "gtdb_species": "s__UBA288 sp017883495", "ani": 82.7951, "matched_fragments": 327, "total_fragments": 768, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanosphaerulaceae;g__UBA288", "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_013331215.1", "gtdb_species": "s__UBA288 sp11384u", "ani": 81.9973, "matched_fragments": 322, "total_fragments": 768, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanosphaerulaceae;g__UBA288", "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_012728895.1", "gtdb_species": "s__UBA288 sp012728895", "ani": 81.1886, "matched_fragments": 400, "total_fragments": 768, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanosphaerulaceae;g__UBA288", "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_001602375.1", "gtdb_species": "s__Methanoculleus horonobensis", "ani": 77.3659, "matched_fragments": 120, "total_fragments": 768, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus", "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_016841955.1", "gtdb_species": "s__Methanoculleus sp016841955", "ani": 77.2034, "matched_fragments": 115, "total_fragments": 768, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.79", "min_intra_species_ani": "99.79", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000021965.1", "gtdb_species": "s__Methanosphaerula palustris", "ani": 76.8388, "matched_fragments": 146, "total_fragments": 768, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanosphaerulaceae;g__Methanosphaerula", "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": -0.348, "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__UBA288", "s__UBA288 sp004332335" ], "_genome_taxon": [ "Methanoregulaceae", "archaeon", "UXB-2016", "d__Archaea", "p__Halobacteriota", "c__Methanomicrobia", "o__Methanomicrobiales", "f__Methanospirillaceae", "g__UBA288", "s__UBA288 sp004332335", "Archaea", "Halobacteriota", "Methanomicrobia", "Methanomicrobiales", "Methanospirillaceae", "UBA288", "UBA288", "sp004332335" ], "_meo": [ { "id": "MEO_0000116", "label": "biofilm" }, { "id": "MEO_0000024", "label": "lake" } ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }