{ "type": "genome", "identifier": "GCF_004114425.1", "organism": "Bradyrhizobium vignae", "title": "Bradyrhizobium vignae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "China Agricultural University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004114425.1", "bioproject": "PRJNA224116", "biosample": "SAMN10259397", "wgs_master": "RDQF00000000.1", "refseq_category": "na", "taxid": "1549949", "species_taxid": "1549949", "organism_name": "Bradyrhizobium vignae", "infraspecific_name": "strain=LMG 28791", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/01/25", "asm_name": "ASM411442v1", "asm_submitter": "China Agricultural University", "gbrs_paired_asm": "GCA_004114425.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/114/425/GCF_004114425.1_ASM411442v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "8175609", "genome_size_ungapped": "8175599", "gc_percent": "63.000000", "replicon_count": "0", "scaffold_count": "156", "contig_count": "156", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004114425.1-RS_2024_05_26", "annotation_date": "2024-05-26", "total_gene_count": "7764", "protein_coding_gene_count": "7443", "non_coding_gene_count": "55", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-01-25", "dateModified": "2019-01-25", "datePublished": "2019-01-25", "_annotation": { "sample_count": 1, "sample_organism": [ "Bradyrhizobium vignae" ], "sample_taxid": [ "1549949" ], "sample_host_organism": [ "Arachis" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Namibia: Kavango region" ], "sample_host_location_id": [], "data_size": "2.282 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)": "8175609", "Number of Sequences": "156", "Longest Sequences (bp)": "348812", "N50 (bp)": "130263", "Gap Ratio (%)": "0.000122", "GCcontent (%)": "63.2", "Number of CDSs": "7724", "Average Protein Length": "292.1", "Coding Ratio (%)": "82.8", "Number of rRNAs": "3", "Number of tRNAs": "50", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bradyrhizobium vignae", "strain": "strain=LMG 28791", "accession": "GCA_004114425.1", "taxid": 1549949, "species_taxid": 1549949, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2639, "total_fragments": 2647, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bradyrhizobium forestalis", "strain": "strain=INPA54B", "accession": "GCA_002795245.1", "taxid": 1419263, "species_taxid": 1419263, "relation_to_type": "type", "validated": true, "ani": 91.834, "matched_fragments": 1951, "total_fragments": 2647, "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": 89.9544, "matched_fragments": 1904, "total_fragments": 2647, "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": 89.9357, "matched_fragments": 1789, "total_fragments": 2647, "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": 89.918, "matched_fragments": 1832, "total_fragments": 2647, "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": 89.6591, "matched_fragments": 1866, "total_fragments": 2647, "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": 89.3153, "matched_fragments": 2050, "total_fragments": 2647, "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": 89.2749, "matched_fragments": 1908, "total_fragments": 2647, "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": 88.9918, "matched_fragments": 1912, "total_fragments": 2647, "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": 88.9636, "matched_fragments": 1843, "total_fragments": 2647, "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": 88.9363, "matched_fragments": 1806, "total_fragments": 2647, "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": 88.7126, "matched_fragments": 1902, "total_fragments": 2647, "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": 88.6118, "matched_fragments": 1685, "total_fragments": 2647, "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": 88.341, "matched_fragments": 1833, "total_fragments": 2647, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium daqingense", "strain": "strain=CGMCC 1.10947", "accession": "GCA_007830205.1", "taxid": 993502, "species_taxid": 993502, "relation_to_type": "type", "validated": true, "ani": 88.3405, "matched_fragments": 1803, "total_fragments": 2647, "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": 88.1357, "matched_fragments": 1614, "total_fragments": 2647, "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": 82.6742, "matched_fragments": 1368, "total_fragments": 2647, "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": 82.5758, "matched_fragments": 1382, "total_fragments": 2647, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004114425.1", "gtdb_species": "s__Bradyrhizobium vignae", "ani": 100.0, "matched_fragments": 2639, "total_fragments": 2647, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.87", 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