{ "type": "genome", "identifier": "GCF_001641635.1", "organism": "Bradyrhizobium centrolobii", "title": "Bradyrhizobium centrolobii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Embrapa Agrobiologia", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001641635.1", "bioproject": "PRJNA224116", "biosample": "SAMN04448272", "wgs_master": "LUUB00000000.1", "refseq_category": "reference genome", "taxid": "1505087", "species_taxid": "1505087", "organism_name": "Bradyrhizobium centrolobii", "infraspecific_name": "strain=BR 10245", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/05/10", "asm_name": "ASM164163v1", "asm_submitter": "Embrapa Agrobiologia", "gbrs_paired_asm": "GCA_001641635.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/641/635/GCF_001641635.1_ASM164163v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "10111113", "genome_size_ungapped": "10107039", "gc_percent": "63.000000", "replicon_count": "0", "scaffold_count": "133", "contig_count": "133", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001641635.1-RS_2024_05_26", "annotation_date": "2024-05-26", "total_gene_count": "9563", "protein_coding_gene_count": "9054", "non_coding_gene_count": "75", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-05-10", "dateModified": "2016-05-10", "datePublished": "2016-05-10", "_annotation": { "sample_count": 1, "sample_organism": [ "Bradyrhizobium centrolobii" ], "sample_taxid": [ "1505087" ], "sample_host_organism": [ "Centrolobium paraense" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Brazil" ], "sample_host_location_id": [], "data_size": "2.819 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)": "10111113", "Number of Sequences": "133", "Longest Sequences (bp)": "535223", "N50 (bp)": "140269", "Gap Ratio (%)": "0.042696", "GCcontent (%)": "63.2", "Number of CDSs": "9504", "Average Protein Length": "292.8", "Coding Ratio (%)": "82.6", "Number of rRNAs": "12", "Number of tRNAs": "64", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bradyrhizobium centrolobii", "strain": "strain=BR 10245", "accession": "GCA_001641635.1", "taxid": 1505087, "species_taxid": 1505087, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 3285, 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95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium diazoefficiens", "strain": "strain=USDA110", "accession": "GCA_000011365.1", "taxid": 1355477, "species_taxid": 1355477, "relation_to_type": "type", "validated": true, "ani": 87.8223, "matched_fragments": 2047, "total_fragments": 3306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium cajani", "strain": "strain=1010", "accession": "GCA_009759665.1", "taxid": 1928661, "species_taxid": 1928661, "relation_to_type": "type", "validated": true, "ani": 87.7801, "matched_fragments": 1950, "total_fragments": 3306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium arachidis", "strain": "strain=CCBAU 051107", "accession": "GCA_015291705.1", "taxid": 858423, "species_taxid": 858423, "relation_to_type": "type", "validated": true, "ani": 87.5035, "matched_fragments": 2096, "total_fragments": 3306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium huanghuaihaiense", "strain": "strain=CGMCC 1.10948", "accession": "GCA_007830635.1", "taxid": 990078, "species_taxid": 990078, "relation_to_type": "type", "validated": true, "ani": 87.4798, "matched_fragments": 2033, "total_fragments": 3306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium zhanjiangense", "strain": "strain=CCBAU 51778", "accession": "GCA_004114935.1", "taxid": 1325107, "species_taxid": 1325107, "relation_to_type": "type", "validated": true, "ani": 87.2693, "matched_fragments": 1975, "total_fragments": 3306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium betae", "strain": "strain=CECT 5829", "accession": "GCA_024806875.1", "taxid": 244734, "species_taxid": 244734, "relation_to_type": "type", "validated": true, "ani": 87.2673, "matched_fragments": 1804, "total_fragments": 3306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium hipponense", "strain": "strain=aSej3", "accession": "GCA_008123965.1", "taxid": 2605638, "species_taxid": 2605638, "relation_to_type": "type", "validated": true, "ani": 87.2118, "matched_fragments": 1835, "total_fragments": 3306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium shewense", "strain": "strain=ERR11", "accession": "GCA_900094605.1", "taxid": 1761772, "species_taxid": 1761772, "relation_to_type": "type", "validated": true, "ani": 87.1271, "matched_fragments": 1937, "total_fragments": 3306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium sacchari", "strain": "strain=p9-20", "accession": "GCA_002068095.1", "taxid": 1399419, "species_taxid": 1399419, "relation_to_type": "type", "validated": true, "ani": 87.0364, "matched_fragments": 1985, "total_fragments": 3306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium vignae", "strain": "strain=LMG 28791", "accession": "GCA_004114425.1", "taxid": 1549949, "species_taxid": 1549949, "relation_to_type": "type", "validated": true, "ani": 87.0238, "matched_fragments": 1786, "total_fragments": 3306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium guangxiense", "strain": "strain=CCBAU 53363", "accession": "GCA_004114915.1", "taxid": 1325115, "species_taxid": 1325115, "relation_to_type": "type", "validated": true, "ani": 86.9219, "matched_fragments": 1888, "total_fragments": 3306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium agreste", "strain": "strain=CNPSo 4010", "accession": "GCA_016031625.1", "taxid": 2751811, "species_taxid": 2751811, "relation_to_type": "type", "validated": true, "ani": 86.8656, "matched_fragments": 1773, "total_fragments": 3306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium diversitatis", "strain": "strain=CNPSo 4019", "accession": "GCA_016031635.1", "taxid": 2755406, "species_taxid": 2755406, "relation_to_type": "type", "validated": true, "ani": 86.8438, "matched_fragments": 1864, "total_fragments": 3306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium glycinis", "strain": "strain=CNPSo 4016", "accession": "GCA_016031655.1", "taxid": 2751812, "species_taxid": 2751812, "relation_to_type": "type", "validated": true, "ani": 86.7826, "matched_fragments": 1775, "total_fragments": 3306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium daqingense", "strain": "strain=CCBAU 15774", "accession": "GCA_021044685.1", "taxid": 993502, "species_taxid": 993502, "relation_to_type": "type", "validated": true, "ani": 86.7238, "matched_fragments": 1844, "total_fragments": 3306, "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": 82.7013, "matched_fragments": 1534, "total_fragments": 3306, "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": 82.6656, "matched_fragments": 1472, "total_fragments": 3306, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001641635.1", "gtdb_species": "s__Bradyrhizobium centrolobii", "ani": 100.0, "matched_fragments": 3286, "total_fragments": 3306, "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_001641695.1", "gtdb_species": "s__Bradyrhizobium neotropicale", "ani": 91.0174, "matched_fragments": 2325, "total_fragments": 3306, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.90", "min_intra_species_ani": "97.90", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000011365.1", "gtdb_species": "s__Bradyrhizobium diazoefficiens", "ani": 87.8582, "matched_fragments": 2041, "total_fragments": 3306, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.15", "min_intra_species_ani": "98.13", 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"mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000282615.1", "gtdb_species": "s__Bradyrhizobium sp000282615", "ani": 87.4464, "matched_fragments": 1775, "total_fragments": 3306, "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_004212635.1", "gtdb_species": "s__Bradyrhizobium sp004212635", "ani": 87.3595, "matched_fragments": 1856, "total_fragments": 3306, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.55", "min_intra_species_ani": "95.55", 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