{ "type": "genome", "identifier": "GCF_008123965.1", "organism": "Bradyrhizobium hipponense", "title": "Bradyrhizobium hipponense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "LMU Munich", "publication": [ {} ], "properties": { "assembly_accession": "GCF_008123965.1", "bioproject": "PRJNA224116", "biosample": "SAMN12616695", "wgs_master": "VSTH00000000.1", "refseq_category": "reference genome", "taxid": "2605638", "species_taxid": "2605638", "organism_name": "Bradyrhizobium hipponense", "infraspecific_name": "strain=aSej3", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/08/29", "asm_name": "ASM812396v1", "asm_submitter": "LMU Munich", "gbrs_paired_asm": "GCA_008123965.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/008/123/965/GCF_008123965.1_ASM812396v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "8826946", "genome_size_ungapped": "8825540", "gc_percent": "63.000000", "replicon_count": "0", "scaffold_count": "315", "contig_count": "315", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_008123965.1-RS_2024_05_26", "annotation_date": "2024-05-26", "total_gene_count": "8401", "protein_coding_gene_count": "7982", "non_coding_gene_count": "59", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-08-29", "dateModified": "2019-08-29", "datePublished": "2019-08-29", "_annotation": { "sample_count": 1, "sample_organism": [ "Bradyrhizobium hipponense" ], "sample_taxid": [ "2605638" ], "sample_host_organism": [ "Lupinus angustifolius" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Tunisia: Bizerte" ], "sample_host_location_id": [], "data_size": "2.478 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)": "8826946", "Number of Sequences": "315", "Longest Sequences (bp)": "326860", "N50 (bp)": "63341", "Gap Ratio (%)": "0.016042", "GCcontent (%)": "62.9", "Number of CDSs": "8246", "Average Protein Length": "292.2", "Coding Ratio (%)": "81.9", "Number of rRNAs": "3", "Number of tRNAs": "55", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bradyrhizobium hipponense", "strain": "strain=aSej3", "accession": "GCA_008123965.1", "taxid": 2605638, "species_taxid": 2605638, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2775, "total_fragments": 2790, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bradyrhizobium niftali", "strain": "strain=CNPSo 3448", "accession": "GCA_004571025.1", "taxid": 2560055, "species_taxid": 2560055, "relation_to_type": "type", "validated": true, "ani": 88.0536, "matched_fragments": 1937, "total_fragments": 2790, "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": 87.7941, "matched_fragments": 1799, "total_fragments": 2790, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium japonicum", "strain": "strain=NBRC 14783", "accession": "GCA_006539645.1", "taxid": 375, "species_taxid": 375, "relation_to_type": "type", "validated": true, "ani": 87.7436, "matched_fragments": 1810, "total_fragments": 2790, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium japonicum", "strain": "strain=USDA 6", "accession": "GCA_000284375.1", "taxid": 375, "species_taxid": 375, "relation_to_type": "type", "validated": true, "ani": 87.7411, "matched_fragments": 1838, "total_fragments": 2790, "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": 87.7169, "matched_fragments": 1874, "total_fragments": 2790, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium japonicum", "strain": "strain=USDA 6", "accession": "GCA_000472985.1", "taxid": 375, "species_taxid": 375, "relation_to_type": "type", "validated": true, "ani": 87.706, "matched_fragments": 1839, "total_fragments": 2790, "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": 87.6773, "matched_fragments": 1634, "total_fragments": 2790, "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": 87.6765, "matched_fragments": 1637, "total_fragments": 2790, "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": 87.4778, "matched_fragments": 1705, "total_fragments": 2790, "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": 87.3806, "matched_fragments": 1793, "total_fragments": 2790, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium nitroreducens", "strain": "strain=TSA1", "accession": "GCA_002776695.1", "taxid": 709803, "species_taxid": 709803, "relation_to_type": "type", "validated": true, "ani": 87.3557, "matched_fragments": 1759, "total_fragments": 2790, "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": 87.3222, "matched_fragments": 1826, "total_fragments": 2790, "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": 87.2793, "matched_fragments": 1963, "total_fragments": 2790, "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": 87.2772, "matched_fragments": 1829, "total_fragments": 2790, "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": 87.2101, "matched_fragments": 1832, "total_fragments": 2790, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium neotropicale", "strain": "strain=BR 10247", "accession": "GCA_001641695.1", "taxid": 1497615, "species_taxid": 1497615, "relation_to_type": "type", "validated": true, "ani": 87.0659, "matched_fragments": 1761, "total_fragments": 2790, "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": 86.9758, "matched_fragments": 1727, "total_fragments": 2790, "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": 86.8451, "matched_fragments": 1775, "total_fragments": 2790, "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": 86.4644, "matched_fragments": 1709, "total_fragments": 2790, "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": 82.5734, "matched_fragments": 1396, "total_fragments": 2790, "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": 82.4644, "matched_fragments": 1315, "total_fragments": 2790, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_008123965.1", "gtdb_species": "s__Bradyrhizobium hipponense", "ani": 100.0, "matched_fragments": 2775, "total_fragments": 2790, "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_000011365.1", "gtdb_species": "s__Bradyrhizobium diazoefficiens", "ani": 88.1431, "matched_fragments": 1897, "total_fragments": 2790, "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", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.84", "num_clustered_genomes": 23, "status": "-" }, { "accession": "GCF_018129995.1", "gtdb_species": "s__Bradyrhizobium japonicum_G", "ani": 88.1349, "matched_fragments": 1740, "total_fragments": 2790, "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": 88.061, "matched_fragments": 1937, "total_fragments": 2790, "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_000938255.1", "gtdb_species": "s__Bradyrhizobium sp000938255", "ani": 87.8871, "matched_fragments": 1747, "total_fragments": 2790, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.09", "min_intra_species_ani": "98.09", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_018130825.1", "gtdb_species": "s__Bradyrhizobium liaoningense_B", "ani": 87.8495, "matched_fragments": 1783, "total_fragments": 2790, "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_018130785.1", "gtdb_species": "s__Bradyrhizobium liaoningense_A", "ani": 87.7991, "matched_fragments": 1749, 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"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_015624505.1", "gtdb_species": "s__Bradyrhizobium sp015624505", "ani": 87.4649, "matched_fragments": 1679, "total_fragments": 2790, "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_001641335.1", "gtdb_species": "s__Bradyrhizobium stylosanthis", "ani": 87.3849, "matched_fragments": 1792, "total_fragments": 2790, "gtdb_taxonomy": 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