{ "type": "genome", "identifier": "GCA_018436405.1", "organism": "Methanosarcina mazei", "title": "Methanosarcina mazei", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "University of California, Berkeley", "publication": [ {} ], "properties": { "assembly_accession": "GCA_018436405.1", "bioproject": "PRJNA655520", "biosample": "SAMN16056027", "wgs_master": "JAHDLT000000000.1", "refseq_category": "na", "taxid": "2209", "species_taxid": "2209", "organism_name": "Methanosarcina mazei", "infraspecific_name": "", "isolate": "M1-B22.1", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/05/21", "asm_name": "M1", "submitter": "University of California, Berkeley", "gbrs_paired_asm": "GCF_018436405.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/018/436/405/GCA_018436405.1_M1", "excluded_from_refseq": "derived from metagenome", "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": [ "Methanosarcina mazei" ], "sample_taxid": [ "2209" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Mill Valley, CA" ], "sample_host_location_id": [], "data_size": "1.035 MB", "sample_ph_range": { "min": 7.0, "max": 7.0 }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 87.5, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3639394", "Number of Sequences": "377", "Longest Sequences (bp)": "66939", "N50 (bp)": "15785", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "41.8", "Number of CDSs": "2889", "Average Protein Length": "283.9", "Coding Ratio (%)": "67.6", "Number of rRNAs": "0", "Number of tRNAs": "46", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Methanosarcina mazei", "strain": "strain=S-6", "accession": "GCA_000970205.1", "taxid": 2209, "species_taxid": 2209, "relation_to_type": "suspected-type", "validated": true, "ani": 98.8945, "matched_fragments": 989, "total_fragments": 1020, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Methanosarcina horonobensis", "strain": "strain=HB-1", "accession": "GCA_000970285.1", "taxid": 418008, "species_taxid": 418008, "relation_to_type": "type", "validated": true, "ani": 83.1015, "matched_fragments": 801, "total_fragments": 1020, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanosarcina acetivorans", "strain": "strain=C2A", "accession": "GCA_000007345.1", "taxid": 2214, "species_taxid": 2214, "relation_to_type": "type", "validated": true, "ani": 81.1667, "matched_fragments": 711, "total_fragments": 1020, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanosarcina siciliae", "strain": "strain=T4/M", "accession": "GCA_000970085.1", "taxid": 38027, "species_taxid": 38027, "relation_to_type": "type", "validated": true, "ani": 81.0464, "matched_fragments": 674, "total_fragments": 1020, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanosarcina thermophila", "strain": "strain=TM-1", "accession": "GCA_000969885.1", "taxid": 2210, "species_taxid": 2210, "relation_to_type": "type", "validated": true, "ani": 78.482, "matched_fragments": 352, "total_fragments": 1020, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanosarcina vacuolata", "strain": "strain=Z-761", "accession": "GCA_000969905.1", "taxid": 2215, "species_taxid": 2215, "relation_to_type": "type", "validated": true, "ani": 78.4724, "matched_fragments": 428, "total_fragments": 1020, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 87.5, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000970205.1", "gtdb_species": "s__Methanosarcina mazei", "ani": 98.8945, "matched_fragments": 989, "total_fragments": 1020, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.56", "min_intra_species_ani": "98.01", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.88", "num_clustered_genomes": 73, "status": "conclusive" }, { "accession": "GCA_013331265.1", "gtdb_species": "s__Methanosarcina sp10923u", "ani": 83.3859, "matched_fragments": 617, "total_fragments": 1020, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina", "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_000970285.1", "gtdb_species": "s__Methanosarcina horonobensis", "ani": 83.1015, "matched_fragments": 801, "total_fragments": 1020, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.79", "min_intra_species_ani": "99.79", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000979455.1", "gtdb_species": "s__Methanosarcina sp000979455", "ani": 81.3919, "matched_fragments": 705, "total_fragments": 1020, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.06", "min_intra_species_ani": "95.85", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.85", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_000970265.1", "gtdb_species": "s__Methanosarcina lacustris", "ani": 81.0572, "matched_fragments": 649, "total_fragments": 1020, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina", "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_000969965.1", "gtdb_species": "s__Methanosarcina sp000969965", "ani": 81.0413, "matched_fragments": 670, "total_fragments": 1020, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.47", "min_intra_species_ani": "99.47", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_017883485.1", "gtdb_species": "s__Methanosarcina sp017883485", "ani": 78.1229, "matched_fragments": 233, "total_fragments": 1020, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina", "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": 0.0, "cell_length": 0.0, "doubling_h": 0.726, "growth_tmp": 36.5, "optimum_tmp": 35.6, "optimum_ph": 7.1, "genome_size": 4046179.641, "gc_content": 41.7, "coding_genes": 3337.583, "rRNA16S_genes": 3.0, "tRNA_genes": 54.5, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 0.0, "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": 0.0, "coccus_cell_shape": 1.0, "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__Methanosarcinia", "o__Methanosarcinales", "f__Methanosarcinaceae", "g__Methanosarcina", "s__Methanosarcina mazei" ], "_genome_taxon": [ "Methanosarcina", "mazei", "d__Archaea", "p__Halobacteriota", "c__Methanosarcinia", "o__Methanosarcinales", "f__Methanosarcinaceae", "g__Methanosarcina", "s__Methanosarcina mazei", "Archaea", "Halobacteriota", "Methanosarcinia", "Methanosarcinales", "Methanosarcinaceae", "Methanosarcina", "Methanosarcina", "mazei" ], "_meo": [ { "id": "MEO_0000035", "label": "waste water" }, { "id": "MEO_0000014", "label": "activated sludge" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }