{ "type": "genome", "identifier": "GCF_019793465.1", "organism": "Rhizobium croatiense", "title": "Rhizobium croatiense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "CSIC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_019793465.1", "bioproject": "PRJNA224116", "biosample": "SAMN20700944", "wgs_master": "JAILYJ000000000.1", "refseq_category": "reference genome", "taxid": "2867516", "species_taxid": "2867516", "organism_name": "Rhizobium croatiense", "infraspecific_name": "strain=13T", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/08/28", "asm_name": "ASM1979346v1", "asm_submitter": "CSIC", "gbrs_paired_asm": "GCA_019793465.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/019/793/465/GCF_019793465.1_ASM1979346v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6408074", "genome_size_ungapped": "6408074", "gc_percent": "61.500000", "replicon_count": "0", "scaffold_count": "124", "contig_count": "124", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_019793465.1-RS_2024_08_03", "annotation_date": "2024-08-03", "total_gene_count": "6253", "protein_coding_gene_count": "5925", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-08-28", "dateModified": "2021-08-28", "datePublished": "2021-08-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhizobium croatiense" ], "sample_taxid": [ "2867516" ], "sample_host_organism": [ "Phaseolus vulgaris" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Croatia" ], "sample_host_location_id": [], "data_size": "1.785 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)": "6408074", "Number of Sequences": "124", "Longest Sequences (bp)": "586315", "N50 (bp)": "284628", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "61.6", "Number of CDSs": "6069", "Average Protein Length": "302.7", "Coding Ratio (%)": "86.0", "Number of rRNAs": "3", "Number of tRNAs": "53", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhizobium croatiense", "strain": "strain=13T", "accession": "GCA_019793465.1", "taxid": 2867516, "species_taxid": 2867516, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2103, "total_fragments": 2103, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhizobium sophoriradicis", "strain": "strain=CCBAU 03470", "accession": "GCA_003939025.1", "taxid": 1535245, "species_taxid": 1535245, "relation_to_type": "type", "validated": true, "ani": 93.594, "matched_fragments": 1861, "total_fragments": 2103, "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": 92.4404, "matched_fragments": 1761, "total_fragments": 2103, "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": 91.3491, "matched_fragments": 1647, "total_fragments": 2103, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium binae", "strain": "strain=BLR195", "accession": "GCA_019684455.1", "taxid": 1138190, "species_taxid": 1138190, "relation_to_type": "type", "validated": true, "ani": 91.303, "matched_fragments": 1636, "total_fragments": 2103, "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": 90.0913, "matched_fragments": 1727, "total_fragments": 2103, "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": 89.8196, "matched_fragments": 1725, "total_fragments": 2103, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium esperanzae", "strain": "strain=CNPSo 668", "accession": "GCA_002204185.1", "taxid": 1967781, "species_taxid": 1967781, "relation_to_type": "suspected-type", "validated": true, "ani": 89.2893, "matched_fragments": 1683, "total_fragments": 2103, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium anhuiense", "strain": "strain=CGMCC 1.12621", "accession": "GCA_014638185.1", "taxid": 1184720, "species_taxid": 1184720, "relation_to_type": "type", "validated": true, "ani": 88.3107, "matched_fragments": 1635, "total_fragments": 2103, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium anhuiense", "strain": "strain=CCBAU 23252", "accession": "GCA_003985145.1", "taxid": 1184720, "species_taxid": 1184720, "relation_to_type": "type", "validated": true, "ani": 88.2622, "matched_fragments": 1650, "total_fragments": 2103, "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": 81.4991, "matched_fragments": 1163, "total_fragments": 2103, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium dioscoreae", "strain": "strain=S-93", "accession": "GCA_009176305.1", "taxid": 2653122, "species_taxid": 2653122, "relation_to_type": "type", "validated": true, "ani": 80.6119, "matched_fragments": 945, "total_fragments": 2103, "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": 80.1306, "matched_fragments": 746, "total_fragments": 2103, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002531955.1", "gtdb_species": "s__Rhizobium sp002531955", "ani": 95.8213, "matched_fragments": 1852, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.59", "min_intra_species_ani": "95.76", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.85", "num_clustered_genomes": 5, "status": "conclusive" }, { "accession": "GCF_001662075.1", "gtdb_species": "s__Rhizobium bangladeshense_B", "ani": 94.4494, "matched_fragments": 1797, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "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_014200175.1", "gtdb_species": "s__Rhizobium lentis_A", "ani": 93.6819, "matched_fragments": 1768, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.98", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_003939025.1", "gtdb_species": "s__Rhizobium sophoriradicis", "ani": 93.594, "matched_fragments": 1861, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.45", "min_intra_species_ani": "97.30", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.88", "num_clustered_genomes": 16, "status": "-" }, { "accession": "GCF_003985125.1", "gtdb_species": "s__Rhizobium phaseoli", "ani": 92.4426, "matched_fragments": 1761, "total_fragments": 2103, "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_017357225.1", "gtdb_species": "s__Rhizobium binae", "ani": 91.3467, "matched_fragments": 1647, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "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_002531825.1", "gtdb_species": "s__Rhizobium sp002531825", "ani": 89.6439, "matched_fragments": 1645, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "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_002531905.1", "gtdb_species": "s__Rhizobium sp002531905", "ani": 89.4182, "matched_fragments": 1711, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.24", "min_intra_species_ani": "98.93", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.86", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_002531755.2", "gtdb_species": "s__Rhizobium acidisoli", "ani": 89.1904, "matched_fragments": 1692, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.96", "min_intra_species_ani": "96.40", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.80", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_002211305.1", "gtdb_species": "s__Rhizobium sp002211305", "ani": 89.054, "matched_fragments": 1613, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.97", "min_intra_species_ani": "96.97", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003985145.1", "gtdb_species": "s__Rhizobium anhuiense", "ani": 88.2943, "matched_fragments": 1646, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.85", "min_intra_species_ani": "98.46", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 19, "status": "-" }, { "accession": "GCF_014193025.1", "gtdb_species": "s__Rhizobium sp014193025", "ani": 87.3751, "matched_fragments": 1435, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "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": -0.23, "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", "croatiense" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }