{ "type": "genome", "identifier": "GCF_000427365.1", "organism": "Rikenella microfusus DSM 15922", "title": "Rikenella microfusus DSM 15922", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000427365.1", "bioproject": "PRJNA224116", "biosample": "SAMN02441234", "wgs_master": "ATXW00000000.1", "refseq_category": "reference genome", "taxid": "880526", "species_taxid": "28139", "organism_name": "Rikenella microfusus DSM 15922", "infraspecific_name": "strain=DSM 15922", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/07/15", "asm_name": "ASM42736v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000427365.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/427/365/GCF_000427365.1_ASM42736v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2880076", "genome_size_ungapped": "2879976", "gc_percent": "57.000000", "replicon_count": "0", "scaffold_count": "2", "contig_count": "3", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000427365.1-RS_2024_03_12", "annotation_date": "2024-03-12", "total_gene_count": "2309", "protein_coding_gene_count": "2234", "non_coding_gene_count": "58", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-07-15", "dateModified": "2013-07-15", "datePublished": "2013-07-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Rikenella microfusus DSM 15922" ], "sample_taxid": [ "880526" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan" ], "sample_host_location_id": [], "data_size": "0.809 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "2880076", "Number of Sequences": "2", "Longest Sequences (bp)": "2693782", "N50 (bp)": "2693782", "Gap Ratio (%)": "0.003472", "GCcontent (%)": "57.0", "Number of CDSs": "2271", "Average Protein Length": "345.1", "Coding Ratio (%)": "81.6", "Number of rRNAs": "8", "Number of tRNAs": "47", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rikenella microfusus", "strain": "strain=DSM 15922", "accession": "GCA_000427365.1", "taxid": 28139, "species_taxid": 28139, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 959, "total_fragments": 959, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rikenella microfusus", "strain": "strain=NCTC11190", "accession": "GCA_900455755.1", "taxid": 28139, "species_taxid": 28139, "relation_to_type": "type", "validated": true, "ani": 99.9946, "matched_fragments": 958, "total_fragments": 959, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Alistipes onderdonkii", "strain": "strain=DSM 19147", "accession": "GCA_025145285.1", "taxid": 328813, "species_taxid": 328813, "relation_to_type": "type", "validated": true, "ani": 80.482, "matched_fragments": 113, "total_fragments": 959, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alistipes communis", "strain": "strain=5CBH24", "accession": "GCA_006542665.1", "taxid": 2585118, "species_taxid": 2585118, "relation_to_type": "type", "validated": true, "ani": 80.3915, "matched_fragments": 109, "total_fragments": 959, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gallalistipes aquisgranensis", "strain": "strain=DSM 108975", "accession": "GCA_014982715.1", "taxid": 2779358, "species_taxid": 2779358, "relation_to_type": "type", "validated": true, "ani": 79.1995, "matched_fragments": 124, "total_fragments": 959, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alistipes shahii", "strain": "strain=WAL 8301", "accession": "GCA_025145845.1", "taxid": 328814, "species_taxid": 328814, "relation_to_type": "suspected-type", "validated": true, "ani": 78.8204, "matched_fragments": 112, "total_fragments": 959, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alistipes shahii", "strain": "strain=WAL 8301", "accession": "GCA_000210575.1", "taxid": 328814, "species_taxid": 328814, "relation_to_type": "suspected-type", "validated": true, "ani": 78.7427, "matched_fragments": 109, "total_fragments": 959, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alistipes ihumii", "strain": "strain=AP11", "accession": "GCA_025144665.1", "taxid": 1470347, "species_taxid": 1470347, "relation_to_type": "type", "validated": true, "ani": 77.4327, "matched_fragments": 101, "total_fragments": 959, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alistipes indistinctus", "strain": "strain=YIT 12060", "accession": "GCA_000231275.1", "taxid": 626932, "species_taxid": 626932, "relation_to_type": "type", "validated": true, "ani": 77.2109, "matched_fragments": 100, "total_fragments": 959, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alistipes megaguti", "strain": "strain=Marseille-P5997", "accession": "GCA_900604385.1", "taxid": 2364787, "species_taxid": 2364787, "relation_to_type": "type", "validated": true, "ani": 77.2101, "matched_fragments": 71, "total_fragments": 959, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alistipes indistinctus", "strain": "strain=YIT 12060", "accession": "GCA_025144995.1", "taxid": 626932, "species_taxid": 626932, "relation_to_type": "type", "validated": true, "ani": 77.154, "matched_fragments": 101, "total_fragments": 959, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alistipes ihumii", "strain": "strain=AP11", "accession": "GCA_000321205.1", "taxid": 1470347, "species_taxid": 1470347, "relation_to_type": "type", "validated": true, "ani": 77.0446, "matched_fragments": 99, "total_fragments": 959, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000427365.1", "gtdb_species": "s__Rikenella microfusus", "ani": 100.0, "matched_fragments": 959, "total_fragments": 959, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Rikenella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_900104655.1", "gtdb_species": "s__Rikenella massiliensis", "ani": 80.2034, "matched_fragments": 476, "total_fragments": 959, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Rikenella", "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_009557455.1", "gtdb_species": "s__Alistipes_A pullistercoris", "ani": 79.4474, "matched_fragments": 117, "total_fragments": 959, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.39", "min_intra_species_ani": "98.63", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.90", "num_clustered_genomes": 13, "status": "-" }, { "accession": "GCA_910577125.1", "gtdb_species": "s__Rikenella sp910577125", "ani": 79.1669, "matched_fragments": 356, "total_fragments": 959, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Rikenella", "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_910579375.1", "gtdb_species": "s__Rikenella sp910579375", "ani": 79.0841, "matched_fragments": 364, "total_fragments": 959, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Rikenella", "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_019113395.1", "gtdb_species": "s__Rikenella faecigallinarum", "ani": 78.5543, "matched_fragments": 308, "total_fragments": 959, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Rikenella", "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_910577885.1", "gtdb_species": "s__Rikenella sp910577885", "ani": 78.1948, "matched_fragments": 297, "total_fragments": 959, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Rikenella", "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_000321205.1", "gtdb_species": "s__Alistipes_A ihumii", "ani": 77.0198, "matched_fragments": 100, "total_fragments": 959, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.03", "min_intra_species_ani": "98.23", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.93", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCA_905214725.1", "gtdb_species": "s__Alistipes sp905214725", "ani": 76.9387, "matched_fragments": 54, "total_fragments": 959, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes", "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_019115605.1", "gtdb_species": "s__Alistipes faecigallinarum", "ani": 76.8781, "matched_fragments": 55, "total_fragments": 959, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes", "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_019119615.1", "gtdb_species": "s__Alistipes stercoravium", "ani": 76.4478, "matched_fragments": 56, "total_fragments": 959, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.09", "min_intra_species_ani": "99.09", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": null, "optimum_ph": null, "genome_size": 2880076.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "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": [ "Rikenella", "microfusus", "DSM", "15922" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }