{ "type": "genome", "identifier": "GCF_008802355.1", "organism": "Oryzomonas sagensis", "title": "Oryzomonas sagensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "The University of Tokyo", "publication": [ {} ], "properties": { "assembly_accession": "GCF_008802355.1", "bioproject": "PRJNA224116", "biosample": "SAMN12811330", "wgs_master": "VZRA00000000.1", "refseq_category": "reference genome", "taxid": "2603857", "species_taxid": "2603857", "organism_name": "Oryzomonas sagensis", "infraspecific_name": "strain=Red100", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/10/01", "asm_name": "ASM880235v1", "asm_submitter": "The University of Tokyo", "gbrs_paired_asm": "GCA_008802355.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/008/802/355/GCF_008802355.1_ASM880235v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3609742", "genome_size_ungapped": "3609722", "gc_percent": "59.500000", "replicon_count": "0", "scaffold_count": "18", "contig_count": "18", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_008802355.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "3420", "protein_coding_gene_count": "3342", "non_coding_gene_count": "58", "pubmed_id": "32349406" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-10-01", "dateModified": "2019-10-01", "datePublished": "2019-10-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Oryzomonas sagensis" ], "sample_taxid": [ "2603857" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan: Kanzaki" ], "sample_host_location_id": [], "data_size": "1.017 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)": "3609742", "Number of Sequences": "18", "Longest Sequences (bp)": "1701635", "N50 (bp)": "672663", "Gap Ratio (%)": "0.000914", "GCcontent (%)": "59.7", "Number of CDSs": "3386", "Average Protein Length": "312.8", "Coding Ratio (%)": "88.0", "Number of rRNAs": "3", "Number of tRNAs": "52", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Oryzomonas sagensis", "strain": "strain=Red100", "accession": "GCA_008802355.1", "taxid": 2603857, "species_taxid": 2603857, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1198, "total_fragments": 1198, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Oryzomonas rubra", "strain": "strain=Red88", "accession": "GCA_008369015.1", "taxid": 2509454, "species_taxid": 2509454, "relation_to_type": "type", "validated": true, "ani": 95.1331, "matched_fragments": 1029, "total_fragments": 1198, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Oryzomonas japonica", "strain": "strain=Red96", "accession": "GCA_008802365.1", "taxid": 2603858, "species_taxid": 2603858, "relation_to_type": "type", "validated": true, "ani": 94.6167, "matched_fragments": 1047, "total_fragments": 1198, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pelobacter propionicus", "strain": "strain=DSM 2379", "accession": "GCA_000015045.1", "taxid": 29543, "species_taxid": 29543, "relation_to_type": "type", "validated": true, "ani": 79.0957, "matched_fragments": 382, "total_fragments": 1198, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Geobacter argillaceus", "strain": "strain=ATCC BAA-1139", "accession": "GCA_007830735.1", "taxid": 345631, "species_taxid": 345631, "relation_to_type": "type", "validated": true, "ani": 78.2575, "matched_fragments": 288, "total_fragments": 1198, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Geomonas silvestris", "strain": "strain=Red330", "accession": "GCA_014193515.1", "taxid": 2740184, "species_taxid": 2740184, "relation_to_type": "type", "validated": true, "ani": 77.5659, "matched_fragments": 309, "total_fragments": 1198, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrifermentans pelophilum", "strain": "strain=DSM 12255", "accession": "GCA_018476885.1", "taxid": 60036, "species_taxid": 60036, "relation_to_type": "type", "validated": true, "ani": 77.0641, "matched_fragments": 159, "total_fragments": 1198, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Geobacter chapellei", "strain": "strain=DSM 13688", "accession": "GCA_018531195.1", "taxid": 44671, "species_taxid": 44671, "relation_to_type": "type", "validated": true, "ani": 77.0539, "matched_fragments": 199, "total_fragments": 1198, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rubrivivax gelatinosus", "strain": "strain=DSM 1709", "accession": "GCA_016583525.1", "taxid": 28068, "species_taxid": 28068, "relation_to_type": "suspected-type", "validated": true, "ani": 76.2668, "matched_fragments": 53, "total_fragments": 1198, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rubrivivax gelatinosus", "strain": "strain=DSM 1709", "accession": "GCA_004340905.1", "taxid": 28068, "species_taxid": 28068, "relation_to_type": "suspected-type", "validated": true, "ani": 76.1994, "matched_fragments": 52, "total_fragments": 1198, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_008802355.1", "gtdb_species": "s__Oryzomonas sagensis", "ani": 100.0, "matched_fragments": 1198, "total_fragments": 1198, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Oryzomonas", "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_008802365.1", "gtdb_species": "s__Oryzomonas japonica", "ani": 94.6167, "matched_fragments": 1047, "total_fragments": 1198, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Oryzomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.07", "min_intra_species_ani": "96.07", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_008330225.1", "gtdb_species": "s__Oryzomonas sp008330225", "ani": 89.3446, "matched_fragments": 986, "total_fragments": 1198, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Oryzomonas", "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_003151775.1", "gtdb_species": "s__Oryzomonas sp003151775", "ani": 85.199, "matched_fragments": 567, "total_fragments": 1198, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Oryzomonas", "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_016182975.1", "gtdb_species": "s__JACPFJ01 sp016182975", "ani": 80.5879, "matched_fragments": 368, "total_fragments": 1198, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACPFJ01", "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_015688915.1", "gtdb_species": "s__JACPFJ01 sp015688915", "ani": 80.1147, "matched_fragments": 438, "total_fragments": 1198, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACPFJ01", "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_002298925.1", "gtdb_species": "s__Pelotalea sp002298925", "ani": 79.1287, "matched_fragments": 388, "total_fragments": 1198, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Pelotalea", "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_000015045.1", "gtdb_species": "s__Pseudopelobacter propionicus", "ani": 79.1012, "matched_fragments": 381, "total_fragments": 1198, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Pseudopelobacter", "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_016650295.1", "gtdb_species": "s__CAIPTY01 sp016650295", "ani": 78.8213, "matched_fragments": 376, "total_fragments": 1198, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__CAIPTY01", "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_016865365.1", "gtdb_species": "s__Pelotalea sp012556225", "ani": 78.7831, "matched_fragments": 436, "total_fragments": 1198, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Pelotalea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Oryzomonas", "sagensis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }