{ "type": "genome", "identifier": "GCF_002531935.1", "organism": "Rhizobium chutanense", "title": "Rhizobium chutanense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Northwest A&F University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002531935.1", "bioproject": "PRJNA224116", "biosample": "SAMN07627103", "wgs_master": "NWSV00000000.1", "refseq_category": "reference genome", "taxid": "2035448", "species_taxid": "2035448", "organism_name": "Rhizobium chutanense", "infraspecific_name": "strain=C5", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/10/12", "asm_name": "ASM253193v1", "asm_submitter": "Northwest A&F University", "gbrs_paired_asm": "GCA_002531935.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/531/935/GCF_002531935.1_ASM253193v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6883664", "genome_size_ungapped": "6883664", "gc_percent": "61.500000", "replicon_count": "0", "scaffold_count": "97", "contig_count": "97", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002531935.1-RS_2024_04_30", "annotation_date": "2024-04-30", "total_gene_count": "6639", "protein_coding_gene_count": "6415", "non_coding_gene_count": "52", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-10-12", "dateModified": "2017-10-12", "datePublished": "2017-10-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhizobium chutanense" ], "sample_taxid": [ "2035448" ], "sample_host_organism": [ "Phaseolus vulgaris" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Chutan, Jiangxi" ], "sample_host_location_id": [], "data_size": "1.920 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)": "6883664", "Number of Sequences": "97", "Longest Sequences (bp)": "512775", "N50 (bp)": "230095", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "61.4", "Number of CDSs": "6502", "Average Protein Length": "304.9", "Coding Ratio (%)": "86.4", "Number of rRNAs": "0", "Number of tRNAs": "50", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhizobium chutanense", "strain": "strain=C5", "accession": "GCA_002531935.1", "taxid": 2035448, "species_taxid": 2035448, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2245, "total_fragments": 2252, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhizobium hidalgonense", "strain": "strain=FH14", "accession": "GCA_002914525.1", "taxid": 1538159, "species_taxid": 1538159, "relation_to_type": "type", "validated": true, "ani": 90.9559, "matched_fragments": 1770, "total_fragments": 2252, "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": 90.9465, "matched_fragments": 1771, "total_fragments": 2252, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium ecuadorense", "strain": "strain=CNPSO 671", "accession": "GCA_001187535.1", "taxid": 1671795, "species_taxid": 1671795, "relation_to_type": "type", "validated": true, "ani": 90.5033, "matched_fragments": 1706, "total_fragments": 2252, "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": 89.9531, "matched_fragments": 1767, "total_fragments": 2252, "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": 89.5825, "matched_fragments": 1717, "total_fragments": 2252, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium anhuiense", "strain": "strain=CCBAU 23252", "accession": "GCA_003985145.1", "taxid": 1184720, "species_taxid": 1184720, "relation_to_type": "type", "validated": true, "ani": 89.5523, "matched_fragments": 1720, "total_fragments": 2252, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium vallis", "strain": "strain=CCBAU 65647", "accession": "GCA_003985155.1", "taxid": 634290, "species_taxid": 634290, "relation_to_type": "type", "validated": true, "ani": 89.4574, "matched_fragments": 1743, "total_fragments": 2252, "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": 89.2742, "matched_fragments": 1571, "total_fragments": 2252, "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": 89.0646, "matched_fragments": 1694, "total_fragments": 2252, "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": 89.0504, "matched_fragments": 1686, "total_fragments": 2252, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium croatiense", "strain": "strain=13T", "accession": "GCA_019793465.1", "taxid": 2867516, "species_taxid": 2867516, "relation_to_type": "type", "validated": true, "ani": 88.9687, "matched_fragments": 1658, "total_fragments": 2252, "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": 88.9429, "matched_fragments": 1661, "total_fragments": 2252, "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": 88.8476, "matched_fragments": 1617, "total_fragments": 2252, "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": 88.7842, "matched_fragments": 1639, "total_fragments": 2252, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium phaseoli", "strain": "strain=ATCC 14482", "accession": "GCA_003985125.1", "taxid": 396, "species_taxid": 396, "relation_to_type": "type", "validated": true, "ani": 88.7663, "matched_fragments": 1694, "total_fragments": 2252, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium aethiopicum", "strain": "strain=HBR26", "accession": "GCA_900094625.1", "taxid": 1138170, "species_taxid": 1138170, "relation_to_type": "type", "validated": true, "ani": 88.5541, "matched_fragments": 1654, "total_fragments": 2252, "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": 81.4157, "matched_fragments": 1163, "total_fragments": 2252, "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": 80.615, "matched_fragments": 1008, "total_fragments": 2252, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ciceribacter ferrooxidans", "strain": "strain=F8825", "accession": "GCA_004137355.1", "taxid": 2509717, "species_taxid": 2509717, "relation_to_type": "type", "validated": true, "ani": 79.5804, "matched_fragments": 688, "total_fragments": 2252, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002531935.1", "gtdb_species": "s__Rhizobium chutanense", "ani": 100.0, "matched_fragments": 2245, "total_fragments": 2252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.76", "min_intra_species_ani": "96.76", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_014197615.1", "gtdb_species": "s__Rhizobium esperanzae_A", "ani": 93.6465, "matched_fragments": 1695, "total_fragments": 2252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "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_000172795.2", "gtdb_species": "s__Rhizobium sp000172795", "ani": 93.374, "matched_fragments": 1800, "total_fragments": 2252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "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_014198335.1", "gtdb_species": "s__Rhizobium leguminosarum_N", "ani": 92.0276, "matched_fragments": 1652, "total_fragments": 2252, "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_002531725.1", "gtdb_species": "s__Rhizobium sp002531725", "ani": 91.8569, "matched_fragments": 1831, "total_fragments": 2252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "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_002914525.1", "gtdb_species": "s__Rhizobium hidalgonense", "ani": 90.9559, "matched_fragments": 1770, "total_fragments": 2252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.87", "min_intra_species_ani": "98.55", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.84", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_001664485.1", "gtdb_species": "s__Rhizobium sp001664485", "ani": 90.137, "matched_fragments": 1825, "total_fragments": 2252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.08", "min_intra_species_ani": "96.02", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.83", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_000271845.1", "gtdb_species": "s__Rhizobium leguminosarum_G", "ani": 90.0765, "matched_fragments": 1725, "total_fragments": 2252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "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_002531905.1", "gtdb_species": "s__Rhizobium sp002531905", "ani": 89.9364, "matched_fragments": 1767, "total_fragments": 2252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.24", "min_intra_species_ani": "98.93", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.86", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_002531755.2", "gtdb_species": "s__Rhizobium acidisoli", "ani": 89.8606, "matched_fragments": 1784, "total_fragments": 2252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.96", "min_intra_species_ani": "96.40", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.80", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_003985145.1", "gtdb_species": "s__Rhizobium anhuiense", "ani": 89.561, "matched_fragments": 1719, "total_fragments": 2252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.85", "min_intra_species_ani": "98.46", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 19, "status": "-" }, { "accession": "GCF_003985155.1", "gtdb_species": "s__Rhizobium vallis", "ani": 89.4688, "matched_fragments": 1741, "total_fragments": 2252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "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_002211285.1", "gtdb_species": "s__Rhizobium sp002211285", "ani": 89.3729, "matched_fragments": 1601, "total_fragments": 2252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "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_001657485.1", "gtdb_species": "s__Rhizobium sp001657485", "ani": 89.1006, "matched_fragments": 1645, "total_fragments": 2252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.95", "min_intra_species_ani": "97.95", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_012349115.1", "gtdb_species": "s__Rhizobium ruizarguesonis", "ani": 89.0493, "matched_fragments": 1685, "total_fragments": 2252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.01", "min_intra_species_ani": "96.15", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.84", "num_clustered_genomes": 170, "status": "-" }, { "accession": "GCF_013087515.1", "gtdb_species": "s__Rhizobium sophorae", "ani": 88.9494, "matched_fragments": 1661, "total_fragments": 2252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.85", "min_intra_species_ani": "95.49", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.83", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_900094625.1", "gtdb_species": "s__Rhizobium aethiopicum", "ani": 88.5455, "matched_fragments": 1655, "total_fragments": 2252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.33", "min_intra_species_ani": "98.33", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002211305.1", "gtdb_species": "s__Rhizobium sp002211305", "ani": 88.2883, "matched_fragments": 1674, "total_fragments": 2252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.97", "min_intra_species_ani": "96.97", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.23, "cell_length": 0.207, "doubling_h": 0.225, "growth_tmp": 28.733, "optimum_tmp": 28.423, "optimum_ph": 6.983, "genome_size": 6239444.624, "gc_content": 60.147, "coding_genes": 6587.615, "rRNA16S_genes": 3.0, "tRNA_genes": 51.725, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.793, "range_salinity": null, "facultative_respiration": 0.05, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.95, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Rhizobium", "chutanense" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }