{ "type": "genome", "identifier": "GCF_001982635.1", "organism": "Bradyrhizobium mercantei", "title": "Bradyrhizobium mercantei", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Embrapa", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001982635.1", "bioproject": "PRJNA224116", "biosample": "SAMN05826124", "wgs_master": "MKFI00000000.1", "refseq_category": "reference genome", "taxid": "1904807", "species_taxid": "1904807", "organism_name": "Bradyrhizobium mercantei", "infraspecific_name": "strain=SEMIA 6399", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/02/01", "asm_name": "ASM198263v1", "asm_submitter": "Embrapa", "gbrs_paired_asm": "GCA_001982635.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/982/635/GCF_001982635.1_ASM198263v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "8842857", "genome_size_ungapped": "8842857", "gc_percent": "64.000000", "replicon_count": "0", "scaffold_count": "72", "contig_count": "72", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001982635.1-RS_2024_10_22", "annotation_date": "2024-10-22", "total_gene_count": "8261", "protein_coding_gene_count": "8082", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-02-01", "dateModified": "2017-02-01", "datePublished": "2017-02-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Bradyrhizobium mercantei" ], "sample_taxid": [ "1904807" ], "sample_host_organism": [ "Deguelia costata" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Brazil" ], "sample_host_location_id": [], "data_size": "2.441 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "8842857", "Number of Sequences": "72", "Longest Sequences (bp)": "1570373", "N50 (bp)": "1006110", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "64.0", "Number of CDSs": "8134", "Average Protein Length": "307.7", "Coding Ratio (%)": "84.9", "Number of rRNAs": "3", "Number of tRNAs": "51", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bradyrhizobium mercantei", "strain": "strain=SEMIA 6399", "accession": "GCA_001982635.1", "taxid": 1904807, "species_taxid": 1904807, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2920, "total_fragments": 2920, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bradyrhizobium tropiciagri", "strain": "strain=SEMIA 6148", "accession": "GCA_001189845.1", "taxid": 312253, "species_taxid": 312253, "relation_to_type": "type", "validated": true, "ani": 91.7422, "matched_fragments": 2106, "total_fragments": 2920, "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": 91.3049, "matched_fragments": 2141, "total_fragments": 2920, "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": 91.2157, "matched_fragments": 1939, "total_fragments": 2920, "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": 91.2098, "matched_fragments": 2094, "total_fragments": 2920, "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": 91.1441, "matched_fragments": 2126, "total_fragments": 2920, "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": 91.1433, "matched_fragments": 2122, "total_fragments": 2920, "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": 91.1324, "matched_fragments": 1988, "total_fragments": 2920, "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": 91.1133, "matched_fragments": 1961, "total_fragments": 2920, "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": 90.9404, "matched_fragments": 1977, "total_fragments": 2920, "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": 90.7968, "matched_fragments": 2053, "total_fragments": 2920, "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": 90.4844, "matched_fragments": 2149, "total_fragments": 2920, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001982635.1", "gtdb_species": "s__Bradyrhizobium mercantei", "ani": 100.0, "matched_fragments": 2920, "total_fragments": 2920, "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_003001755.1", "gtdb_species": "s__Bradyrhizobium sp003001755", "ani": 92.1814, "matched_fragments": 2067, "total_fragments": 2920, "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": 92.15, "matched_fragments": 2230, "total_fragments": 2920, "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": 91.8103, "matched_fragments": 2063, "total_fragments": 2920, "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": 91.7455, "matched_fragments": 2106, "total_fragments": 2920, "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": 91.5091, "matched_fragments": 2100, "total_fragments": 2920, "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": 91.2868, "matched_fragments": 2144, "total_fragments": 2920, "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_015291625.1", "gtdb_species": "s__Bradyrhizobium sp015291625", "ani": 91.2859, "matched_fragments": 2185, "total_fragments": 2920, "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": 91.1958, "matched_fragments": 2017, "total_fragments": 2920, "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_013373795.1", "gtdb_species": "s__Bradyrhizobium quebecense", "ani": 91.1957, "matched_fragments": 2127, "total_fragments": 2920, "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_000379145.1", "gtdb_species": "s__Bradyrhizobium elkanii", "ani": 91.1492, "matched_fragments": 2121, "total_fragments": 2920, "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_001189235.2", "gtdb_species": "s__Bradyrhizobium embrapense", "ani": 90.8048, "matched_fragments": 2052, "total_fragments": 2920, "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_002831585.1", "gtdb_species": "s__Bradyrhizobium sp002831585", "ani": 90.4737, "matched_fragments": 2015, "total_fragments": 2920, "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", "mercantei" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }