{ "type": "genome", "identifier": "GCF_003985155.1", "organism": "Rhizobium vallis", "title": "Rhizobium vallis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "North West Agriculture and Forestry University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003985155.1", "bioproject": "PRJNA224116", "biosample": "SAMN10390720", "wgs_master": "RJTH00000000.1", "refseq_category": "reference genome", "taxid": "634290", "species_taxid": "634290", "organism_name": "Rhizobium vallis", "infraspecific_name": "strain=CCBAU 65647", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/12/28", "asm_name": "ASM398515v1", "asm_submitter": "North West Agriculture and Forestry University", "gbrs_paired_asm": "GCA_003985155.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/985/155/GCF_003985155.1_ASM398515v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7115113", "genome_size_ungapped": "7115083", "gc_percent": "61.000000", "replicon_count": "0", "scaffold_count": "62", "contig_count": "65", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003985155.1-RS_2024_05_01", "annotation_date": "2024-05-01", "total_gene_count": "6909", "protein_coding_gene_count": "6624", "non_coding_gene_count": "54", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-12-28", "dateModified": "2018-12-28", "datePublished": "2018-12-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhizobium vallis" ], "sample_taxid": [ "634290" ], "sample_host_organism": [ "Phaseolus vulgaris" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Yunnan" ], "sample_host_location_id": [], "data_size": "1.988 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)": "7115113", "Number of Sequences": "62", "Longest Sequences (bp)": "1044850", "N50 (bp)": "440881", "Gap Ratio (%)": "0.000422", "GCcontent (%)": "60.8", "Number of CDSs": "6807", "Average Protein Length": "301.8", "Coding Ratio (%)": "86.6", "Number of rRNAs": "3", "Number of tRNAs": "48", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhizobium vallis", "strain": "strain=CCBAU 65647", "accession": "GCA_003985155.1", "taxid": 634290, "species_taxid": 634290, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2340, "total_fragments": 2343, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhizobium fabae", "strain": "strain=CCBAU 33202", "accession": "GCA_003985135.1", "taxid": 573179, "species_taxid": 573179, "relation_to_type": "type", "validated": true, "ani": 91.0877, "matched_fragments": 1794, "total_fragments": 2343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium pisi", "strain": "strain=DSM 30132", "accession": "GCA_003938655.1", "taxid": 574561, "species_taxid": 574561, "relation_to_type": "type", "validated": true, "ani": 91.015, "matched_fragments": 1801, "total_fragments": 2343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium fabae", "strain": "strain=DSM 19331", "accession": "GCA_014196235.1", "taxid": 573179, "species_taxid": 573179, "relation_to_type": "type", "validated": true, "ani": 90.9731, "matched_fragments": 1818, "total_fragments": 2343, "ani_threshold": 95, "status": "below_threshold" }, { 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"strain=13T", "accession": "GCA_019793465.1", "taxid": 2867516, "species_taxid": 2867516, "relation_to_type": "type", "validated": true, "ani": 88.6585, "matched_fragments": 1652, "total_fragments": 2343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium anhuiense", "strain": "strain=CGMCC 1.12621", "accession": "GCA_014638185.1", "taxid": 1184720, "species_taxid": 1184720, "relation_to_type": "type", "validated": true, "ani": 88.6512, "matched_fragments": 1681, "total_fragments": 2343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium hidalgonense", "strain": "strain=FH14", "accession": "GCA_002914525.1", "taxid": 1538159, "species_taxid": 1538159, "relation_to_type": "type", "validated": true, "ani": 88.6455, "matched_fragments": 1750, "total_fragments": 2343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium hidalgonense", "strain": "strain=FH14", "accession": "GCA_002531855.1", "taxid": 1538159, "species_taxid": 1538159, "relation_to_type": "type", "validated": true, "ani": 88.628, "matched_fragments": 1753, "total_fragments": 2343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium redzepovicii", "strain": "strain=18T", "accession": "GCA_019793435.1", "taxid": 2867518, "species_taxid": 2867518, "relation_to_type": "type", "validated": true, "ani": 88.6161, "matched_fragments": 1729, "total_fragments": 2343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium changzhiense", "strain": "strain=WYCCWR 11279", "accession": "GCA_013087625.1", "taxid": 2692317, "species_taxid": 2692317, "relation_to_type": "type", "validated": true, "ani": 88.4795, "matched_fragments": 1553, "total_fragments": 2343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium indicum", "strain": "strain=JKLM 12A2", "accession": "GCA_005862305.2", "taxid": 2583231, "species_taxid": 2583231, "relation_to_type": "type", "validated": true, "ani": 88.4469, "matched_fragments": 1645, "total_fragments": 2343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium ruizarguesonis", "strain": "strain=UPM1133", "accession": "GCA_012349115.1", "taxid": 2081791, "species_taxid": 2081791, "relation_to_type": "type", "validated": true, "ani": 88.3562, "matched_fragments": 1661, "total_fragments": 2343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium sophorae", "strain": "strain=CCBAU 03386", "accession": "GCA_013087515.1", "taxid": 1535242, "species_taxid": 1535242, "relation_to_type": "type", "validated": true, "ani": 88.2971, "matched_fragments": 1622, "total_fragments": 2343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium laguerreae", "strain": "strain=FB206", "accession": "GCA_002008165.1", "taxid": 1076926, "species_taxid": 1076926, "relation_to_type": "type", "validated": true, "ani": 88.1171, "matched_fragments": 1623, "total_fragments": 2343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium laguerreae", "strain": "strain=CECT 8280", "accession": "GCA_014192445.1", "taxid": 1076926, "species_taxid": 1076926, "relation_to_type": "type", "validated": true, "ani": 88.0705, "matched_fragments": 1643, "total_fragments": 2343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium mongolense subsp. loessense", "strain": "strain=CGMCC 1.3401", "accession": "GCA_900099775.1", "taxid": 158890, "species_taxid": 57676, "relation_to_type": "type", "validated": true, "ani": 81.4267, "matched_fragments": 1124, "total_fragments": 2343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium dioscoreae", "strain": "strain=S-93", "accession": "GCA_009176305.1", "taxid": 2653122, "species_taxid": 2653122, "relation_to_type": "type", "validated": true, "ani": 80.4999, "matched_fragments": 971, 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"GCF_003938655.1", "gtdb_species": "s__Rhizobium pisi", "ani": 91.0298, "matched_fragments": 1799, "total_fragments": 2343, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.78", "min_intra_species_ani": "97.55", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.90", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_014198335.1", "gtdb_species": "s__Rhizobium leguminosarum_N", "ani": 89.6097, "matched_fragments": 1605, "total_fragments": 2343, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.95", "min_intra_species_ani": "99.93", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_002531935.1", "gtdb_species": 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