{ "type": "genome", "identifier": "GCF_001938985.1", "organism": "Allorhizobium taibaishanense", "title": "Allorhizobium taibaishanense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Chinese Academy of Agricultural Sciences", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001938985.1", "bioproject": "PRJNA224116", "biosample": "SAMN05832037", "wgs_master": "MKIN00000000.1", "refseq_category": "reference genome", "taxid": "887144", "species_taxid": "887144", "organism_name": "Allorhizobium taibaishanense", "infraspecific_name": "strain=14971", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/01/06", "asm_name": "ASM193898v1", "asm_submitter": "Chinese Academy of Agricultural Sciences", "gbrs_paired_asm": "GCA_001938985.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/938/985/GCF_001938985.1_ASM193898v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5418020", "genome_size_ungapped": "5417930", "gc_percent": "59.500000", "replicon_count": "0", "scaffold_count": "28", "contig_count": "28", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001938985.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "4919", "protein_coding_gene_count": "4807", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-01-06", "dateModified": "2017-01-06", "datePublished": "2017-01-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Allorhizobium taibaishanense" ], "sample_taxid": [ "887144" ], "sample_host_organism": [ "Kummerowia striata" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.523 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)": "5418020", "Number of Sequences": "28", "Longest Sequences (bp)": "1283339", "N50 (bp)": "465074", "Gap Ratio (%)": "0.001698", "GCcontent (%)": "59.3", "Number of CDSs": "4956", "Average Protein Length": "317.3", "Coding Ratio (%)": "87.1", "Number of rRNAs": "3", "Number of tRNAs": "48", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhizobium taibaishanense", "strain": "strain=14971", "accession": "GCA_001938985.1", "taxid": 887144, "species_taxid": 887144, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1793, "total_fragments": 1793, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhizobium taibaishanense", "strain": "strain=DSM 100021", "accession": "GCA_014196735.1", "taxid": 887144, "species_taxid": 887144, "relation_to_type": "type", "validated": true, "ani": 99.9982, "matched_fragments": 1793, "total_fragments": 1793, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Ciceribacter selenitireducens", "strain": "strain=ATCC BAA-1503", "accession": "GCA_000518785.1", "taxid": 448181, "species_taxid": 448181, "relation_to_type": "type", "validated": true, "ani": 79.429, "matched_fragments": 677, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium wuzhouense", "strain": "strain=W44", "accession": "GCA_003205195.1", "taxid": 1986026, "species_taxid": 1986026, "relation_to_type": "type", "validated": true, "ani": 79.3671, "matched_fragments": 635, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium halophytocola", "strain": "strain=DSM 21600", "accession": "GCA_017873095.1", "taxid": 735519, "species_taxid": 735519, "relation_to_type": "type", "validated": true, "ani": 79.3221, "matched_fragments": 642, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium glycinendophyticum", "strain": "strain=CL12", "accession": "GCA_006443685.1", "taxid": 2589807, "species_taxid": 2589807, "relation_to_type": "type", "validated": true, "ani": 79.2435, "matched_fragments": 609, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium rosettiformans", "strain": "strain=DSM 26376", "accession": "GCA_014202175.1", "taxid": 1368430, "species_taxid": 1368430, "relation_to_type": "type", "validated": true, "ani": 79.1294, "matched_fragments": 615, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium rhizophilum", "strain": "strain=7209-2", "accession": "GCA_004912145.1", "taxid": 1850373, "species_taxid": 1850373, "relation_to_type": "type", "validated": true, "ani": 79.1285, "matched_fragments": 586, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium rosettiformans", "strain": "strain=W3", "accession": "GCA_004912135.1", "taxid": 1368430, "species_taxid": 1368430, "relation_to_type": "type", "validated": true, "ani": 79.0947, "matched_fragments": 614, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neorhizobium vignae", "strain": "strain=CCBAU 05176", "accession": "GCA_000732195.1", "taxid": 690585, "species_taxid": 690585, "relation_to_type": "type", "validated": true, "ani": 78.9112, "matched_fragments": 597, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neorhizobium galegae", "strain": "strain=HAMBI 540", "accession": "GCA_000731315.1", "taxid": 399, "species_taxid": 399, "relation_to_type": "suspected-type", "validated": true, "ani": 78.7327, "matched_fragments": 577, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ciceribacter lividus", "strain": "strain=DSM 25528", "accession": "GCA_003337715.1", "taxid": 1197950, "species_taxid": 1197950, "relation_to_type": "type", "validated": true, "ani": 78.6584, "matched_fragments": 533, "total_fragments": 1793, "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": 78.6581, "matched_fragments": 625, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ciceribacter thiooxidans", "strain": "strain=F43B", "accession": "GCA_014126615.1", "taxid": 1969821, "species_taxid": 1969821, "relation_to_type": "type", "validated": true, "ani": 78.6357, "matched_fragments": 516, "total_fragments": 1793, "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": 78.6352, "matched_fragments": 520, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium binae", "strain": "strain=BLR195", "accession": "GCA_017357225.1", "taxid": 1138190, "species_taxid": 1138190, "relation_to_type": "type", "validated": true, "ani": 78.6231, "matched_fragments": 616, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ciceribacter naphthalenivorans", "strain": "strain=NBRC 107585", "accession": "GCA_007992095.1", "taxid": 1118451, "species_taxid": 1118451, "relation_to_type": "type", "validated": true, "ani": 78.5758, "matched_fragments": 522, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella sumterensis", "strain": "strain=MEC087", "accession": "GCA_004514425.2", "taxid": 1967501, "species_taxid": 1967501, "relation_to_type": "type", "validated": true, "ani": 78.5607, "matched_fragments": 539, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella curvata", "strain": "strain=C3", "accession": "GCA_022899935.1", "taxid": 1817964, "species_taxid": 1817964, "relation_to_type": "type", "validated": true, "ani": 78.5568, "matched_fragments": 543, "total_fragments": 1793, "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": 78.507, "matched_fragments": 637, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella pollutisoli", "strain": "strain=KCTC 52677", "accession": "GCA_024609765.1", "taxid": 2250594, "species_taxid": 2250594, "relation_to_type": "type", "validated": true, "ani": 78.4422, "matched_fragments": 483, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neorhizobium lilium", "strain": "strain=24NR", "accession": "GCA_004053875.1", "taxid": 2503024, "species_taxid": 2503024, "relation_to_type": "type", "validated": true, "ani": 78.2643, "matched_fragments": 513, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001938985.1", "gtdb_species": "s__Allorhizobium taibaishanense", "ani": 100.0, "matched_fragments": 1793, "total_fragments": 1793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_009744115.1", "gtdb_species": "s__Allorhizobium vitis_E", "ani": 82.3544, "matched_fragments": 1153, "total_fragments": 1793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "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_001541345.2", "gtdb_species": "s__Allorhizobium vitis", "ani": 82.2989, "matched_fragments": 1172, "total_fragments": 1793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.04", "min_intra_species_ani": "96.12", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.85", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_001758275.2", "gtdb_species": "s__Allorhizobium vitis_B", "ani": 82.287, "matched_fragments": 1187, "total_fragments": 1793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.87", "min_intra_species_ani": "95.34", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.85", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_013426735.1", "gtdb_species": "s__Allorhizobium vitis_D", "ani": 82.2765, "matched_fragments": 1179, "total_fragments": 1793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.49", "min_intra_species_ani": "97.49", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009744025.1", "gtdb_species": "s__Allorhizobium vitis_A", "ani": 82.2032, "matched_fragments": 1194, "total_fragments": 1793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.14", "min_intra_species_ani": "95.73", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.84", "num_clustered_genomes": 24, "status": "-" }, { "accession": "GCF_000621665.1", "gtdb_species": "s__Allorhizobium undicola", "ani": 79.5022, "matched_fragments": 680, "total_fragments": 1793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "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_000300855.1", "gtdb_species": "s__Allorhizobium albertimagni", "ani": 79.2882, "matched_fragments": 605, "total_fragments": 1793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "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_014237835.1", "gtdb_species": "s__Allorhizobium sp014237835", "ani": 79.1998, "matched_fragments": 592, "total_fragments": 1793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "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_004912135.1", "gtdb_species": "s__Allorhizobium rosettiformans", "ani": 79.0906, "matched_fragments": 614, "total_fragments": 1793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.40", "min_intra_species_ani": "95.42", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.84", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCA_900466945.1", "gtdb_species": "s__Allorhizobium sp900466945", "ani": 79.0242, "matched_fragments": 583, "total_fragments": 1793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002855515.1", "gtdb_species": "s__Allorhizobium sp002855515", "ani": 79.0162, "matched_fragments": 616, "total_fragments": 1793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "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_005860795.2", "gtdb_species": "s__Allorhizobium desertarenae", "ani": 78.7329, "matched_fragments": 458, "total_fragments": 1793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "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": 78.6746, "matched_fragments": 623, "total_fragments": 1793, "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_003985125.1", "gtdb_species": "s__Rhizobium phaseoli", "ani": 78.6443, "matched_fragments": 627, "total_fragments": 1793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.51", "min_intra_species_ani": "96.92", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.87", "num_clustered_genomes": 41, "status": "-" }, { "accession": "GCF_000009265.1", "gtdb_species": "s__Rhizobium leguminosarum_L", "ani": 78.5629, "matched_fragments": 640, "total_fragments": 1793, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.59", "min_intra_species_ani": "95.46", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.82", "num_clustered_genomes": 60, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Allorhizobium", "taibaishanense" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }