{ "type": "genome", "identifier": "GCF_020329495.1", "organism": "Bradyrhizobium australafricanum", "title": "Bradyrhizobium australafricanum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Empresa Brasileira de Pesquisa Agropecuaria", "publication": [ {} ], "properties": { "assembly_accession": "GCF_020329495.1", "bioproject": "PRJNA224116", "biosample": "SAMN18497705", "wgs_master": "JAGKJL000000000.1", "refseq_category": "reference genome", "taxid": "2821406", "species_taxid": "2821406", "organism_name": "Bradyrhizobium australafricanum", "infraspecific_name": "strain=WSM 4400", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/10/06", "asm_name": "ASM2032949v1", "asm_submitter": "Empresa Brasileira de Pesquisa Agropecuaria", "gbrs_paired_asm": "GCA_020329495.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/020/329/495/GCF_020329495.1_ASM2032949v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "9684669", "genome_size_ungapped": "9684669", "gc_percent": "63.500000", "replicon_count": "0", "scaffold_count": "221", "contig_count": "221", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_020329495.1-RS_2024_09_27", "annotation_date": "2024-09-27", "total_gene_count": "9365", "protein_coding_gene_count": "8963", "non_coding_gene_count": "61", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-10-06", "dateModified": "2021-10-06", "datePublished": "2021-10-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Bradyrhizobium australafricanum" ], "sample_taxid": [ "2821406" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Africa: Amathole District" ], "sample_host_location_id": [], "data_size": "2.697 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)": "9684669", "Number of Sequences": "221", "Longest Sequences (bp)": "399449", "N50 (bp)": "125914", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "63.5", "Number of CDSs": "9153", "Average Protein Length": "289.0", "Coding Ratio (%)": "81.9", "Number of rRNAs": "3", "Number of tRNAs": "55", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bradyrhizobium pachyrhizi", "strain": "strain=PAC 48", "accession": "GCA_001189245.1", "taxid": 280333, "species_taxid": 280333, "relation_to_type": "type", "validated": true, "ani": 95.3332, "matched_fragments": 2421, "total_fragments": 3128, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bradyrhizobium elkanii", "strain": "strain=NBRC 14791", "accession": "GCA_006539665.1", "taxid": 29448, "species_taxid": 29448, "relation_to_type": "type", "validated": true, "ani": 94.6203, "matched_fragments": 2423, "total_fragments": 3128, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium elkanii", "strain": "strain=USDA 76", "accession": "GCA_000379145.1", "taxid": 29448, "species_taxid": 29448, "relation_to_type": "type", "validated": true, "ani": 94.6038, "matched_fragments": 2510, "total_fragments": 3128, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium elkanii", "strain": "strain=USDA 76", "accession": "GCA_023278185.1", "taxid": 29448, "species_taxid": 29448, "relation_to_type": "type", "validated": true, "ani": 94.5816, "matched_fragments": 2508, "total_fragments": 3128, "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": 90.7069, "matched_fragments": 2192, "total_fragments": 3128, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium altum", "strain": "strain=Pear77", "accession": "GCA_020889705.1", "taxid": 1571202, "species_taxid": 1571202, "relation_to_type": "type", "validated": true, "ani": 90.5944, "matched_fragments": 2031, "total_fragments": 3128, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium oropedii", "strain": "strain=Pear76", "accession": "GCA_020889685.1", "taxid": 1571201, "species_taxid": 1571201, "relation_to_type": "type", "validated": true, "ani": 90.5268, "matched_fragments": 2045, "total_fragments": 3128, "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": 90.3911, "matched_fragments": 2054, "total_fragments": 3128, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium tropiciagri", "strain": "strain=SEMIA 6148", "accession": "GCA_001189845.1", "taxid": 312253, "species_taxid": 312253, "relation_to_type": "type", "validated": true, "ani": 90.3517, "matched_fragments": 2218, "total_fragments": 3128, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium uaiense", "strain": "strain=UFLA03-164", "accession": "GCA_010811875.1", "taxid": 2594946, "species_taxid": 2594946, "relation_to_type": "type", "validated": true, "ani": 90.32, "matched_fragments": 2084, "total_fragments": 3128, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium septentrionale", "strain": "strain=1S1", "accession": "GCA_011516645.4", "taxid": 1404411, "species_taxid": 1404411, "relation_to_type": "type", "validated": true, "ani": 90.2998, "matched_fragments": 2244, "total_fragments": 3128, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium embrapense", "strain": "strain=SEMIA 6208", "accession": "GCA_001189235.2", "taxid": 630921, "species_taxid": 630921, "relation_to_type": "type", "validated": true, "ani": 90.1845, "matched_fragments": 2145, "total_fragments": 3128, "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": 90.1587, "matched_fragments": 2171, "total_fragments": 3128, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001189245.1", "gtdb_species": "s__Bradyrhizobium pachyrhizi", "ani": 95.358, "matched_fragments": 2418, "total_fragments": 3128, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.66", "min_intra_species_ani": "95.38", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.82", "num_clustered_genomes": 8, "status": "conclusive" }, { "accession": "GCF_000379145.1", "gtdb_species": "s__Bradyrhizobium elkanii", "ani": 94.6047, "matched_fragments": 2510, "total_fragments": 3128, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.89", "min_intra_species_ani": "95.57", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.83", "num_clustered_genomes": 18, "status": "-" }, { "accession": "GCF_001982635.1", "gtdb_species": "s__Bradyrhizobium mercantei", "ani": 91.0954, "matched_fragments": 2121, "total_fragments": 3128, "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_003001755.1", "gtdb_species": "s__Bradyrhizobium sp003001755", "ani": 91.0387, "matched_fragments": 2113, "total_fragments": 3128, "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_900105845.1", "gtdb_species": "s__Bradyrhizobium erythrophlei_E", "ani": 90.9939, "matched_fragments": 2125, "total_fragments": 3128, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.1616, "mean_intra_species_ani": "95.48", "min_intra_species_ani": "95.46", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.83", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_015291625.1", "gtdb_species": "s__Bradyrhizobium sp015291625", "ani": 90.7376, "matched_fragments": 2338, "total_fragments": 3128, "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_018130545.1", "gtdb_species": "s__Bradyrhizobium tropiciagri_A", "ani": 90.7197, "matched_fragments": 2087, "total_fragments": 3128, "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_013373795.1", "gtdb_species": "s__Bradyrhizobium quebecense", "ani": 90.6946, "matched_fragments": 2172, "total_fragments": 3128, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.1616, "mean_intra_species_ani": "96.90", "min_intra_species_ani": "95.60", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.83", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002532045.1", "gtdb_species": "s__Bradyrhizobium sp002532045", "ani": 90.6267, "matched_fragments": 2185, "total_fragments": 3128, "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_001908235.1", "gtdb_species": "s__Bradyrhizobium sp001908235", "ani": 90.5527, "matched_fragments": 2066, "total_fragments": 3128, "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_001189845.1", "gtdb_species": "s__Bradyrhizobium tropiciagri", "ani": 90.3404, "matched_fragments": 2220, "total_fragments": 3128, "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_011516645.2", "gtdb_species": "s__Bradyrhizobium septentrionale", "ani": 90.2018, "matched_fragments": 2256, "total_fragments": 3128, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.80", "min_intra_species_ani": "95.80", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.78", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_001189235.2", "gtdb_species": "s__Bradyrhizobium embrapense", "ani": 90.1845, "matched_fragments": 2145, "total_fragments": 3128, "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": "GCA_001238275.1", "gtdb_species": "s__Bradyrhizobium viridifuturi", "ani": 90.1565, "matched_fragments": 2171, "total_fragments": 3128, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.73", "min_intra_species_ani": "98.73", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002831585.1", "gtdb_species": "s__Bradyrhizobium sp002831585", "ani": 89.9717, "matched_fragments": 1984, "total_fragments": 3128, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.70", "min_intra_species_ani": "98.62", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.93", "num_clustered_genomes": 5, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.132, "cell_length": 0.272, "doubling_h": 1.189, "growth_tmp": 28.766, "optimum_tmp": 28.773, "optimum_ph": 7.035, "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", "australafricanum" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }