{ "type": "genome", "identifier": "GCF_011046895.1", "organism": "Rhizobium rhizoryzae", "title": "Rhizobium rhizoryzae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Kyungpook National University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_011046895.1", "bioproject": "PRJNA224116", "biosample": "SAMN14167853", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "451876", "species_taxid": "451876", "organism_name": "Rhizobium rhizoryzae", "infraspecific_name": "strain=DSM 29514", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/03/02", "asm_name": "ASM1104689v1", "asm_submitter": "Kyungpook National University", "gbrs_paired_asm": "GCA_011046895.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/011/046/895/GCF_011046895.1_ASM1104689v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4984090", "genome_size_ungapped": "4984090", "gc_percent": "58.000000", "replicon_count": "6", "scaffold_count": "6", "contig_count": "6", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_011046895.1-RS_2024_05_05", "annotation_date": "2024-05-05", "total_gene_count": "4660", "protein_coding_gene_count": "4532", "non_coding_gene_count": "78", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-03-02", "dateModified": "2020-03-02", "datePublished": "2020-03-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhizobium rhizoryzae" ], "sample_taxid": [ "451876" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea" ], "sample_host_location_id": [], "data_size": "1.405 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)": "4984090", "Number of Sequences": "6", "Longest Sequences (bp)": "3375736", "N50 (bp)": "3375736", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "58.0", "Number of CDSs": "4665", "Average Protein Length": "315.3", "Coding Ratio (%)": "88.5", "Number of rRNAs": "15", "Number of tRNAs": "59", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhizobium rhizoryzae", "strain": "strain=DSM 29514", "accession": "GCA_011046895.1", "taxid": 451876, "species_taxid": 451876, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1657, "total_fragments": 1659, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhizobium rhizoryzae", "strain": "strain=DSM 29514", "accession": "GCA_014196605.1", "taxid": 451876, "species_taxid": 451876, "relation_to_type": "type", "validated": true, "ani": 99.9953, "matched_fragments": 1624, "total_fragments": 1659, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhizobium pseudoryzae", "strain": "strain=DSM 19479", "accession": "GCA_011046245.1", "taxid": 379684, "species_taxid": 379684, "relation_to_type": "type", "validated": true, "ani": 80.4601, "matched_fragments": 797, "total_fragments": 1659, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agrobacterium larrymoorei", "strain": "strain=CFBP5473", "accession": "GCA_005145045.1", "taxid": 160699, "species_taxid": 160699, "relation_to_type": "type", "validated": true, "ani": 78.5891, "matched_fragments": 442, "total_fragments": 1659, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neorhizobium vignae", "strain": "strain=CCBAU 05176", "accession": "GCA_000732195.1", "taxid": 690585, "species_taxid": 690585, "relation_to_type": "type", "validated": true, "ani": 78.5698, "matched_fragments": 536, "total_fragments": 1659, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudorhizobium flavum", "strain": "strain=YW14", "accession": "GCA_902502825.2", "taxid": 1335061, "species_taxid": 1335061, "relation_to_type": "type", "validated": true, "ani": 78.549, "matched_fragments": 397, "total_fragments": 1659, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ciceribacter thiooxidans", "strain": "strain=F43B", "accession": "GCA_014126615.1", "taxid": 1969821, "species_taxid": 1969821, "relation_to_type": "type", "validated": true, "ani": 78.5076, "matched_fragments": 367, "total_fragments": 1659, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium daejeonense", "strain": "strain=L61", "accession": "GCA_014280875.1", "taxid": 240521, "species_taxid": 240521, "relation_to_type": "type", "validated": true, "ani": 78.5032, "matched_fragments": 425, "total_fragments": 1659, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella zoogloeoides", "strain": "strain=ATCC 19623", "accession": "GCA_020883495.1", "taxid": 352475, "species_taxid": 352475, "relation_to_type": "type", "validated": true, "ani": 78.4569, "matched_fragments": 411, "total_fragments": 1659, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudorhizobium flavum", "strain": "strain=YW14", "accession": "GCA_002000045.1", "taxid": 1335061, "species_taxid": 1335061, "relation_to_type": "type", "validated": true, "ani": 78.4267, "matched_fragments": 394, "total_fragments": 1659, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ciceribacter lividus", "strain": "strain=DSM 25528", "accession": "GCA_003337715.1", "taxid": 1197950, "species_taxid": 1197950, "relation_to_type": "type", "validated": true, "ani": 78.4209, "matched_fragments": 367, "total_fragments": 1659, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neorhizobium alkalisoli", "strain": "strain=DSM 21826", "accession": "GCA_002968635.1", "taxid": 528178, "species_taxid": 528178, "relation_to_type": "type", "validated": true, "ani": 78.3155, "matched_fragments": 486, "total_fragments": 1659, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agrobacterium larrymoorei", "strain": "strain=ATCC 51759", "accession": "GCA_000518585.1", "taxid": 160699, "species_taxid": 160699, "relation_to_type": "type", "validated": true, "ani": 78.2836, "matched_fragments": 433, "total_fragments": 1659, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium wenxiniae", "strain": "strain=CGMCC 1.15279", "accession": "GCA_014641515.1", "taxid": 1737357, "species_taxid": 1737357, "relation_to_type": "type", "validated": true, "ani": 78.263, "matched_fragments": 518, "total_fragments": 1659, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neorhizobium lilium", "strain": "strain=24NR", "accession": "GCA_004053875.1", "taxid": 2503024, "species_taxid": 2503024, "relation_to_type": "type", "validated": true, "ani": 78.2446, "matched_fragments": 452, "total_fragments": 1659, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agrobacterium leguminum", "strain": "strain=MOPV5", "accession": "GCA_015704895.1", "taxid": 2792015, "species_taxid": 2792015, "relation_to_type": "type", "validated": true, "ani": 78.2177, "matched_fragments": 474, "total_fragments": 1659, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium pusense", "strain": "strain=LMG 25623", "accession": "GCA_900102105.1", "taxid": 648995, "species_taxid": 648995, "relation_to_type": "type", "validated": true, "ani": 78.2088, "matched_fragments": 433, "total_fragments": 1659, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium petrolearium", "strain": "strain=DSM 26482", "accession": "GCA_017873175.1", "taxid": 515361, "species_taxid": 515361, "relation_to_type": "type", "validated": true, "ani": 78.1083, "matched_fragments": 520, "total_fragments": 1659, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella curvata", "strain": "strain=C3", "accession": "GCA_022899935.1", "taxid": 1817964, "species_taxid": 1817964, "relation_to_type": "type", "validated": true, "ani": 78.0647, "matched_fragments": 399, "total_fragments": 1659, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium skierniewicense", "strain": "strain=Ch11", "accession": "GCA_023757665.1", "taxid": 984260, "species_taxid": 984260, "relation_to_type": "type", "validated": true, "ani": 77.9561, "matched_fragments": 369, "total_fragments": 1659, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_011046895.1", "gtdb_species": "s__Rhizobium_A rhizoryzae", "ani": 100.0, "matched_fragments": 1657, "total_fragments": 1659, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.45", "min_intra_species_ani": "98.91", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_005222835.1", "gtdb_species": "s__Rhizobium_A sp005222835", "ani": 90.3061, "matched_fragments": 1319, "total_fragments": 1659, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A", "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_011046245.1", "gtdb_species": "s__Rhizobium_A pseudoryzae", "ani": 80.4193, "matched_fragments": 796, "total_fragments": 1659, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A", "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_007004135.1", "gtdb_species": "s__Rhizobium_A straminoryzae", "ani": 80.2738, "matched_fragments": 736, "total_fragments": 1659, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.62", "min_intra_species_ani": "98.62", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_018760785.1", "gtdb_species": "s__Rhizobium_A sp018760785", "ani": 80.2583, "matched_fragments": 806, "total_fragments": 1659, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A", "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_017877135.1", "gtdb_species": "s__Rhizobium_A galegae_A", "ani": 79.7945, "matched_fragments": 714, "total_fragments": 1659, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A", "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_005222845.1", "gtdb_species": "s__Rhizobium_A sp005222845", "ani": 79.3936, "matched_fragments": 718, "total_fragments": 1659, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A", "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_900466005.1", "gtdb_species": "s__Allorhizobium sp900466005", "ani": 78.3133, "matched_fragments": 372, "total_fragments": 1659, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.03", "min_intra_species_ani": "99.00", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001429725.1", "gtdb_species": "s__Rhizobium sp001429725", "ani": 78.0872, "matched_fragments": 377, "total_fragments": 1659, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "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_002307905.1", "gtdb_species": "s__Allorhizobium sp002307905", "ani": 77.8699, "matched_fragments": 314, "total_fragments": 1659, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "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": -0.23, "cell_length": 0.207, "doubling_h": 0.225, "growth_tmp": 30.0, "optimum_tmp": 28.423, "optimum_ph": 6.983, "genome_size": 4862048.0, "gc_content": 60.147, "coding_genes": 6587.615, "rRNA16S_genes": 3.0, "tRNA_genes": 51.725, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.793, "range_salinity": null, "facultative_respiration": 0.05, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.95, "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": [ "Rhizobium", "rhizoryzae" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }