{ "type": "genome", "identifier": "GCF_017873135.1", "organism": "Rhizobium herbae", "title": "Rhizobium herbae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_017873135.1", "bioproject": "PRJNA224116", "biosample": "SAMN18247418", "wgs_master": "JAGGJV000000000.1", "refseq_category": "reference genome", "taxid": "508661", "species_taxid": "508661", "organism_name": "Rhizobium herbae", "infraspecific_name": "strain=DSM 26427", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/04/08", "asm_name": "ASM1787313v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_017873135.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/017/873/135/GCF_017873135.1_ASM1787313v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6125009", "genome_size_ungapped": "6125009", "gc_percent": "60.500000", "replicon_count": "0", "scaffold_count": "25", "contig_count": "25", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_017873135.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "5849", "protein_coding_gene_count": "5719", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-04-08", "dateModified": "2021-04-08", "datePublished": "2021-04-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhizobium herbae" ], "sample_taxid": [ "508661" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.712 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)": "6125009", "Number of Sequences": "25", "Longest Sequences (bp)": "1099193", "N50 (bp)": "509968", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "60.5", "Number of CDSs": "5782", "Average Protein Length": "308.6", "Coding Ratio (%)": "87.4", "Number of rRNAs": "3", "Number of tRNAs": "50", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhizobium giardinii", "strain": "strain=H152", "accession": "GCA_000379605.1", "taxid": 56731, "species_taxid": 56731, "relation_to_type": "type", "validated": true, "ani": 84.8223, "matched_fragments": 1296, "total_fragments": 2028, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pararhizobium antarcticum", "strain": "strain=NAQVI 59", "accession": "GCA_001885585.1", "taxid": 1798805, "species_taxid": 1798805, "relation_to_type": "type", "validated": true, "ani": 82.1539, "matched_fragments": 1078, "total_fragments": 2028, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella zoogloeoides", "strain": "strain=DSM 287", "accession": "GCA_009826855.1", "taxid": 352475, "species_taxid": 352475, "relation_to_type": "type", "validated": true, "ani": 80.6825, "matched_fragments": 780, "total_fragments": 2028, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ensifer sesbaniae", "strain": "strain=CCBAU 65729", "accession": "GCA_013283665.1", "taxid": 1214071, "species_taxid": 1214071, "relation_to_type": "type", "validated": true, "ani": 80.5903, "matched_fragments": 960, "total_fragments": 2028, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella yambaruensis", "strain": "strain=DSM 18801", "accession": "GCA_022899355.1", "taxid": 415996, "species_taxid": 415996, "relation_to_type": "type", "validated": true, "ani": 80.4706, "matched_fragments": 947, "total_fragments": 2028, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella kummerowiae", "strain": "strain=CCBAU 25048", "accession": "GCA_009827055.1", "taxid": 417745, "species_taxid": 417745, "relation_to_type": "type", "validated": true, "ani": 80.3718, "matched_fragments": 882, "total_fragments": 2028, "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": 80.2752, "matched_fragments": 782, "total_fragments": 2028, "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": 80.2691, "matched_fragments": 857, "total_fragments": 2028, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sinorhizobium fredii", "strain": "strain=NBRC 14780", "accession": "GCA_006539605.1", "taxid": 380, "species_taxid": 380, "relation_to_type": "type", "validated": true, "ani": 80.1907, "matched_fragments": 875, "total_fragments": 2028, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sinorhizobium fredii", "strain": "strain=USDA205", "accession": "GCA_009601405.1", "taxid": 380, "species_taxid": 380, "relation_to_type": "type", "validated": true, "ani": 80.1737, "matched_fragments": 890, "total_fragments": 2028, "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": 80.1686, "matched_fragments": 822, "total_fragments": 2028, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sinorhizobium fredii", "strain": "strain=USDA 205", "accession": "GCA_001461695.1", "taxid": 380, "species_taxid": 380, "relation_to_type": "type", "validated": true, "ani": 80.1591, "matched_fragments": 888, "total_fragments": 2028, "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": 80.0123, "matched_fragments": 832, "total_fragments": 2028, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium chutanense", "strain": "strain=C5", "accession": "GCA_002531935.1", "taxid": 2035448, "species_taxid": 2035448, "relation_to_type": "type", "validated": true, "ani": 79.9994, "matched_fragments": 864, "total_fragments": 2028, "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": 79.9609, "matched_fragments": 860, "total_fragments": 2028, "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": 79.9399, "matched_fragments": 892, "total_fragments": 2028, "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": 79.9266, "matched_fragments": 857, "total_fragments": 2028, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium fabae", "strain": "strain=CCBAU 33202", "accession": "GCA_003985135.1", "taxid": 573179, "species_taxid": 573179, "relation_to_type": "type", "validated": true, "ani": 79.9107, "matched_fragments": 834, "total_fragments": 2028, "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": 79.9051, "matched_fragments": 828, "total_fragments": 2028, "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": 79.8837, "matched_fragments": 854, "total_fragments": 2028, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium etli", "strain": "strain=CFN 42", "accession": "GCA_000092045.1", "taxid": 29449, "species_taxid": 29449, "relation_to_type": "suspected-type", "validated": true, "ani": 79.7679, "matched_fragments": 814, "total_fragments": 2028, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ensifer psoraleae", "strain": "strain=CCBAU 65732", "accession": "GCA_013283645.1", "taxid": 520838, "species_taxid": 520838, "relation_to_type": "type", "validated": true, "ani": 79.6922, "matched_fragments": 862, "total_fragments": 2028, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neorhizobium alkalisoli", "strain": "strain=DSM 21826", "accession": "GCA_002968635.1", "taxid": 528178, "species_taxid": 528178, "relation_to_type": "type", "validated": true, "ani": 79.0751, "matched_fragments": 619, "total_fragments": 2028, "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": 79.0135, "matched_fragments": 625, "total_fragments": 2028, "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": 77.79, "matched_fragments": 418, "total_fragments": 2028, "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": 77.7235, "matched_fragments": 416, "total_fragments": 2028, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_017873135.1", "gtdb_species": "s__Pararhizobium herbae", "ani": 100.0, "matched_fragments": 2028, "total_fragments": 2028, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium", "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": "conclusive" }, { "accession": "GCF_001687365.1", "gtdb_species": "s__Pararhizobium polonicum", "ani": 88.8037, "matched_fragments": 1448, "total_fragments": 2028, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium", "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_000745255.1", "gtdb_species": "s__Pararhizobium sp000745255", "ani": 87.5556, "matched_fragments": 1521, "total_fragments": 2028, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.24", "min_intra_species_ani": "95.31", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.85", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_900468065.1", "gtdb_species": "s__Pararhizobium sp900468065", "ani": 85.9625, "matched_fragments": 1325, "total_fragments": 2028, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium", "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": "GCA_900473045.1", "gtdb_species": "s__Pararhizobium sp900473045", "ani": 85.6996, "matched_fragments": 1328, "total_fragments": 2028, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium", "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_000745575.1", "gtdb_species": "s__Pararhizobium sp000745575", "ani": 85.476, "matched_fragments": 1360, "total_fragments": 2028, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.55", "min_intra_species_ani": "96.55", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001426685.1", "gtdb_species": "s__Pararhizobium sp001426685", "ani": 85.4642, "matched_fragments": 1282, "total_fragments": 2028, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium", "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": "GCA_900472175.1", "gtdb_species": "s__Pararhizobium sp900472175", "ani": 85.305, "matched_fragments": 1295, "total_fragments": 2028, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium", "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_001426665.1", "gtdb_species": "s__Pararhizobium sp001426665", "ani": 84.9369, "matched_fragments": 1313, "total_fragments": 2028, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.66", "min_intra_species_ani": "98.98", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.87", "num_clustered_genomes": 4, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.23, "cell_length": 0.207, "doubling_h": 0.225, "growth_tmp": 30.0, "optimum_tmp": 28.423, "optimum_ph": 6.983, "genome_size": 6116837.0, "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", "herbae" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }