{ "type": "genome", "identifier": "GCF_014727215.1", "organism": "Rhizobium leucaenae USDA 9039", "title": "Rhizobium leucaenae USDA 9039", "description": "na", "data type": "Genome sequencing and assembly", "organization": "LNCC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014727215.1", "bioproject": "PRJNA224116", "biosample": "SAMN04231515", "wgs_master": "LNCJ00000000.1", "refseq_category": "na", "taxid": "1041147", "species_taxid": "29450", "organism_name": "Rhizobium leucaenae USDA 9039", "infraspecific_name": "strain=CFN 299", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/09/24", "asm_name": "ASM1472721v1", "asm_submitter": "LNCC", "gbrs_paired_asm": "GCA_014727215.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/727/215/GCF_014727215.1_ASM1472721v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6694130", "genome_size_ungapped": "6694130", "gc_percent": "59.500000", "replicon_count": "0", "scaffold_count": "95", "contig_count": "95", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014727215.1-RS_2024_05_06", "annotation_date": "2024-05-06", "total_gene_count": "6463", "protein_coding_gene_count": "6208", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-09-24", "dateModified": "2020-09-24", "datePublished": "2020-09-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhizobium leucaenae USDA 9039" ], "sample_taxid": [ "1041147" ], "sample_host_organism": [ "Phaseolus vulgaris" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Brazil" ], "sample_host_location_id": [], "data_size": "1.886 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)": "6694130", "Number of Sequences": "95", "Longest Sequences (bp)": "553642", "N50 (bp)": "296137", "Gap Ratio (%)": "0.000015", "GCcontent (%)": "59.4", "Number of CDSs": "6518", "Average Protein Length": "293.3", "Coding Ratio (%)": "85.7", "Number of rRNAs": "3", "Number of tRNAs": "49", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhizobium leucaenae", "strain": "strain=CFN 299", "accession": "GCA_014727215.1", "taxid": 29450, "species_taxid": 29450, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2187, "total_fragments": 2190, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhizobium leucaenae", "strain": "strain=USDA 9039", "accession": "GCA_000426285.1", "taxid": 29450, "species_taxid": 29450, "relation_to_type": "type", "validated": true, "ani": 99.9817, "matched_fragments": 2159, "total_fragments": 2190, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhizobium jaguaris", "strain": "strain=CCGE525", "accession": "GCA_003627755.1", "taxid": 1312183, "species_taxid": 1312183, "relation_to_type": "type", "validated": true, "ani": 87.4258, "matched_fragments": 1577, "total_fragments": 2190, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium freirei", "strain": "strain=PRF 81", "accession": "GCA_000359745.1", "taxid": 1353277, "species_taxid": 1353277, "relation_to_type": "type", "validated": true, "ani": 85.8012, "matched_fragments": 1410, "total_fragments": 2190, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium tropici", "strain": "strain=CIAT 899", "accession": "GCA_000330885.1", "taxid": 398, "species_taxid": 398, "relation_to_type": "type", "validated": true, "ani": 85.5636, "matched_fragments": 1408, "total_fragments": 2190, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agrobacterium rhizogenes", "strain": "strain=NBRC 13257", "accession": "GCA_000696095.1", "taxid": 359, "species_taxid": 359, "relation_to_type": "type", "validated": true, "ani": 85.0334, "matched_fragments": 1296, "total_fragments": 2190, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agrobacterium rhizogenes", "strain": "strain=LMG150", "accession": "GCA_007002985.1", "taxid": 359, "species_taxid": 359, "relation_to_type": "type", "validated": true, "ani": 85.0106, "matched_fragments": 1294, "total_fragments": 2190, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium hainanense", "strain": "strain=CCBAU 57015", "accession": "GCA_900094555.1", "taxid": 52131, "species_taxid": 52131, "relation_to_type": "type", "validated": true, "ani": 83.1719, "matched_fragments": 1253, "total_fragments": 2190, "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": 82.971, "matched_fragments": 1256, "total_fragments": 2190, "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": 80.8172, "matched_fragments": 976, "total_fragments": 2190, "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": 80.6403, "matched_fragments": 1025, "total_fragments": 2190, "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": 79.3787, "matched_fragments": 619, "total_fragments": 2190, "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": 78.9168, "matched_fragments": 568, "total_fragments": 2190, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000426285.1", "gtdb_species": "s__Rhizobium leucaenae", "ani": 99.9817, "matched_fragments": 2159, "total_fragments": 2190, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.87", "min_intra_species_ani": "99.71", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.93", "num_clustered_genomes": 5, "status": "conclusive" }, { "accession": "GCF_003025035.1", "gtdb_species": "s__Rhizobium paranaense", "ani": 91.9314, "matched_fragments": 1204, "total_fragments": 2190, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002944315.1", "gtdb_species": "s__Rhizobium sp002944315", "ani": 89.633, "matched_fragments": 1720, "total_fragments": 2190, "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_004362445.1", "gtdb_species": "s__Rhizobium sp004362445", "ani": 87.5965, "matched_fragments": 1465, "total_fragments": 2190, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003627755.1", "gtdb_species": "s__Rhizobium jaguaris", "ani": 87.4021, "matched_fragments": 1580, "total_fragments": 2190, "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_000359745.1", "gtdb_species": "s__Rhizobium freirei", "ani": 85.8253, "matched_fragments": 1407, "total_fragments": 2190, "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_000696095.1", "gtdb_species": "s__Rhizobium rhizogenes", "ani": 85.0395, "matched_fragments": 1295, "total_fragments": 2190, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.11", "min_intra_species_ani": "97.39", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.86", "num_clustered_genomes": 92, "status": "-" }, { "accession": "GCF_009498525.1", "gtdb_species": "s__Rhizobium sp009498525", "ani": 85.0156, "matched_fragments": 1308, "total_fragments": 2190, "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_003024605.1", "gtdb_species": "s__Rhizobium sp003024605", "ani": 83.5988, "matched_fragments": 1027, "total_fragments": 2190, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.03", "min_intra_species_ani": "99.00", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.95", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCA_900468625.1", "gtdb_species": "s__Rhizobium sp900468625", "ani": 83.2554, "matched_fragments": 1198, "total_fragments": 2190, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.33", "min_intra_species_ani": "98.37", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.89", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCA_900469475.1", "gtdb_species": "s__Rhizobium sp900469475", "ani": 82.9821, "matched_fragments": 1194, "total_fragments": 2190, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.70", "min_intra_species_ani": "97.21", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.88", "num_clustered_genomes": 20, "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", "leucaenae", "USDA", "9039" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }