{ "type": "genome", "identifier": "GCF_014196515.1", "organism": "Rhizobium skierniewicense", "title": "Rhizobium skierniewicense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014196515.1", "bioproject": "PRJNA224116", "biosample": "SAMN13173413", "wgs_master": "JACIDV000000000.1", "refseq_category": "na", "taxid": "984260", "species_taxid": "984260", "organism_name": "Rhizobium skierniewicense", "infraspecific_name": "strain=DSM 26438", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/08/14", "asm_name": "ASM1419651v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_014196515.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/196/515/GCF_014196515.1_ASM1419651v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4798976", "genome_size_ungapped": "4798976", "gc_percent": "57.000000", "replicon_count": "0", "scaffold_count": "33", "contig_count": "33", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-01-27", "total_gene_count": "4580", "protein_coding_gene_count": "4447", "non_coding_gene_count": "51", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-08-14", "dateModified": "2020-08-14", "datePublished": "2020-08-14", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhizobium skierniewicense" ], "sample_taxid": [ "984260" ], "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": "1.360 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)": "4798976", "Number of Sequences": "33", "Longest Sequences (bp)": "614440", "N50 (bp)": "348058", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "56.9", "Number of CDSs": "4554", "Average Protein Length": "307.5", "Coding Ratio (%)": "87.5", "Number of rRNAs": "2", "Number of tRNAs": "43", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhizobium skierniewicense", "strain": "strain=DSM 26438", "accession": "GCA_014196515.1", "taxid": 984260, "species_taxid": 984260, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1581, "total_fragments": 1582, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhizobium skierniewicense", "strain": "strain=Ch11", "accession": "GCA_023757665.1", "taxid": 984260, "species_taxid": 984260, "relation_to_type": "type", "validated": true, "ani": 99.9906, "matched_fragments": 1571, "total_fragments": 1582, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Agrobacterium rubi", "strain": "strain=NBRC 13261", "accession": "GCA_000739935.1", "taxid": 28099, "species_taxid": 28099, "relation_to_type": "type", "validated": true, "ani": 85.0965, "matched_fragments": 1194, "total_fragments": 1582, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agrobacterium rubi", "strain": "strain=DSM 6772", "accession": "GCA_017873055.1", "taxid": 28099, "species_taxid": 28099, "relation_to_type": "type", "validated": true, "ani": 85.0277, "matched_fragments": 1193, "total_fragments": 1582, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agrobacterium rosae", "strain": "strain=NCPPB 1650", "accession": "GCA_002915175.1", "taxid": 1972867, "species_taxid": 1972867, "relation_to_type": "type", "validated": true, "ani": 83.6155, "matched_fragments": 1032, "total_fragments": 1582, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agrobacterium bohemicum", "strain": "strain=R90", "accession": "GCA_002896715.1", "taxid": 2052828, "species_taxid": 2052828, "relation_to_type": "type", "validated": true, "ani": 83.0579, "matched_fragments": 957, "total_fragments": 1582, "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": 78.078, "matched_fragments": 404, "total_fragments": 1582, "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": 77.5894, "matched_fragments": 330, "total_fragments": 1582, "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": 77.5148, "matched_fragments": 385, "total_fragments": 1582, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014196515.1", "gtdb_species": "s__Agrobacterium skierniewicense", "ani": 100.0, "matched_fragments": 1581, "total_fragments": 1582, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.07", "min_intra_species_ani": "98.07", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_000739935.1", "gtdb_species": "s__Agrobacterium rubi", "ani": 85.0895, "matched_fragments": 1195, "total_fragments": 1582, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.45", "min_intra_species_ani": "95.90", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.87", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_002915175.1", "gtdb_species": "s__Agrobacterium rosae", "ani": 83.6334, "matched_fragments": 1030, "total_fragments": 1582, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.78", "min_intra_species_ani": "95.28", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.82", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCA_900468015.1", "gtdb_species": "s__Agrobacterium sp900468015", "ani": 83.4451, "matched_fragments": 940, "total_fragments": 1582, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.47", "min_intra_species_ani": "95.47", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900472925.1", "gtdb_species": "s__Agrobacterium sp900472925", "ani": 83.3815, "matched_fragments": 988, "total_fragments": 1582, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium", "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_001422245.1", "gtdb_species": "s__Agrobacterium sp001422245", "ani": 83.2661, "matched_fragments": 926, "total_fragments": 1582, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium", "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_002896715.1", "gtdb_species": "s__Agrobacterium bohemicum", "ani": 83.0562, "matched_fragments": 958, "total_fragments": 1582, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.81", "min_intra_species_ani": "99.81", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000834635.1", "gtdb_species": "s__Agrobacterium tumefaciens_C", "ani": 82.5638, "matched_fragments": 954, "total_fragments": 1582, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.02", "min_intra_species_ani": "95.99", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000949865.1", "gtdb_species": "s__Agrobacterium nepotum", "ani": 79.9124, "matched_fragments": 675, "total_fragments": 1582, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium", "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_900012615.1", "gtdb_species": "s__Agrobacterium sp900012615", "ani": 79.8478, "matched_fragments": 690, "total_fragments": 1582, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.47", "min_intra_species_ani": "97.45", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_017744915.1", "gtdb_species": "s__Agrobacterium tumefaciens_I", "ani": 79.7316, "matched_fragments": 684, "total_fragments": 1582, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium", "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": -0.302, "cell_length": 0.397, "doubling_h": 0.225, "growth_tmp": 30.0, "optimum_tmp": 28.423, "optimum_ph": 6.983, "genome_size": 4774682.0, "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": 0.0, "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": [ "Rhizobium", "skierniewicense" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }