{ "type": "genome", "identifier": "GCF_001641335.1", "organism": "Bradyrhizobium stylosanthis", "title": "Bradyrhizobium stylosanthis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Embrapa Soja", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001641335.1", "bioproject": "PRJNA224116", "biosample": "SAMN04549886", "wgs_master": "LVEM00000000.1", "refseq_category": "reference genome", "taxid": "1803665", "species_taxid": "1803665", "organism_name": "Bradyrhizobium stylosanthis", "infraspecific_name": "strain=BR 446", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/05/10", "asm_name": "ASM164133v1", "asm_submitter": "Embrapa Soja", "gbrs_paired_asm": "GCA_001641335.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/641/335/GCF_001641335.1_ASM164133v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "8801717", "genome_size_ungapped": "8801717", "gc_percent": "64.500000", "replicon_count": "0", "scaffold_count": "22", "contig_count": "22", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001641335.1-RS_2024_05_26", "annotation_date": "2024-05-26", "total_gene_count": "8244", "protein_coding_gene_count": "8071", "non_coding_gene_count": "67", "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 stylosanthis" ], "sample_taxid": [ "1803665" ], "sample_host_organism": [ "Stylosanthes guianensis" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Brazil: Rio de Janeiro" ], "sample_host_location_id": [], "data_size": "2.420 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 2.08, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "8801717", "Number of Sequences": "22", "Longest Sequences (bp)": "2454055", "N50 (bp)": "1501053", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "64.6", "Number of CDSs": "8234", "Average Protein Length": "303.6", "Coding Ratio (%)": "85.2", "Number of rRNAs": "4", "Number of tRNAs": "54", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bradyrhizobium stylosanthis", "strain": "strain=BR 446", "accession": "GCA_001641335.1", "taxid": 1803665, "species_taxid": 1803665, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2923, "total_fragments": 2925, "ani_threshold": 95, "status": "conclusive" }, { "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": 90.8567, "matched_fragments": 2240, "total_fragments": 2925, "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": 90.2087, "matched_fragments": 2137, "total_fragments": 2925, "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": 89.7869, "matched_fragments": 2157, "total_fragments": 2925, "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": 89.7663, "matched_fragments": 2159, "total_fragments": 2925, "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": 89.7622, "matched_fragments": 2160, "total_fragments": 2925, "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": 89.7443, "matched_fragments": 2194, "total_fragments": 2925, "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": 89.2775, "matched_fragments": 1945, "total_fragments": 2925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium ottawaense", "strain": "strain=OO99", "accession": "GCA_002278135.2", "taxid": 931866, "species_taxid": 931866, "relation_to_type": "type", "validated": true, "ani": 89.1302, "matched_fragments": 2060, "total_fragments": 2925, "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": 89.0841, "matched_fragments": 2041, "total_fragments": 2925, "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": 89.024, "matched_fragments": 1847, "total_fragments": 2925, "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": 88.9072, "matched_fragments": 1989, "total_fragments": 2925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium amphicarpaeae", "strain": "strain=39S1MB", "accession": "GCA_002266435.2", "taxid": 1404768, "species_taxid": 1404768, "relation_to_type": "type", "validated": true, "ani": 88.9022, "matched_fragments": 1941, "total_fragments": 2925, "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": 88.828, "matched_fragments": 1909, "total_fragments": 2925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium frederickii", "strain": "strain=CNPSo 3426", "accession": "GCA_004570865.1", "taxid": 2560054, "species_taxid": 2560054, "relation_to_type": "type", "validated": true, "ani": 88.783, "matched_fragments": 1926, "total_fragments": 2925, "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": 88.742, "matched_fragments": 1954, "total_fragments": 2925, "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": 88.4863, "matched_fragments": 1943, "total_fragments": 2925, "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": 88.1623, "matched_fragments": 1833, "total_fragments": 2925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium rifense", "strain": "strain=CTAW71", "accession": "GCA_008123425.1", "taxid": 515499, "species_taxid": 515499, "relation_to_type": "type", "validated": true, "ani": 88.0726, "matched_fragments": 1963, "total_fragments": 2925, "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": 83.1688, "matched_fragments": 1600, "total_fragments": 2925, "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": 83.0451, "matched_fragments": 1458, "total_fragments": 2925, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 2.08, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001641335.1", "gtdb_species": "s__Bradyrhizobium stylosanthis", "ani": 100.0, "matched_fragments": 2923, "total_fragments": 2925, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.54", "min_intra_species_ani": "96.50", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.85", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_018130825.1", "gtdb_species": "s__Bradyrhizobium liaoningense_B", "ani": 91.1143, "matched_fragments": 2206, "total_fragments": 2925, "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_018130765.1", "gtdb_species": "s__Bradyrhizobium iriomotense_A", "ani": 90.7604, "matched_fragments": 2224, "total_fragments": 2925, "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", 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"N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_002068095.1", "gtdb_species": "s__Bradyrhizobium sacchari", "ani": 90.2179, "matched_fragments": 2135, "total_fragments": 2925, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000011365.1", "gtdb_species": "s__Bradyrhizobium diazoefficiens", "ani": 89.7723, "matched_fragments": 2158, "total_fragments": 2925, "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", 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