{ "type": "genome", "identifier": "GCF_000472965.1", "organism": "Bradyrhizobium murdochi", "title": "Bradyrhizobium murdochi", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000472965.1", "bioproject": "PRJNA224116", "biosample": "SAMN02441128", "wgs_master": "AXAU00000000.1", "refseq_category": "reference genome", "taxid": "1038859", "species_taxid": "1038859", "organism_name": "Bradyrhizobium murdochi", "infraspecific_name": "strain=WSM 1741", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/09/30", "asm_name": "ASM47296v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000472965.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/472/965/GCF_000472965.1_ASM47296v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7952346", "genome_size_ungapped": "7952271", "gc_percent": "62.000000", "replicon_count": "0", "scaffold_count": "69", "contig_count": "70", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000472965.1-RS_2024_05_26", "annotation_date": "2024-05-26", "total_gene_count": "7524", "protein_coding_gene_count": "7223", "non_coding_gene_count": "56", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-09-30", "dateModified": "2013-09-30", "datePublished": "2013-09-30", "_annotation": { "sample_count": 1, "sample_organism": [ "Bradyrhizobium murdochi" ], "sample_taxid": [ "1038859" ], "sample_host_organism": [ "Rhynchosia minima" ], "sample_host_organism_id": [], "sample_host_disease": [ "None" ], "sample_host_disease_id": [], "sample_host_location": [ "Australia" ], "sample_host_location_id": [], "data_size": "2.227 MB", "sample_ph_range": { "min": 58.0, "max": 58.0 }, "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)": "7952346", "Number of Sequences": "69", "Longest Sequences (bp)": "1450744", "N50 (bp)": "311400", "Gap Ratio (%)": "0.002213", "GCcontent (%)": "62.1", "Number of CDSs": "7487", "Average Protein Length": "294.2", "Coding Ratio (%)": "83.1", "Number of rRNAs": "3", "Number of tRNAs": "51", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bradyrhizobium murdochi", "strain": "strain=WSM 1741", "accession": "GCA_000472965.1", "taxid": 1038859, "species_taxid": 1038859, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2607, "total_fragments": 2613, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bradyrhizobium retamae", "strain": "strain=Ro19", "accession": "GCA_001440415.1", "taxid": 1300035, "species_taxid": 1300035, "relation_to_type": "type", "validated": true, "ani": 93.5462, "matched_fragments": 2039, "total_fragments": 2613, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium icense", "strain": "strain=LMTR 13", "accession": "GCA_001693385.1", "taxid": 1274631, "species_taxid": 1274631, "relation_to_type": "type", "validated": true, "ani": 91.3787, "matched_fragments": 2062, "total_fragments": 2613, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium australiense", "strain": "strain=WSM 1791", "accession": "GCA_013114825.1", "taxid": 2721161, "species_taxid": 2721161, "relation_to_type": "type", "validated": true, "ani": 90.4517, "matched_fragments": 1931, "total_fragments": 2613, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium valentinum", "strain": "strain=LmjM3", "accession": "GCA_001440405.1", "taxid": 1518501, "species_taxid": 1518501, "relation_to_type": "type", "validated": true, "ani": 88.5, "matched_fragments": 1922, "total_fragments": 2613, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium paxllaeri", "strain": "strain=LMTR 21", "accession": "GCA_001693515.2", "taxid": 190148, "species_taxid": 190148, "relation_to_type": "type", "validated": true, "ani": 88.2436, "matched_fragments": 1956, "total_fragments": 2613, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium lablabi", "strain": "strain=CCBAU 23086", "accession": "GCA_001440475.1", "taxid": 722472, "species_taxid": 722472, "relation_to_type": "suspected-type", "validated": true, "ani": 88.0928, "matched_fragments": 1922, "total_fragments": 2613, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium jicamae", "strain": "strain=PAC68", "accession": "GCA_001440395.1", "taxid": 280332, "species_taxid": 280332, "relation_to_type": "type", "validated": true, "ani": 87.498, "matched_fragments": 1840, "total_fragments": 2613, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium sediminis", "strain": "strain=S2-20-1", "accession": "GCA_018736085.1", "taxid": 2840469, "species_taxid": 2840469, "relation_to_type": "type", "validated": true, "ani": 83.1076, "matched_fragments": 1225, "total_fragments": 2613, "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": 82.6856, "matched_fragments": 1456, "total_fragments": 2613, "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": 82.5176, "matched_fragments": 1332, "total_fragments": 2613, "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": 82.5052, "matched_fragments": 1337, "total_fragments": 2613, "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": 82.4905, "matched_fragments": 1411, "total_fragments": 2613, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000472965.1", "gtdb_species": "s__Bradyrhizobium murdochi", "ani": 100.0, "matched_fragments": 2607, "total_fragments": 2613, "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_018398875.1", "gtdb_species": "s__Bradyrhizobium sp018398875", "ani": 94.5167, "matched_fragments": 2102, "total_fragments": 2613, "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_001693485.1", "gtdb_species": "s__Bradyrhizobium sp001693485", "ani": 93.7708, "matched_fragments": 2131, "total_fragments": 2613, "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_001440415.1", "gtdb_species": "s__Bradyrhizobium retamae", "ani": 93.5422, "matched_fragments": 2039, "total_fragments": 2613, "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_018398895.1", "gtdb_species": "s__Bradyrhizobium sp018398895", "ani": 91.7508, "matched_fragments": 2021, "total_fragments": 2613, "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_001693385.1", "gtdb_species": "s__Bradyrhizobium icense", "ani": 91.3553, "matched_fragments": 2065, "total_fragments": 2613, "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_013114825.1", "gtdb_species": "s__Bradyrhizobium australiense", "ani": 90.4557, "matched_fragments": 1931, "total_fragments": 2613, "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_003062295.1", "gtdb_species": "s__Bradyrhizobium algeriense", "ani": 88.2633, "matched_fragments": 1939, "total_fragments": 2613, "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_001693515.2", "gtdb_species": "s__Bradyrhizobium paxllaeri", "ani": 88.2581, "matched_fragments": 1953, "total_fragments": 2613, "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_018596315.1", "gtdb_species": "s__Bradyrhizobium sp018596315", "ani": 88.1408, "matched_fragments": 1914, "total_fragments": 2613, "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_001440475.1", "gtdb_species": "s__Bradyrhizobium lablabi", "ani": 88.0908, "matched_fragments": 1922, "total_fragments": 2613, "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_017305715.1", "gtdb_species": "s__Bradyrhizobium sp017305715", "ani": 83.902, "matched_fragments": 1435, "total_fragments": 2613, "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", "murdochi" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }