{ "type": "genome", "identifier": "GCF_024806875.1", "organism": "Bradyrhizobium betae", "title": "Bradyrhizobium betae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_024806875.1", "bioproject": "PRJNA224116", "biosample": "SAMN12025190", "wgs_master": "JANTYR000000000.1", "refseq_category": "na", "taxid": "244734", "species_taxid": "244734", "organism_name": "Bradyrhizobium betae", "infraspecific_name": "strain=CECT 5829", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/08/31", "asm_name": "ASM2480687v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_024806875.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/024/806/875/GCF_024806875.1_ASM2480687v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7334789", "genome_size_ungapped": "7334789", "gc_percent": "64.500000", "replicon_count": "0", "scaffold_count": "28", "contig_count": "28", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_024806875.1-RS_2024_09_16", "annotation_date": "2024-09-16", "total_gene_count": "7062", "protein_coding_gene_count": "6892", "non_coding_gene_count": "54", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-08-31", "dateModified": "2022-08-31", "datePublished": "2022-08-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Bradyrhizobium betae" ], "sample_taxid": [ "244734" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "2.024 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)": "7334789", "Number of Sequences": "28", "Longest Sequences (bp)": "1377641", "N50 (bp)": "565778", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "64.4", "Number of CDSs": "7030", "Average Protein Length": "304.0", "Coding Ratio (%)": "87.4", "Number of rRNAs": "3", "Number of tRNAs": "51", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bradyrhizobium betae", "strain": "strain=CECT 5829", "accession": "GCA_024806875.1", "taxid": 244734, "species_taxid": 244734, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2430, "total_fragments": 2431, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bradyrhizobium betae", "strain": "strain=PL7HG1", "accession": "GCA_008932115.1", "taxid": 244734, "species_taxid": 244734, "relation_to_type": "type", "validated": true, "ani": 99.9981, "matched_fragments": 2431, "total_fragments": 2431, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bradyrhizobium cosmicum", "strain": "strain=58S1", "accession": "GCA_007290395.1", "taxid": 1404864, "species_taxid": 1404864, "relation_to_type": "type", "validated": true, "ani": 94.11, "matched_fragments": 1962, "total_fragments": 2431, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium japonicum", "strain": "strain=NBRC 14783", "accession": "GCA_006539645.1", "taxid": 375, "species_taxid": 375, "relation_to_type": "type", "validated": true, "ani": 89.6898, "matched_fragments": 1816, "total_fragments": 2431, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium diazoefficiens", "strain": "strain=USDA 110", "accession": "GCA_001642675.1", "taxid": 1355477, "species_taxid": 1355477, "relation_to_type": "type", "validated": true, "ani": 89.6836, "matched_fragments": 1838, "total_fragments": 2431, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium japonicum", "strain": "strain=USDA 6", "accession": "GCA_000472985.1", "taxid": 375, "species_taxid": 375, "relation_to_type": "type", "validated": true, "ani": 89.6652, "matched_fragments": 1838, "total_fragments": 2431, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium diazoefficiens", "strain": "strain=USDA110", "accession": "GCA_000011365.1", "taxid": 1355477, "species_taxid": 1355477, "relation_to_type": "type", "validated": true, "ani": 89.5937, "matched_fragments": 1841, "total_fragments": 2431, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium niftali", "strain": "strain=CNPSo 3448", "accession": "GCA_004571025.1", "taxid": 2560055, "species_taxid": 2560055, "relation_to_type": "type", "validated": true, "ani": 89.479, "matched_fragments": 1784, "total_fragments": 2431, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium symbiodeficiens", "strain": "strain=85S1MB", "accession": "GCA_002266465.2", "taxid": 1404367, "species_taxid": 1404367, "relation_to_type": "type", "validated": true, "ani": 89.018, "matched_fragments": 1779, "total_fragments": 2431, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium amphicarpaeae", "strain": "strain=39S1MB", "accession": "GCA_002266435.2", "taxid": 1404768, "species_taxid": 1404768, "relation_to_type": "type", "validated": true, "ani": 88.9195, "matched_fragments": 1841, "total_fragments": 2431, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium cajani", "strain": "strain=1010", "accession": "GCA_009759665.1", "taxid": 1928661, "species_taxid": 1928661, "relation_to_type": "type", "validated": true, "ani": 88.8693, "matched_fragments": 1761, "total_fragments": 2431, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium nitroreducens", "strain": "strain=TSA1", "accession": "GCA_002776695.1", "taxid": 709803, "species_taxid": 709803, "relation_to_type": "type", "validated": true, "ani": 88.7661, "matched_fragments": 1839, "total_fragments": 2431, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium daqingense", "strain": "strain=CCBAU 15774", "accession": "GCA_021044685.1", "taxid": 993502, "species_taxid": 993502, "relation_to_type": "type", "validated": true, "ani": 87.9921, "matched_fragments": 1699, "total_fragments": 2431, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium viridifuturi", "strain": "strain=SEMIA 690", "accession": "GCA_001238275.1", "taxid": 1654716, "species_taxid": 1654716, "relation_to_type": "type", "validated": true, "ani": 82.9581, "matched_fragments": 1399, "total_fragments": 2431, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium acaciae", "strain": "strain=10BB", "accession": "GCA_020889785.1", "taxid": 2683706, "species_taxid": 2683706, "relation_to_type": "type", "validated": true, "ani": 82.8045, "matched_fragments": 1322, "total_fragments": 2431, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ancylobacter oerskovii", "strain": "strain=CCM 7435", "accession": "GCA_018390555.1", "taxid": 459519, "species_taxid": 459519, "relation_to_type": "type", "validated": true, "ani": 78.0446, "matched_fragments": 514, "total_fragments": 2431, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium helmanticense", "strain": "strain=CSLC115N", "accession": "GCA_003034915.1", "taxid": 1776423, "species_taxid": 1776423, "relation_to_type": "type", "validated": true, "ani": 77.2091, "matched_fragments": 362, "total_fragments": 2431, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Fulvimarina pelagi", "strain": "strain=HTCC2506", "accession": "GCA_000153705.1", "taxid": 217511, "species_taxid": 217511, "relation_to_type": "type", "validated": true, "ani": 76.2602, "matched_fragments": 153, "total_fragments": 2431, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Fulvimarina pelagi", "strain": "strain=DSM 15513", "accession": "GCA_001463845.1", "taxid": 217511, "species_taxid": 217511, "relation_to_type": "type", "validated": true, "ani": 76.1886, "matched_fragments": 151, "total_fragments": 2431, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_008932115.1", "gtdb_species": "s__Bradyrhizobium betae", "ani": 99.9981, "matched_fragments": 2431, "total_fragments": 2431, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "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_007290395.1", "gtdb_species": "s__Bradyrhizobium cosmicum", "ani": 94.1, "matched_fragments": 1963, "total_fragments": 2431, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.90", "min_intra_species_ani": "97.90", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_018129965.1", "gtdb_species": "s__Bradyrhizobium diazoefficiens_A", "ani": 90.4032, "matched_fragments": 1796, "total_fragments": 2431, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_018130785.1", "gtdb_species": "s__Bradyrhizobium liaoningense_A", "ani": 89.7196, "matched_fragments": 1810, "total_fragments": 2431, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "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_011516635.3", "gtdb_species": "s__Bradyrhizobium sp011516635", "ani": 89.6844, "matched_fragments": 1841, "total_fragments": 2431, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.65", "min_intra_species_ani": "95.57", "mean_intra_species_af": "0.79", "min_intra_species_af": "0.75", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCF_000282615.1", "gtdb_species": "s__Bradyrhizobium sp000282615", "ani": 89.6785, "matched_fragments": 1729, "total_fragments": 2431, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "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_000011365.1", "gtdb_species": "s__Bradyrhizobium diazoefficiens", "ani": 89.5979, "matched_fragments": 1840, "total_fragments": 2431, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.15", "min_intra_species_ani": "98.13", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.84", "num_clustered_genomes": 23, "status": "-" }, { "accession": "GCF_004571025.1", "gtdb_species": "s__Bradyrhizobium niftali", "ani": 89.4905, "matched_fragments": 1783, "total_fragments": 2431, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.00", "min_intra_species_ani": "95.49", "mean_intra_species_af": "0.80", "min_intra_species_af": "0.80", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_018129995.1", "gtdb_species": "s__Bradyrhizobium japonicum_G", "ani": 89.3664, "matched_fragments": 1766, "total_fragments": 2431, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "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_002266465.2", "gtdb_species": "s__Bradyrhizobium symbiodeficiens", "ani": 89.0031, "matched_fragments": 1781, "total_fragments": 2431, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.63", "min_intra_species_ani": "98.60", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_002266435.2", "gtdb_species": "s__Bradyrhizobium amphicarpaeae", "ani": 88.9155, "matched_fragments": 1842, "total_fragments": 2431, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "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_900114915.1", "gtdb_species": "s__Bradyrhizobium sp900114915", "ani": 88.8192, "matched_fragments": 1779, "total_fragments": 2431, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.76", "min_intra_species_ani": "97.31", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.88", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_002776695.1", "gtdb_species": "s__Bradyrhizobium nitroreducens", "ani": 88.7958, "matched_fragments": 1835, "total_fragments": 2431, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.68", "min_intra_species_ani": "98.68", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000938255.1", "gtdb_species": "s__Bradyrhizobium sp000938255", "ani": 88.5331, "matched_fragments": 1752, "total_fragments": 2431, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.09", "min_intra_species_ani": "98.09", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000617845.2", "gtdb_species": "s__Bradyrhizobium sp000617845", "ani": 88.2355, "matched_fragments": 1718, "total_fragments": 2431, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "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_018131185.1", "gtdb_species": "s__Bradyrhizobium diazoefficiens_G", "ani": 88.1655, "matched_fragments": 1725, "total_fragments": 2431, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "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_016612535.1", "gtdb_species": "s__Bradyrhizobium diazoefficiens_C", "ani": 88.0767, "matched_fragments": 1688, "total_fragments": 2431, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "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_018129685.1", "gtdb_species": "s__Bradyrhizobium manausense_D", "ani": 87.7701, "matched_fragments": 1760, "total_fragments": 2431, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "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_016839165.1", "gtdb_species": "s__Bradyrhizobium sp003020075", "ani": 83.0808, "matched_fragments": 1398, "total_fragments": 2431, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.93", "min_intra_species_ani": "99.86", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 16, "status": "-" }, { "accession": "GCF_000314735.2", "gtdb_species": "s__Afipia felis", "ani": 79.9344, "matched_fragments": 588, "total_fragments": 2431, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.60", "min_intra_species_ani": "95.79", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.87", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_017308135.1", "gtdb_species": "s__Tagaea sp017308135", "ani": 77.5282, "matched_fragments": 297, "total_fragments": 2431, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__Tagaea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.31", "min_intra_species_ani": "97.31", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.132, "cell_length": 0.272, "doubling_h": 1.189, "growth_tmp": 28.0, "optimum_tmp": 28.0, "optimum_ph": 7.25, "genome_size": 8573557.767, "gc_content": 63.651, "coding_genes": 7833.366, "rRNA16S_genes": 1.416, "tRNA_genes": 52.57, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.071, "aerobic_respiration": 0.928, "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": [ "Bradyrhizobium", "betae" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }