{ "type": "genome", "identifier": "GCF_020889685.1", "organism": "Bradyrhizobium oropedii", "title": "Bradyrhizobium oropedii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Pretoria", "publication": [ {} ], "properties": { "assembly_accession": "GCF_020889685.1", "bioproject": "PRJNA224116", "biosample": "SAMN15826094", "wgs_master": "JACMYO000000000.1", "refseq_category": "reference genome", "taxid": "1571201", "species_taxid": "1571201", "organism_name": "Bradyrhizobium oropedii", "infraspecific_name": "strain=Pear76", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/11/19", "asm_name": "ASM2088968v1", "asm_submitter": "University of Pretoria", "gbrs_paired_asm": "GCA_020889685.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/020/889/685/GCF_020889685.1_ASM2088968v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "9043029", "genome_size_ungapped": "9043029", "gc_percent": "63.500000", "replicon_count": "0", "scaffold_count": "513", "contig_count": "513", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_020889685.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "8732", "protein_coding_gene_count": "8198", "non_coding_gene_count": "69", "pubmed_id": "34757168" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-11-19", "dateModified": "2021-11-19", "datePublished": "2021-11-19", "_annotation": { "sample_count": 1, "sample_organism": [ "Bradyrhizobium oropedii" ], "sample_taxid": [ "1571201" ], "sample_host_organism": [ "Pearsonia obovata" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Africa" ], "sample_host_location_id": [], "data_size": "2.524 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)": "9043029", "Number of Sequences": "513", "Longest Sequences (bp)": "203105", "N50 (bp)": "36050", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "63.6", "Number of CDSs": "8306", "Average Protein Length": "289.5", "Coding Ratio (%)": "79.8", "Number of rRNAs": "3", "Number of tRNAs": "61", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bradyrhizobium oropedii", "strain": "strain=Pear76", "accession": "GCA_020889685.1", "taxid": 1571201, "species_taxid": 1571201, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2761, 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"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": 91.1339, "matched_fragments": 1995, "total_fragments": 2774, "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": 91.0854, "matched_fragments": 2098, "total_fragments": 2774, "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": 90.7948, "matched_fragments": 2156, "total_fragments": 2774, "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": 90.734, "matched_fragments": 2068, "total_fragments": 2774, "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": 90.6441, "matched_fragments": 2053, "total_fragments": 2774, "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": 90.6407, "matched_fragments": 1999, "total_fragments": 2774, "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": 90.6261, "matched_fragments": 2067, "total_fragments": 2774, "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": 90.0594, "matched_fragments": 2052, "total_fragments": 2774, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium campsiandrae", "strain": "strain=INPA 394B", "accession": "GCA_014529705.1", "taxid": 1729892, "species_taxid": 1729892, "relation_to_type": "type", "validated": true, "ani": 82.5042, "matched_fragments": 1383, "total_fragments": 2774, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Afipia carboxidovorans", "strain": "strain=OM5", "accession": "GCA_000218565.1", "taxid": 40137, "species_taxid": 40137, "relation_to_type": "type", "validated": true, "ani": 79.5371, "matched_fragments": 544, "total_fragments": 2774, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium metallidurans", "strain": "strain=STM 2683", "accession": "GCA_000350085.1", "taxid": 489722, "species_taxid": 489722, "relation_to_type": "type", "validated": true, "ani": 77.0242, "matched_fragments": 381, "total_fragments": 2774, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aureimonas flava", "strain": "strain=M2BS4Y-1", "accession": "GCA_003583935.1", "taxid": 2320271, "species_taxid": 2320271, "relation_to_type": "type", "validated": true, "ani": 76.9404, "matched_fragments": 298, "total_fragments": 2774, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium sediminum", "strain": "strain=KCTC 42205", "accession": "GCA_013240295.1", "taxid": 1849104, "species_taxid": 1849104, "relation_to_type": "type", "validated": true, "ani": 76.875, "matched_fragments": 298, "total_fragments": 2774, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agrobacterium leguminum", "strain": "strain=MOPV5", "accession": "GCA_015704895.1", "taxid": 2792015, "species_taxid": 2792015, "relation_to_type": "type", "validated": true, "ani": 76.585, "matched_fragments": 203, "total_fragments": 2774, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_018130545.1", "gtdb_species": "s__Bradyrhizobium tropiciagri_A", "ani": 91.6218, "matched_fragments": 2001, "total_fragments": 2774, "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": 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