{ "type": "genome", "identifier": "GCA_024280975.1", "organism": "Methanosarcina sp.", "title": "Methanosarcina sp.", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "Center for Nuclear Energy in Agriculture - University of Sao Paulo", "publication": [ {} ], "properties": { "assembly_accession": "GCA_024280975.1", "bioproject": "PRJNA842732", "biosample": "SAMN28861739", "wgs_master": "JAMXLQ000000000.1", "refseq_category": "na", "taxid": "2213", "species_taxid": "2213", "organism_name": "Methanosarcina sp.", "infraspecific_name": "", "isolate": "Bin.035_Pasture", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/07/15", "asm_name": "ASM2428097v1", "submitter": "Center for Nuclear Energy in Agriculture - University of Sao Paulo", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/024/280/975/GCA_024280975.1_ASM2428097v1", "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": "2022-07-15", "dateModified": "2022-07-15", "datePublished": "2022-07-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Methanosarcina sp." ], "sample_taxid": [ "2213" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Brazil: Eastern Amazon" ], "sample_host_location_id": [], "data_size": "0.749 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 63.8, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2614668", "Number of Sequences": "335", "Longest Sequences (bp)": "60370", "N50 (bp)": "8975", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "39.9", "Number of CDSs": "2111", "Average Protein Length": "258.4", "Coding Ratio (%)": "62.6", "Number of rRNAs": "0", "Number of tRNAs": "40", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Methanosarcina barkeri", "strain": "strain=MS", "accession": "GCA_000970025.1", "taxid": 2208, "species_taxid": 2208, "relation_to_type": "type", "validated": true, "ani": 83.6538, "matched_fragments": 569, "total_fragments": 706, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanosarcina barkeri", "strain": "strain=JCM 10043", "accession": "GCA_001316305.1", "taxid": 2208, "species_taxid": 2208, "relation_to_type": "type", "validated": true, "ani": 83.4732, "matched_fragments": 554, "total_fragments": 706, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanosarcina spelaei", "strain": "strain=MC-15", "accession": "GCA_002287235.1", "taxid": 1036679, "species_taxid": 1036679, "relation_to_type": "type", "validated": true, "ani": 83.2936, "matched_fragments": 544, "total_fragments": 706, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanosarcina flavescens", "strain": "strain=E03.2", "accession": "GCA_001304615.2", "taxid": 1715806, "species_taxid": 1715806, "relation_to_type": "type", "validated": true, "ani": 81.6765, "matched_fragments": 473, "total_fragments": 706, "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": 81.3209, "matched_fragments": 473, "total_fragments": 706, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 63.8, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_002505485.1", "gtdb_species": "s__Methanosarcina sp002505485", "ani": 85.0838, "matched_fragments": 574, "total_fragments": 706, "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_000970305.1", "gtdb_species": "s__Methanosarcina barkeri_A", "ani": 83.3519, "matched_fragments": 570, "total_fragments": 706, "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": "GCA_002509325.1", "gtdb_species": "s__Methanosarcina sp002509325", "ani": 82.9349, "matched_fragments": 399, "total_fragments": 706, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.58", "min_intra_species_ani": "99.58", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_002499445.1", "gtdb_species": "s__Methanosarcina sp002499445", "ani": 82.1192, "matched_fragments": 461, "total_fragments": 706, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.41", "min_intra_species_ani": "96.88", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.88", "num_clustered_genomes": 16, "status": "-" }, { "accession": "GCF_001304615.2", "gtdb_species": "s__Methanosarcina flavescens", "ani": 81.6467, "matched_fragments": 475, "total_fragments": 706, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.75", "min_intra_species_ani": "99.75", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": 0.137, "cell_length": 0.137, "doubling_h": 1.127, "growth_tmp": 34.413, "optimum_tmp": 35.498, "optimum_ph": 7.03, "genome_size": 4436636.291, "gc_content": 40.988, "coding_genes": 3622.727, "rRNA16S_genes": 3.0, "tRNA_genes": 56.135, "gram_stain": 0.142, "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": 0.75, "thermophilic_range_tmp": 0.25, "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 sp024280975" ], "_genome_taxon": [ "Methanosarcina", "sp.", "d__Archaea", "p__Halobacteriota", "c__Methanosarcinia", "o__Methanosarcinales", "f__Methanosarcinaceae", "g__Methanosarcina", "s__Methanosarcina sp024280975", "Archaea", "Halobacteriota", "Methanosarcinia", "Methanosarcinales", "Methanosarcinaceae", "Methanosarcina", "Methanosarcina", "sp024280975" ], "_meo": [ { "id": "MEO_0000007", "label": "soil" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }