{ "type": "genome", "identifier": "GCF_001542415.1", "organism": "Bradyrhizobium macuxiense", "title": "Bradyrhizobium macuxiense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Embrapa Agrobiologia", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001542415.1", "bioproject": "PRJNA224116", "biosample": "SAMN04262301", "wgs_master": "LNCU00000000.1", "refseq_category": "reference genome", "taxid": "1755647", "species_taxid": "1755647", "organism_name": "Bradyrhizobium macuxiense", "infraspecific_name": "strain=BR 10303", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/01/28", "asm_name": "ASM154241v1", "asm_submitter": "Embrapa Agrobiologia", "gbrs_paired_asm": "GCA_001542415.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/542/415/GCF_001542415.1_ASM154241v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "8722143", "genome_size_ungapped": "8715681", "gc_percent": "63.000000", "replicon_count": "0", "scaffold_count": "137", "contig_count": "137", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001542415.1-RS_2024_05_26", "annotation_date": "2024-05-26", "total_gene_count": "8313", "protein_coding_gene_count": "7900", "non_coding_gene_count": "58", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-01-28", "dateModified": "2016-01-28", "datePublished": "2016-01-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Bradyrhizobium macuxiense" ], "sample_taxid": [ "1755647" ], "sample_host_organism": [ "Centrolobium paraense" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Brazil: Roraima State" ], "sample_host_location_id": [], "data_size": "2.426 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)": "8722143", "Number of Sequences": "137", "Longest Sequences (bp)": "392524", "N50 (bp)": "173122", "Gap Ratio (%)": "0.078089", "GCcontent (%)": "63.2", "Number of CDSs": "8109", "Average Protein Length": "296.8", "Coding Ratio (%)": "82.8", "Number of rRNAs": "3", "Number of tRNAs": "55", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bradyrhizobium macuxiense", "strain": "strain=BR 10303", "accession": "GCA_001542415.1", "taxid": 1755647, "species_taxid": 1755647, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2834, "total_fragments": 2839, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bradyrhizobium mercantei", "strain": "strain=SEMIA 6399", "accession": "GCA_001982635.1", "taxid": 1904807, "species_taxid": 1904807, "relation_to_type": "type", "validated": true, "ani": 87.8818, "matched_fragments": 1979, "total_fragments": 2839, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium elkanii", "strain": "strain=NBRC 14791", "accession": "GCA_006539665.1", "taxid": 29448, "species_taxid": 29448, "relation_to_type": "type", "validated": true, "ani": 87.3153, "matched_fragments": 1878, "total_fragments": 2839, "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": 87.2389, "matched_fragments": 1935, "total_fragments": 2839, "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": 87.2278, "matched_fragments": 1945, "total_fragments": 2839, "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": 87.1876, "matched_fragments": 1908, "total_fragments": 2839, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium pachyrhizi", "strain": "strain=PAC 48", "accession": "GCA_001189245.1", "taxid": 280333, "species_taxid": 280333, "relation_to_type": "type", "validated": true, "ani": 87.1617, "matched_fragments": 1931, "total_fragments": 2839, "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": 87.1044, "matched_fragments": 1913, "total_fragments": 2839, "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": 87.0985, "matched_fragments": 1920, "total_fragments": 2839, "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": 87.0935, "matched_fragments": 1783, "total_fragments": 2839, "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": 87.0621, "matched_fragments": 1900, "total_fragments": 2839, "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": 87.0011, "matched_fragments": 1779, "total_fragments": 2839, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium ivorense", "strain": "strain=CI-1B", "accession": "GCA_900696085.2", "taxid": 2511166, "species_taxid": 2511166, "relation_to_type": "type", "validated": true, "ani": 86.9462, "matched_fragments": 1927, "total_fragments": 2839, "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": 86.8957, "matched_fragments": 1772, "total_fragments": 2839, "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": 86.8422, "matched_fragments": 1818, "total_fragments": 2839, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001542415.1", "gtdb_species": "s__Bradyrhizobium macuxiense", "ani": 100.0, "matched_fragments": 2835, "total_fragments": 2839, "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_001982635.1", "gtdb_species": "s__Bradyrhizobium mercantei", "ani": 87.914, "matched_fragments": 1974, "total_fragments": 2839, "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_007993935.1", "gtdb_species": "s__Bradyrhizobium macuxiense_A", "ani": 87.6131, "matched_fragments": 2004, "total_fragments": 2839, "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": 87.4835, "matched_fragments": 1845, "total_fragments": 2839, "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": 87.4394, "matched_fragments": 1877, "total_fragments": 2839, "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": 87.3761, "matched_fragments": 1861, "total_fragments": 2839, "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_000379145.1", "gtdb_species": "s__Bradyrhizobium elkanii", "ani": 87.256, "matched_fragments": 1934, "total_fragments": 2839, "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_013373795.1", "gtdb_species": "s__Bradyrhizobium quebecense", "ani": 87.1812, "matched_fragments": 1897, "total_fragments": 2839, "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_001189245.1", "gtdb_species": "s__Bradyrhizobium pachyrhizi", "ani": 87.1553, "matched_fragments": 1932, "total_fragments": 2839, "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": "-" }, { "accession": "GCF_015291625.1", "gtdb_species": "s__Bradyrhizobium sp015291625", "ani": 87.1508, "matched_fragments": 1984, "total_fragments": 2839, "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": 87.1283, "matched_fragments": 1789, "total_fragments": 2839, "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_011516645.2", "gtdb_species": "s__Bradyrhizobium septentrionale", "ani": 87.0731, "matched_fragments": 1925, "total_fragments": 2839, "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": "GCA_001238275.1", "gtdb_species": "s__Bradyrhizobium viridifuturi", "ani": 87.0466, "matched_fragments": 1904, "total_fragments": 2839, "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_000938305.1", "gtdb_species": "s__Bradyrhizobium sp000938305", "ani": 87.0075, "matched_fragments": 1761, "total_fragments": 2839, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.61", "min_intra_species_ani": "95.61", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900696085.1", "gtdb_species": "s__Bradyrhizobium ivorense", "ani": 86.9252, "matched_fragments": 1931, "total_fragments": 2839, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.20", "min_intra_species_ani": "96.86", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_018130215.1", "gtdb_species": "s__Bradyrhizobium jicamae_A", "ani": 86.7867, "matched_fragments": 1789, "total_fragments": 2839, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.26", "min_intra_species_ani": "99.26", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_018130695.1", "gtdb_species": "s__Bradyrhizobium jicamae_B", "ani": 85.3484, "matched_fragments": 1677, "total_fragments": 2839, "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_018131005.1", "gtdb_species": "s__Bradyrhizobium lablabi_D", "ani": 84.9097, "matched_fragments": 1529, "total_fragments": 2839, "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": "-" } ] }, "_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", "macuxiense" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }