{ "type": "genome", "identifier": "GCF_001189845.1", "organism": "Bradyrhizobium tropiciagri", "title": "Bradyrhizobium tropiciagri", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Embrapa Soja", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001189845.1", "bioproject": "PRJNA224116", "biosample": "SAMN03784761", "wgs_master": "LFLZ00000000.1", "refseq_category": "reference genome", "taxid": "312253", "species_taxid": "312253", "organism_name": "Bradyrhizobium tropiciagri", "infraspecific_name": "strain=SEMIA 6148", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/07/31", "asm_name": "ASM118984v1", "asm_submitter": "Embrapa Soja", "gbrs_paired_asm": "GCA_001189845.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/189/845/GCF_001189845.1_ASM118984v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "9767314", "genome_size_ungapped": "9767314", "gc_percent": "63.500000", "replicon_count": "0", "scaffold_count": "189", "contig_count": "189", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001189845.1-RS_2024_05_26", "annotation_date": "2024-05-26", "total_gene_count": "9164", "protein_coding_gene_count": "8464", "non_coding_gene_count": "56", "pubmed_id": "24031882;26679591" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-07-31", "dateModified": "2015-07-31", "datePublished": "2015-07-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Bradyrhizobium tropiciagri" ], "sample_taxid": [ "312253" ], "sample_host_organism": [ "Neonotonia wightii" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Brazil" ], "sample_host_location_id": [], "data_size": "2.718 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 2.08, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "9767314", "Number of Sequences": "189", "Longest Sequences (bp)": "391851", "N50 (bp)": "111450", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "63.5", "Number of CDSs": "9378", "Average Protein Length": "286.8", "Coding Ratio (%)": "82.6", "Number of rRNAs": "3", "Number of tRNAs": "53", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bradyrhizobium tropiciagri", "strain": "strain=SEMIA 6148", "accession": "GCA_001189845.1", "taxid": 312253, "species_taxid": 312253, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 3155, "total_fragments": 3165, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bradyrhizobium viridifuturi", "strain": "strain=SEMIA 690", "accession": "GCA_001238275.1", "taxid": 1654716, "species_taxid": 1654716, "relation_to_type": "type", "validated": true, "ani": 93.0988, "matched_fragments": 2276, "total_fragments": 3165, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium mercantei", "strain": "strain=SEMIA 6399", "accession": "GCA_001982635.1", "taxid": 1904807, "species_taxid": 1904807, "relation_to_type": "type", "validated": true, "ani": 91.6621, "matched_fragments": 2148, "total_fragments": 3165, "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": 91.3457, "matched_fragments": 2240, "total_fragments": 3165, "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": 91.2245, "matched_fragments": 2191, "total_fragments": 3165, "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": 91.1513, "matched_fragments": 2171, "total_fragments": 3165, "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": 90.786, "matched_fragments": 2136, "total_fragments": 3165, "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": 90.74, "matched_fragments": 2149, "total_fragments": 3165, "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": 90.4479, "matched_fragments": 2134, "total_fragments": 3165, "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": 90.3816, "matched_fragments": 2149, "total_fragments": 3165, "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": 90.3629, "matched_fragments": 2201, "total_fragments": 3165, "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": 90.3258, "matched_fragments": 2214, "total_fragments": 3165, "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": 89.909, "matched_fragments": 2162, "total_fragments": 3165, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 2.08, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001189845.1", "gtdb_species": "s__Bradyrhizobium tropiciagri", "ani": 100.0, "matched_fragments": 3155, "total_fragments": 3165, "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_001908235.1", "gtdb_species": "s__Bradyrhizobium sp001908235", "ani": 94.5311, "matched_fragments": 2230, "total_fragments": 3165, "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": 94.3806, "matched_fragments": 2310, "total_fragments": 3165, "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": 93.1006, "matched_fragments": 2276, "total_fragments": 3165, "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_016839165.1", "gtdb_species": "s__Bradyrhizobium sp003020075", "ani": 92.2536, "matched_fragments": 2068, "total_fragments": 3165, "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_001982635.1", "gtdb_species": "s__Bradyrhizobium mercantei", "ani": 91.6546, "matched_fragments": 2148, "total_fragments": 3165, "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": 91.2967, "matched_fragments": 2190, "total_fragments": 3165, "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_003001755.1", "gtdb_species": "s__Bradyrhizobium sp003001755", "ani": 91.2378, "matched_fragments": 2054, "total_fragments": 3165, "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": 91.1667, "matched_fragments": 2178, "total_fragments": 3165, "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_015291625.1", "gtdb_species": "s__Bradyrhizobium sp015291625", "ani": 91.0887, "matched_fragments": 2351, "total_fragments": 3165, "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_002532045.1", "gtdb_species": "s__Bradyrhizobium sp002532045", "ani": 90.984, "matched_fragments": 2221, "total_fragments": 3165, "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": 90.3579, "matched_fragments": 2022, "total_fragments": 3165, "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": 9767314.0, "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": 0.071, "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", "tropiciagri" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }