{ "type": "genome", "identifier": "GCF_004912145.1", "organism": "Rhizobium rhizophilum", "title": "Rhizobium rhizophilum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Beijing Academy of Agriculture and Forestry Science", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004912145.1", "bioproject": "PRJNA224116", "biosample": "SAMN11458302", "wgs_master": "STGT00000000.1", "refseq_category": "reference genome", "taxid": "1850373", "species_taxid": "1850373", "organism_name": "Rhizobium rhizophilum", "infraspecific_name": "strain=7209-2", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/04/24", "asm_name": "ASM491214v1", "asm_submitter": "Beijing Academy of Agriculture and Forestry Science", "gbrs_paired_asm": "GCA_004912145.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/912/145/GCF_004912145.1_ASM491214v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5248183", "genome_size_ungapped": "5248183", "gc_percent": "61.000000", "replicon_count": "0", "scaffold_count": "20", "contig_count": "20", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004912145.1-RS_2024_12_11", "annotation_date": "2024-12-11", "total_gene_count": "5057", "protein_coding_gene_count": "4941", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-04-24", "dateModified": "2019-04-24", "datePublished": "2019-04-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhizobium rhizophilum" ], "sample_taxid": [ "1850373" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Inner Mongolia" ], "sample_host_location_id": [], "data_size": "1.467 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)": "5248183", "Number of Sequences": "20", "Longest Sequences (bp)": "1263873", "N50 (bp)": "971448", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "61.2", "Number of CDSs": "5059", "Average Protein Length": "305.7", "Coding Ratio (%)": "88.4", "Number of rRNAs": "3", "Number of tRNAs": "47", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhizobium rhizophilum", "strain": "strain=7209-2", "accession": "GCA_004912145.1", "taxid": 1850373, "species_taxid": 1850373, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1741, "total_fragments": 1741, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhizobium rosettiformans", "strain": "strain=DSM 26376", "accession": "GCA_014202175.1", "taxid": 1368430, "species_taxid": 1368430, "relation_to_type": "type", "validated": true, "ani": 85.6638, "matched_fragments": 1186, "total_fragments": 1741, "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": 85.6275, "matched_fragments": 1195, "total_fragments": 1741, "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": 84.0907, "matched_fragments": 1106, "total_fragments": 1741, "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": 83.3035, "matched_fragments": 1076, "total_fragments": 1741, "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": 80.0135, "matched_fragments": 706, "total_fragments": 1741, "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": 79.9251, "matched_fragments": 709, "total_fragments": 1741, "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": 79.2386, "matched_fragments": 686, "total_fragments": 1741, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agrobacterium leguminum", "strain": "strain=MOPV5", "accession": "GCA_015704895.1", "taxid": 2792015, "species_taxid": 2792015, "relation_to_type": "type", "validated": true, "ani": 79.0427, "matched_fragments": 602, "total_fragments": 1741, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium petrolearium", "strain": "strain=DSM 26482", "accession": "GCA_017873175.1", "taxid": 515361, "species_taxid": 515361, "relation_to_type": "type", "validated": true, "ani": 78.9613, "matched_fragments": 620, "total_fragments": 1741, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium skierniewicense", "strain": "strain=Ch11", "accession": "GCA_023757665.1", "taxid": 984260, "species_taxid": 984260, "relation_to_type": "type", "validated": true, "ani": 78.0653, "matched_fragments": 407, "total_fragments": 1741, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium skierniewicense", "strain": "strain=DSM 26438", "accession": "GCA_014196515.1", "taxid": 984260, "species_taxid": 984260, "relation_to_type": "type", "validated": true, "ani": 78.0096, "matched_fragments": 403, "total_fragments": 1741, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004912145.1", "gtdb_species": "s__Allorhizobium rhizophilum", "ani": 100.0, "matched_fragments": 1741, "total_fragments": 1741, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.70", "min_intra_species_ani": "95.70", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCA_900466945.1", "gtdb_species": "s__Allorhizobium sp900466945", "ani": 89.3689, "matched_fragments": 1397, "total_fragments": 1741, "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": "GCA_900473745.1", "gtdb_species": "s__Allorhizobium sp900473745", "ani": 89.2561, "matched_fragments": 1384, "total_fragments": 1741, "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_002855515.1", "gtdb_species": "s__Allorhizobium sp002855515", "ani": 87.3844, "matched_fragments": 1274, "total_fragments": 1741, "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_900156055.1", "gtdb_species": "s__Allorhizobium sp900156055", "ani": 86.3383, "matched_fragments": 1256, "total_fragments": 1741, "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_001713475.1", "gtdb_species": "s__Allorhizobium sp001713475", "ani": 86.1234, "matched_fragments": 1258, "total_fragments": 1741, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.17", "min_intra_species_ani": "97.98", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.89", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_000300855.1", "gtdb_species": "s__Allorhizobium albertimagni", "ani": 85.8381, "matched_fragments": 1305, "total_fragments": 1741, "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": 85.6228, "matched_fragments": 1196, "total_fragments": 1741, "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": "GCF_014237835.1", "gtdb_species": "s__Allorhizobium sp014237835", "ani": 84.9739, "matched_fragments": 1189, "total_fragments": 1741, "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_003205195.1", "gtdb_species": "s__Allorhizobium wuzhouense", "ani": 84.0936, "matched_fragments": 1107, "total_fragments": 1741, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.59", "min_intra_species_ani": "97.59", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900473805.1", "gtdb_species": "s__Allorhizobium sp900473805", "ani": 83.9938, "matched_fragments": 1078, "total_fragments": 1741, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.45", "min_intra_species_ani": "97.28", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.92", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_001429245.1", "gtdb_species": "s__Allorhizobium sp001429245", "ani": 83.7183, "matched_fragments": 1044, "total_fragments": 1741, "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": "GCA_900465605.1", "gtdb_species": "s__Allorhizobium sp900465605", "ani": 80.0096, "matched_fragments": 696, "total_fragments": 1741, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.96", "min_intra_species_ani": "95.85", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.91", "num_clustered_genomes": 5, "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", "rhizophilum" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }