{ "type": "genome", "identifier": "GCF_029892045.1", "organism": "Sinorhizobium numidicum", "title": "Sinorhizobium numidicum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Queen's University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_029892045.1", "bioproject": "PRJNA224116", "biosample": "SAMN33397754", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "680248", "species_taxid": "680248", "organism_name": "Sinorhizobium numidicum", "infraspecific_name": "strain=CIP 109850", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2023/03/30", "asm_name": "ASM2989204v1", "asm_submitter": "Queen's University", "gbrs_paired_asm": "GCA_029892045.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/029/892/045/GCF_029892045.1_ASM2989204v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6722812", "genome_size_ungapped": "6722812", "gc_percent": "60.500000", "replicon_count": "3", "scaffold_count": "3", "contig_count": "3", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_029892045.1-RS_2024_04_28", "annotation_date": "2024-04-28", "total_gene_count": "6429", "protein_coding_gene_count": "5994", "non_coding_gene_count": "77", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2023-03-30", "dateModified": "2023-03-30", "datePublished": "2023-03-30", "_annotation": { "sample_count": 1, "sample_organism": [ "Sinorhizobium numidicum" ], "sample_taxid": [ "680248" ], "sample_host_organism": [ "Argyrolobium uniflorum" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Tunisia" ], "sample_host_location_id": [], "data_size": "1.884 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)": "6722812", "Number of Sequences": "3", "Longest Sequences (bp)": "3768519", "N50 (bp)": "3768519", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "60.7", "Number of CDSs": "6414", "Average Protein Length": "291.3", "Coding Ratio (%)": "83.4", "Number of rRNAs": "9", "Number of tRNAs": "70", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Ensifer psoraleae", "strain": "strain=CCBAU 65732", "accession": "GCA_013283645.1", "taxid": 520838, "species_taxid": 520838, "relation_to_type": "type", "validated": true, "ani": 83.3759, "matched_fragments": 1382, "total_fragments": 2239, "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": 83.1728, "matched_fragments": 1264, "total_fragments": 2239, "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": 83.158, "matched_fragments": 1335, "total_fragments": 2239, "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": 83.0877, "matched_fragments": 1293, "total_fragments": 2239, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ensifer mexicanus", "strain": "strain=DSM 18446", "accession": "GCA_017873105.1", "taxid": 375549, "species_taxid": 375549, "relation_to_type": "type", "validated": true, "ani": 82.8341, "matched_fragments": 1264, "total_fragments": 2239, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ensifer mexicanus", "strain": "strain=ITTG R7", "accession": "GCA_013488225.1", "taxid": 375549, "species_taxid": 375549, "relation_to_type": "type", "validated": true, "ani": 82.8326, "matched_fragments": 1263, "total_fragments": 2239, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sinorhizobium meliloti", "strain": "strain=NBRC 14782", "accession": "GCA_006539625.1", "taxid": 382, "species_taxid": 382, "relation_to_type": "type", "validated": true, "ani": 82.4499, "matched_fragments": 1198, "total_fragments": 2239, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sinorhizobium meliloti", "strain": "strain=USDA 1002", "accession": "GCA_017876815.1", "taxid": 382, "species_taxid": 382, "relation_to_type": "type", "validated": true, "ani": 82.4243, "matched_fragments": 1305, "total_fragments": 2239, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sinorhizobium meliloti", "strain": "strain=USDA1002", "accession": "GCA_009601385.1", "taxid": 382, "species_taxid": 382, "relation_to_type": "type", "validated": true, "ani": 82.3799, "matched_fragments": 1250, "total_fragments": 2239, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sinorhizobium kostiense", "strain": "strain=DSM 13372", "accession": "GCA_017874595.1", "taxid": 76747, "species_taxid": 76747, "relation_to_type": "type", "validated": true, "ani": 82.2953, "matched_fragments": 1188, "total_fragments": 2239, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ensifer sojae", "strain": "strain=CCBAU 05684", "accession": "GCA_000261485.1", "taxid": 716925, "species_taxid": 716925, "relation_to_type": "type", "validated": true, "ani": 82.2304, "matched_fragments": 1146, "total_fragments": 2239, "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": 81.5971, "matched_fragments": 1099, "total_fragments": 2239, "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": 79.9139, "matched_fragments": 709, "total_fragments": 2239, "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": 79.5091, "matched_fragments": 666, "total_fragments": 2239, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella daejeonensis", "strain": "strain=JCM 16236", "accession": "GCA_024281235.1", "taxid": 659017, "species_taxid": 659017, "relation_to_type": "type", "validated": true, "ani": 79.1684, "matched_fragments": 546, "total_fragments": 2239, "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": 79.0004, "matched_fragments": 705, "total_fragments": 2239, "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": 78.6229, "matched_fragments": 684, "total_fragments": 2239, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001651875.1", "gtdb_species": "s__Sinorhizobium saheli", "ani": 83.4388, "matched_fragments": 1233, "total_fragments": 2239, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_001704765.1", "gtdb_species": "s__Sinorhizobium shofinae", "ani": 83.4027, "matched_fragments": 1181, "total_fragments": 2239, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium", "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_002078505.1", "gtdb_species": "s__Sinorhizobium aridi", "ani": 83.3957, "matched_fragments": 1456, "total_fragments": 2239, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.86", "min_intra_species_ani": "98.54", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.82", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_013283645.1", "gtdb_species": "s__Sinorhizobium psoraleae", "ani": 83.3745, "matched_fragments": 1381, "total_fragments": 2239, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium", "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_000513895.1", "gtdb_species": "s__Sinorhizobium sp000513895", "ani": 83.3477, "matched_fragments": 1404, "total_fragments": 2239, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium", "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_000265205.3", "gtdb_species": "s__Sinorhizobium fredii_B", "ani": 83.2914, "matched_fragments": 1408, "total_fragments": 2239, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.03", "min_intra_species_ani": "98.03", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.83", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001651865.1", "gtdb_species": "s__Sinorhizobium glycinis", "ani": 83.201, "matched_fragments": 1287, "total_fragments": 2239, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium", "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_001461695.1", "gtdb_species": "s__Sinorhizobium fredii", "ani": 83.0987, "matched_fragments": 1292, "total_fragments": 2239, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.55", "min_intra_species_ani": "96.82", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.82", "num_clustered_genomes": 17, "status": "-" }, { "accession": "GCF_000018545.1", "gtdb_species": "s__Sinorhizobium fredii_A", "ani": 83.0854, "matched_fragments": 1344, "total_fragments": 2239, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium", "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_004827385.1", "gtdb_species": "s__Sinorhizobium sp004827385", "ani": 82.97, "matched_fragments": 1397, "total_fragments": 2239, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium", "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_002944405.1", "gtdb_species": "s__Sinorhizobium fredii_C", "ani": 82.9517, "matched_fragments": 1306, "total_fragments": 2239, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.60", "min_intra_species_ani": "98.35", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.83", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_000378985.1", "gtdb_species": "s__Sinorhizobium sp000378985", "ani": 82.9494, "matched_fragments": 1326, "total_fragments": 2239, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium", "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_013488225.1", "gtdb_species": "s__Sinorhizobium mexicanum", "ani": 82.8512, "matched_fragments": 1266, "total_fragments": 2239, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium", "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_001651855.1", "gtdb_species": "s__Sinorhizobium americanum", "ani": 82.8497, "matched_fragments": 1270, "total_fragments": 2239, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.81", "min_intra_species_ani": "98.12", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.85", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_009601505.1", "gtdb_species": "s__Sinorhizobium terangae", "ani": 82.7596, "matched_fragments": 1344, "total_fragments": 2239, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002288525.1", "gtdb_species": "s__Sinorhizobium sojae", "ani": 82.3072, "matched_fragments": 1178, "total_fragments": 2239, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_017874595.1", "gtdb_species": "s__Sinorhizobium kostiense", "ani": 82.2736, "matched_fragments": 1190, "total_fragments": 2239, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium", "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_013283665.1", "gtdb_species": "s__Ensifer sesbaniae", "ani": 81.6027, "matched_fragments": 1095, "total_fragments": 2239, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.93", "min_intra_species_ani": "98.93", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002007205.1", "gtdb_species": "s__Ensifer adhaerens_D", "ani": 81.3792, "matched_fragments": 1048, "total_fragments": 2239, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer", "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": 0.176, "growth_tmp": 29.0, "optimum_tmp": 28.86, "optimum_ph": null, "genome_size": 6672173.704, "gc_content": 61.4, "coding_genes": 6241.448, "rRNA16S_genes": 2.977, "tRNA_genes": 53.794, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.5, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "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": [ "Sinorhizobium", "numidicum" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }