{ "type": "genome", "identifier": "GCF_001639265.1", "organism": "Methanobrevibacter filiformis", "title": "Methanobrevibacter filiformis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Goettingen Genomics Laboratory", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001639265.1", "bioproject": "PRJNA224116", "biosample": "SAMN04867340", "wgs_master": "LWMT00000000.1", "refseq_category": "reference genome", "taxid": "55758", "species_taxid": "55758", "organism_name": "Methanobrevibacter filiformis", "infraspecific_name": "strain=DSM 11501", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/04/29", "asm_name": "ASM163926v1", "asm_submitter": "Goettingen Genomics Laboratory", "gbrs_paired_asm": "GCA_001639265.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/639/265/GCF_001639265.1_ASM163926v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "archaea", "genome_size": "2606143", "genome_size_ungapped": "2606143", "gc_percent": "27.000000", "replicon_count": "0", "scaffold_count": "295", "contig_count": "295", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001639265.1-RS_2024_10_22", "annotation_date": "2024-10-22", "total_gene_count": "2057", "protein_coding_gene_count": "1964", "non_coding_gene_count": "43", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-04-29", "dateModified": "2016-04-29", "datePublished": "2016-04-29", "_annotation": { "sample_count": 1, "sample_organism": [ "Methanobrevibacter filiformis" ], "sample_taxid": [ "55758" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not collected" ], "sample_host_location_id": [], "data_size": "0.686 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 91.67, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "2606143", "Number of Sequences": "295", "Longest Sequences (bp)": "68572", "N50 (bp)": "17303", "Gap Ratio (%)": "0.000038", "GCcontent (%)": "27.0", "Number of CDSs": "1916", "Average Protein Length": "311.5", "Coding Ratio (%)": "68.7", "Number of rRNAs": "2", "Number of tRNAs": "30", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Methanobrevibacter filiformis", "strain": "strain=DSM 11501", "accession": "GCA_001639265.1", "taxid": 55758, "species_taxid": 55758, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 713, "total_fragments": 727, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Methanobrevibacter cuticularis", "strain": "strain=DSM 11139", "accession": "GCA_001639285.1", "taxid": 47311, "species_taxid": 47311, "relation_to_type": "type", "validated": true, "ani": 77.696, "matched_fragments": 238, "total_fragments": 727, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanobrevibacter curvatus", "strain": "strain=DSM 11111", "accession": "GCA_001639295.1", "taxid": 49547, "species_taxid": 49547, "relation_to_type": "type", "validated": true, "ani": 77.4343, "matched_fragments": 197, "total_fragments": 727, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanobrevibacter arboriphilus", "strain": "strain=DH1", "accession": "GCA_002072215.1", "taxid": 39441, "species_taxid": 39441, "relation_to_type": "type", "validated": true, "ani": 77.0549, "matched_fragments": 226, "total_fragments": 727, "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": 76.5114, "matched_fragments": 93, "total_fragments": 727, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanobrevibacter oralis", "strain": "strain=DSM 7256", "accession": "GCA_001639275.1", "taxid": 66851, "species_taxid": 66851, "relation_to_type": "type", "validated": true, "ani": 76.2839, "matched_fragments": 115, "total_fragments": 727, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanobrevibacter gottschalkii", "strain": "strain=DSM 11977", "accession": "GCA_003814835.1", "taxid": 190974, "species_taxid": 190974, "relation_to_type": "type", "validated": true, "ani": 76.2209, "matched_fragments": 91, "total_fragments": 727, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 91.67, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001639265.1", "gtdb_species": "s__Methanobrevibacter_D filiformis", "ani": 100.0, "matched_fragments": 713, "total_fragments": 727, "gtdb_taxonomy": "d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_D", "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": "GCF_001639285.1", "gtdb_species": "s__Methanobrevibacter_C cuticularis", "ani": 77.6702, "matched_fragments": 240, "total_fragments": 727, "gtdb_taxonomy": "d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_C", "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_001639295.1", "gtdb_species": "s__Methanobrevibacter_D curvatus", "ani": 77.447, "matched_fragments": 197, "total_fragments": 727, "gtdb_taxonomy": "d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_D", "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_002072215.1", "gtdb_species": "s__Methanobrevibacter_C arboriphilus", "ani": 77.009, "matched_fragments": 229, "total_fragments": 727, "gtdb_taxonomy": "d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_C", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.72", "min_intra_species_ani": "99.72", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000513315.1", "gtdb_species": "s__Methanobrevibacter_C arboriphilus_A", "ani": 76.9914, "matched_fragments": 217, "total_fragments": 727, "gtdb_taxonomy": "d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_C", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.28", "min_intra_species_ani": "97.35", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.82", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_009776495.1", "gtdb_species": "s__Methanobrevibacter_C sp009776495", "ani": 76.98, "matched_fragments": 106, "total_fragments": 727, "gtdb_taxonomy": "d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_C", "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_009784145.1", "gtdb_species": "s__Methanobrevibacter_C sp009784145", "ani": 76.7179, "matched_fragments": 131, "total_fragments": 727, "gtdb_taxonomy": "d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_C", "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_009777005.1", "gtdb_species": "s__Methanobrevibacter_C sp009777005", "ani": 76.6208, "matched_fragments": 188, "total_fragments": 727, "gtdb_taxonomy": "d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_C", "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": -0.639, "cell_length": 0.602, "doubling_h": 1.568, "growth_tmp": 30.0, "optimum_tmp": 30.0, "optimum_ph": 7.1, "genome_size": 2563611.0, "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": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Methanobrevibacter", "filiformis" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }