{ "type": "genome", "identifier": "GCF_015624505.1", "organism": "Bradyrhizobium commune", "title": "Bradyrhizobium commune", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Universite Claude Bernard - Lyon 1", "publication": [ {} ], "properties": { "assembly_accession": "GCF_015624505.1", "bioproject": "PRJNA224116", "biosample": "SAMN16089659", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "83627", "species_taxid": "83627", "organism_name": "Bradyrhizobium commune", "infraspecific_name": "strain=BDV5040", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/11/20", "asm_name": "ASM1562450v1", "asm_submitter": "Universite Claude Bernard - Lyon 1", "gbrs_paired_asm": "GCA_015624505.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/015/624/505/GCF_015624505.1_ASM1562450v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7622528", "genome_size_ungapped": "7622528", "gc_percent": "64.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_015624505.1-RS_2024_07_29", "annotation_date": "2024-07-29", "total_gene_count": "7190", "protein_coding_gene_count": "7073", "non_coding_gene_count": "55", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-11-20", "dateModified": "2020-11-20", "datePublished": "2020-11-20", "_annotation": { "sample_count": 1, "sample_organism": [ "Bradyrhizobium commune" ], "sample_taxid": [ "83627" ], "sample_host_organism": [ "Bossiaea ensata" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Australia: Ben Boyd National Park, NSW" ], "sample_host_location_id": [], "data_size": "2.098 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)": "7622528", "Number of Sequences": "1", "Longest Sequences (bp)": "7622528", "N50 (bp)": "7622528", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "63.9", "Number of CDSs": "7218", "Average Protein Length": "309.7", "Coding Ratio (%)": "88.0", "Number of rRNAs": "3", "Number of tRNAs": "50", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bradyrhizobium rifense", "strain": "strain=CTAW71", "accession": "GCA_008123425.1", "taxid": 515499, "species_taxid": 515499, "relation_to_type": "type", "validated": true, "ani": 88.9201, "matched_fragments": 1947, "total_fragments": 2540, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium diazoefficiens", "strain": "strain=USDA 110", "accession": "GCA_001642675.1", "taxid": 1355477, "species_taxid": 1355477, "relation_to_type": "type", "validated": true, "ani": 88.8535, "matched_fragments": 1873, "total_fragments": 2540, "ani_threshold": 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": 88.7773, "matched_fragments": 1905, "total_fragments": 2540, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium cytisi", "strain": "strain=CTAW11", "accession": "GCA_008123515.1", "taxid": 515489, "species_taxid": 515489, "relation_to_type": "type", "validated": true, "ani": 88.7094, "matched_fragments": 1842, "total_fragments": 2540, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium niftali", "strain": "strain=CNPSo 3448", "accession": "GCA_004571025.1", "taxid": 2560055, "species_taxid": 2560055, "relation_to_type": "type", "validated": true, "ani": 88.7005, "matched_fragments": 1860, "total_fragments": 2540, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium stylosanthis", "strain": "strain=BR 446", "accession": "GCA_001641335.1", "taxid": 1803665, "species_taxid": 1803665, "relation_to_type": "type", "validated": true, "ani": 88.2798, "matched_fragments": 1889, "total_fragments": 2540, "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": 88.2637, "matched_fragments": 1915, "total_fragments": 2540, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium arachidis", "strain": "strain=LMG 26795", "accession": "GCA_900116675.1", "taxid": 858423, "species_taxid": 858423, "relation_to_type": "type", "validated": true, "ani": 88.2581, "matched_fragments": 1907, "total_fragments": 2540, "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": 88.2038, "matched_fragments": 1728, "total_fragments": 2540, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium betae", "strain": "strain=PL7HG1", "accession": "GCA_008932115.1", "taxid": 244734, "species_taxid": 244734, "relation_to_type": "type", "validated": true, "ani": 88.2037, "matched_fragments": 1756, "total_fragments": 2540, "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": 88.0817, "matched_fragments": 1779, "total_fragments": 2540, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium guangzhouense", "strain": "strain=CCBAU 51670", "accession": "GCA_004114955.1", "taxid": 1325095, "species_taxid": 1325095, "relation_to_type": "type", "validated": true, "ani": 88.0719, "matched_fragments": 1786, "total_fragments": 2540, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium cosmicum", "strain": "strain=58S1", "accession": "GCA_007290395.1", "taxid": 1404864, "species_taxid": 1404864, "relation_to_type": "type", "validated": true, "ani": 88.0704, "matched_fragments": 1780, "total_fragments": 2540, "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": 87.9396, "matched_fragments": 1838, "total_fragments": 2540, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium forestalis", "strain": "strain=INPA54B", "accession": "GCA_002795245.1", "taxid": 1419263, "species_taxid": 1419263, "relation_to_type": "type", "validated": true, "ani": 87.9301, "matched_fragments": 1734, "total_fragments": 2540, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium manausense", "strain": "strain=BR 3351", "accession": "GCA_001440035.1", "taxid": 989370, "species_taxid": 989370, "relation_to_type": "suspected-type", "validated": true, "ani": 87.8525, "matched_fragments": 1781, "total_fragments": 2540, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium symbiodeficiens", "strain": "strain=85S1MB", "accession": "GCA_002266465.2", "taxid": 1404367, "species_taxid": 1404367, "relation_to_type": "type", "validated": true, "ani": 87.7374, "matched_fragments": 1766, "total_fragments": 2540, "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": 87.721, "matched_fragments": 1774, "total_fragments": 2540, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium nanningense", "strain": "strain=CCBAU 53390", "accession": "GCA_004114535.1", "taxid": 1325118, "species_taxid": 1325118, "relation_to_type": "type", "validated": true, "ani": 87.6984, "matched_fragments": 1711, "total_fragments": 2540, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium canariense", "strain": "strain=BTA-1", "accession": "GCA_019402665.1", "taxid": 255045, "species_taxid": 255045, "relation_to_type": "suspected-type", "validated": true, "ani": 87.6571, "matched_fragments": 1783, "total_fragments": 2540, "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": 87.5431, "matched_fragments": 1758, "total_fragments": 2540, "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": 87.5199, "matched_fragments": 1658, "total_fragments": 2540, "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": 87.4873, "matched_fragments": 1662, "total_fragments": 2540, "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": 87.4048, "matched_fragments": 1726, "total_fragments": 2540, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium centrolobii", "strain": "strain=BR 10245", "accession": "GCA_001641635.1", "taxid": 1505087, "species_taxid": 1505087, "relation_to_type": "type", "validated": true, "ani": 87.3338, "matched_fragments": 1844, "total_fragments": 2540, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium yuanmingense", "strain": "strain=CCBAU 10071", "accession": "GCA_900094575.1", "taxid": 108015, "species_taxid": 108015, "relation_to_type": "type", "validated": true, "ani": 87.3205, "matched_fragments": 1704, "total_fragments": 2540, "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": 82.9332, "matched_fragments": 1435, "total_fragments": 2540, "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": 82.8267, "matched_fragments": 1335, "total_fragments": 2540, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_015624505.1", "gtdb_species": "s__Bradyrhizobium sp015624505", "ani": 100.0, "matched_fragments": 2539, "total_fragments": 2540, "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_008123425.1", "gtdb_species": "s__Bradyrhizobium rifense", "ani": 88.9113, "matched_fragments": 1949, "total_fragments": 2540, "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_000473045.1", "gtdb_species": "s__Bradyrhizobium sp000473045", "ani": 88.8433, "matched_fragments": 1813, "total_fragments": 2540, "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_008123515.1", "gtdb_species": "s__Bradyrhizobium cytisi", "ani": 88.7315, "matched_fragments": 1839, "total_fragments": 2540, "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_004571025.1", "gtdb_species": "s__Bradyrhizobium niftali", "ani": 88.7237, "matched_fragments": 1857, "total_fragments": 2540, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.00", "min_intra_species_ani": "95.49", "mean_intra_species_af": "0.80", "min_intra_species_af": "0.80", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_016616885.1", "gtdb_species": "s__Bradyrhizobium diazoefficiens_F", "ani": 88.7072, "matched_fragments": 1815, "total_fragments": 2540, "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_000282615.1", "gtdb_species": "s__Bradyrhizobium sp000282615", "ani": 88.5142, "matched_fragments": 1764, "total_fragments": 2540, 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