{ "type": "genome", "identifier": "GCF_001440405.1", "organism": "Bradyrhizobium valentinum", "title": "Bradyrhizobium valentinum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "UPM", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001440405.1", "bioproject": "PRJNA224116", "biosample": "SAMN02688507", "wgs_master": "LLXX00000000.1", "refseq_category": "reference genome", "taxid": "1518501", "species_taxid": "1518501", "organism_name": "Bradyrhizobium valentinum", "infraspecific_name": "strain=LmjM3", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/11/06", "asm_name": "ASM144040v1", "asm_submitter": "UPM", "gbrs_paired_asm": "GCA_001440405.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/440/405/GCF_001440405.1_ASM144040v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "8845258", "genome_size_ungapped": "8825946", "gc_percent": "62.000000", "replicon_count": "0", "scaffold_count": "242", "contig_count": "242", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001440405.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "8655", "protein_coding_gene_count": "8112", "non_coding_gene_count": "62", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-11-06", "dateModified": "2015-11-06", "datePublished": "2015-11-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Bradyrhizobium valentinum" ], "sample_taxid": [ "1518501" ], "sample_host_organism": [ "Lupinus mariae-josephae" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Spain: Monserrat, Valencia" ], "sample_host_location_id": [], "data_size": "2.486 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 98.96, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "8845258", "Number of Sequences": "242", "Longest Sequences (bp)": "347695", "N50 (bp)": "72962", "Gap Ratio (%)": "0.218332", "GCcontent (%)": "61.9", "Number of CDSs": "8437", "Average Protein Length": "279.2", "Coding Ratio (%)": "79.9", "Number of rRNAs": "3", "Number of tRNAs": "55", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bradyrhizobium valentinum", "strain": "strain=LmjM3", "accession": "GCA_001440405.1", "taxid": 1518501, "species_taxid": 1518501, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2812, "total_fragments": 2826, "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": 89.0878, "matched_fragments": 1953, "total_fragments": 2826, "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": 88.5529, "matched_fragments": 1940, "total_fragments": 2826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium murdochi", "strain": "strain=WSM 1741", "accession": "GCA_000472965.1", "taxid": 1038859, "species_taxid": 1038859, "relation_to_type": "type", "validated": true, "ani": 88.4788, "matched_fragments": 1948, "total_fragments": 2826, "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": 88.0434, "matched_fragments": 1823, "total_fragments": 2826, "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": 87.849, "matched_fragments": 1925, "total_fragments": 2826, "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": 87.811, "matched_fragments": 1917, "total_fragments": 2826, "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": 87.4549, "matched_fragments": 1862, "total_fragments": 2826, "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": 83.2526, "matched_fragments": 1238, "total_fragments": 2826, "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": 82.7712, "matched_fragments": 1467, "total_fragments": 2826, "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": 82.681, "matched_fragments": 1356, "total_fragments": 2826, "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": 82.6635, "matched_fragments": 1396, "total_fragments": 2826, "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": 82.6474, "matched_fragments": 1328, "total_fragments": 2826, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 98.96, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001440405.1", "gtdb_species": "s__Bradyrhizobium valentinum", "ani": 100.0, "matched_fragments": 2812, "total_fragments": 2826, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.35", "min_intra_species_ani": "99.35", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_003062295.1", "gtdb_species": "s__Bradyrhizobium algeriense", "ani": 90.2201, "matched_fragments": 2083, "total_fragments": 2826, "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": 89.9005, "matched_fragments": 2071, "total_fragments": 2826, "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_018130385.1", "gtdb_species": "s__Bradyrhizobium sp018130385", "ani": 89.2679, "matched_fragments": 1804, "total_fragments": 2826, "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", 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