{ "type": "genome", "identifier": "GCF_021044685.1", "organism": "Bradyrhizobium daqingense", "title": "Bradyrhizobium daqingense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Agriculture and Agri-Food Canada", "publication": [ {} ], "properties": { "assembly_accession": "GCF_021044685.1", "bioproject": "PRJNA224116", "biosample": "SAMN23310456", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "993502", "species_taxid": "993502", "organism_name": "Bradyrhizobium daqingense", "infraspecific_name": "strain=CCBAU 15774", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/12/05", "asm_name": "ASM2104468v1", "asm_submitter": "Agriculture and Agri-Food Canada", "gbrs_paired_asm": "GCA_021044685.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/021/044/685/GCF_021044685.1_ASM2104468v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7998085", "genome_size_ungapped": "7998085", "gc_percent": "63.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_021044685.1-RS_2024_05_26", "annotation_date": "2024-05-26", "total_gene_count": "7592", "protein_coding_gene_count": "7300", "non_coding_gene_count": "56", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-12-05", "dateModified": "2021-12-05", "datePublished": "2021-12-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Bradyrhizobium daqingense" ], "sample_taxid": [ "993502" ], "sample_host_organism": [ "Glycine max" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Heilongjiang, Daqing" ], "sample_host_location_id": [], "data_size": "2.208 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)": "7998085", "Number of Sequences": "1", "Longest Sequences (bp)": "7998085", "N50 (bp)": "7998085", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "63.7", "Number of CDSs": "7629", "Average Protein Length": "296.2", "Coding Ratio (%)": "84.8", "Number of rRNAs": "3", "Number of tRNAs": "49", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bradyrhizobium daqingense", "strain": "strain=CCBAU 15774", "accession": "GCA_021044685.1", "taxid": 993502, "species_taxid": 993502, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2666, "total_fragments": 2666, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bradyrhizobium daqingense", "strain": "strain=CGMCC 1.10947", "accession": "GCA_007830205.1", "taxid": 993502, "species_taxid": 993502, "relation_to_type": "type", "validated": true, "ani": 99.9529, "matched_fragments": 2574, "total_fragments": 2666, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bradyrhizobium huanghuaihaiense", "strain": "strain=CGMCC 1.10948", "accession": "GCA_007830635.1", "taxid": 990078, "species_taxid": 990078, "relation_to_type": "type", "validated": true, "ani": 89.9442, "matched_fragments": 2099, "total_fragments": 2666, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium zhanjiangense", "strain": "strain=CCBAU 51778", "accession": "GCA_004114935.1", "taxid": 1325107, "species_taxid": 1325107, "relation_to_type": "type", "validated": true, "ani": 89.5422, "matched_fragments": 2013, "total_fragments": 2666, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium forestalis", "strain": "strain=INPA54B", "accession": "GCA_002795245.1", "taxid": 1419263, "species_taxid": 1419263, "relation_to_type": "type", "validated": true, "ani": 88.9682, "matched_fragments": 1983, "total_fragments": 2666, "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": 88.9223, "matched_fragments": 1943, "total_fragments": 2666, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium yuanmingense", "strain": "strain=CCBAU 10071", "accession": "GCA_900094575.1", "taxid": 108015, "species_taxid": 108015, "relation_to_type": "type", "validated": true, "ani": 88.7618, "matched_fragments": 2028, "total_fragments": 2666, "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": 88.6987, "matched_fragments": 1842, "total_fragments": 2666, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium stylosanthis", "strain": "strain=BR 446", "accession": "GCA_001641335.1", "taxid": 1803665, "species_taxid": 1803665, "relation_to_type": "type", "validated": true, "ani": 88.6978, "matched_fragments": 1894, "total_fragments": 2666, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium guangxiense", "strain": "strain=CCBAU 53363", "accession": "GCA_004114915.1", "taxid": 1325115, "species_taxid": 1325115, "relation_to_type": "type", "validated": true, "ani": 88.59, "matched_fragments": 1883, "total_fragments": 2666, "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": 88.4969, "matched_fragments": 1821, "total_fragments": 2666, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium arachidis", "strain": "strain=CCBAU 051107", "accession": "GCA_015291705.1", "taxid": 858423, "species_taxid": 858423, "relation_to_type": "type", "validated": true, "ani": 88.385, "matched_fragments": 2034, "total_fragments": 2666, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium arachidis", "strain": "strain=LMG 26795", "accession": "GCA_900116675.1", "taxid": 858423, "species_taxid": 858423, "relation_to_type": "type", "validated": true, "ani": 88.3829, "matched_fragments": 2023, "total_fragments": 2666, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium betae", "strain": "strain=CECT 5829", "accession": "GCA_024806875.1", "taxid": 244734, "species_taxid": 244734, "relation_to_type": "type", "validated": true, "ani": 88.0634, "matched_fragments": 1708, "total_fragments": 2666, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium quebecense", "strain": "strain=66S1MB, /ecotype=symbiovar septentrionalis", "accession": "GCA_013373795.3", "taxid": 2748629, "species_taxid": 2748629, "relation_to_type": "type", "validated": true, "ani": 82.69, "matched_fragments": 1479, "total_fragments": 2666, "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": 82.4916, "matched_fragments": 1397, "total_fragments": 2666, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_007830205.1", "gtdb_species": "s__Bradyrhizobium daqingense", "ani": 99.9529, "matched_fragments": 2574, "total_fragments": 2666, "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_000296215.2", "gtdb_species": "s__Bradyrhizobium sp000296215", "ani": 94.5636, "matched_fragments": 2093, "total_fragments": 2666, "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": "97.76", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_011602485.1", "gtdb_species": "s__Bradyrhizobium sp011602485", "ani": 91.1761, "matched_fragments": 2028, "total_fragments": 2666, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.68", "min_intra_species_ani": "97.67", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_004212635.1", "gtdb_species": "s__Bradyrhizobium sp004212635", "ani": 89.6505, "matched_fragments": 1858, "total_fragments": 2666, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.55", "min_intra_species_ani": "95.55", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_018130245.1", "gtdb_species": "s__Bradyrhizobium japonicum_F", "ani": 89.2238, "matched_fragments": 1869, "total_fragments": 2666, "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_018130825.1", "gtdb_species": "s__Bradyrhizobium liaoningense_B", "ani": 88.9913, "matched_fragments": 1887, "total_fragments": 2666, "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_000617845.2", "gtdb_species": "s__Bradyrhizobium sp000617845", "ani": 88.9506, "matched_fragments": 1890, "total_fragments": 2666, "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_013240495.1", "gtdb_species": "s__Bradyrhizobium sp013240495", "ani": 88.8465, "matched_fragments": 1983, "total_fragments": 2666, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.36", "min_intra_species_ani": "98.36", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_018130765.1", "gtdb_species": "s__Bradyrhizobium iriomotense_A", "ani": 88.7822, "matched_fragments": 1878, "total_fragments": 2666, "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_004216735.1", "gtdb_species": "s__Bradyrhizobium sp004216735", "ani": 88.6413, "matched_fragments": 1879, "total_fragments": 2666, "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_004571025.1", "gtdb_species": "s__Bradyrhizobium niftali", "ani": 88.6097, "matched_fragments": 1984, "total_fragments": 2666, "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_015291725.1", "gtdb_species": "s__Bradyrhizobium japonicum_D", "ani": 88.5764, "matched_fragments": 1999, "total_fragments": 2666, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.2113, "mean_intra_species_ani": "95.51", "min_intra_species_ani": "95.51", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004114915.1", "gtdb_species": "s__Bradyrhizobium guangxiense", "ani": 88.5723, "matched_fragments": 1887, "total_fragments": 2666, "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_002266435.2", "gtdb_species": "s__Bradyrhizobium amphicarpaeae", "ani": 88.5087, "matched_fragments": 1819, "total_fragments": 2666, "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_003837805.1", "gtdb_species": "s__Bradyrhizobium sp003837805", "ani": 88.4404, "matched_fragments": 1955, "total_fragments": 2666, "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_015291705.1", "gtdb_species": "s__Bradyrhizobium arachidis", "ani": 88.388, "matched_fragments": 2035, "total_fragments": 2666, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.87", "min_intra_species_ani": "98.47", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_018131015.1", "gtdb_species": "s__Bradyrhizobium diazoefficiens_B", "ani": 87.3764, "matched_fragments": 1675, "total_fragments": 2666, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.132, "cell_length": 0.272, "doubling_h": 1.189, "growth_tmp": 28.766, "optimum_tmp": 28.0, "optimum_ph": 7.0, "genome_size": 7889191.0, "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": 0.0, "aerobic_respiration": 1.0, "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": [ "Bradyrhizobium", "daqingense" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }