{ "type": "genome", "identifier": "GCF_900220975.1", "organism": "Rhizobium subbaraonis", "title": "Rhizobium subbaraonis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900220975.1", "bioproject": "PRJNA224116", "biosample": "SAMN05892877", "wgs_master": "OBQD00000000.1", "refseq_category": "reference genome", "taxid": "908946", "species_taxid": "908946", "organism_name": "Rhizobium subbaraonis", "infraspecific_name": "strain=JC85", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/09/28", "asm_name": "IMG-taxon 2740891857 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900220975.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/220/975/GCF_900220975.1_IMG-taxon_2740891857_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6576489", "genome_size_ungapped": "6575903", "gc_percent": "63.000000", "replicon_count": "0", "scaffold_count": "85", "contig_count": "85", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900220975.1-RS_2024_12_01", "annotation_date": "2024-12-01", "total_gene_count": "6382", "protein_coding_gene_count": "6168", "non_coding_gene_count": "55", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-09-28", "dateModified": "2017-09-28", "datePublished": "2017-09-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhizobium subbaraonis" ], "sample_taxid": [ "908946" ], "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": "1.832 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)": "6576489", "Number of Sequences": "85", "Longest Sequences (bp)": "502747", "N50 (bp)": "280913", "Gap Ratio (%)": "0.008911", "GCcontent (%)": "63.1", "Number of CDSs": "6305", "Average Protein Length": "303.5", "Coding Ratio (%)": "87.3", "Number of rRNAs": "3", "Number of tRNAs": "49", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhizobium subbaraonis", "strain": "strain=JC85", "accession": "GCA_900220975.1", "taxid": 908946, "species_taxid": 908946, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2149, "total_fragments": 2152, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhizobium rhizolycopersici", "strain": "strain=DBTS2", "accession": "GCA_013378445.1", "taxid": 2746702, "species_taxid": 2746702, "relation_to_type": "type", "validated": true, "ani": 92.2988, "matched_fragments": 1541, "total_fragments": 2152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium azooxidifex", "strain": "strain=DSM 100211", "accession": "GCA_014196765.1", "taxid": 1636188, "species_taxid": 1636188, "relation_to_type": "type", "validated": true, "ani": 83.9275, "matched_fragments": 1208, "total_fragments": 2152, "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": 81.9508, "matched_fragments": 927, "total_fragments": 2152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella granuli", "strain": "strain=DSM 18401", "accession": "GCA_004341885.1", "taxid": 323621, "species_taxid": 323621, "relation_to_type": "type", "validated": true, "ani": 81.9182, "matched_fragments": 1061, "total_fragments": 2152, "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": 81.7243, "matched_fragments": 918, "total_fragments": 2152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella zoogloeoides", "strain": "strain=ATCC 19623", "accession": "GCA_020883495.1", "taxid": 352475, "species_taxid": 352475, "relation_to_type": "type", "validated": true, "ani": 81.6818, "matched_fragments": 920, "total_fragments": 2152, "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": 81.6791, "matched_fragments": 1039, "total_fragments": 2152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella fusca", "strain": "strain=DSM 21319", "accession": "GCA_014203155.1", "taxid": 544480, "species_taxid": 544480, "relation_to_type": "type", "validated": true, "ani": 81.587, "matched_fragments": 904, "total_fragments": 2152, "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": 81.1991, "matched_fragments": 883, "total_fragments": 2152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella oryzae", "strain": "strain=Z-25", "accession": "GCA_023038235.1", "taxid": 2871820, "species_taxid": 2871820, "relation_to_type": "type", "validated": true, "ani": 81.1044, "matched_fragments": 886, "total_fragments": 2152, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900220975.1", "gtdb_species": "s__Mycoplana subbaraonis", "ani": 100.0, "matched_fragments": 2149, "total_fragments": 2152, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana", "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_013378445.1", "gtdb_species": "s__Mycoplana rhizolycopersici", "ani": 92.3049, "matched_fragments": 1540, "total_fragments": 2152, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana", "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_900469965.1", "gtdb_species": "s__Mycoplana sp900469965", "ani": 84.5776, "matched_fragments": 1213, "total_fragments": 2152, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.03", "min_intra_species_ani": "97.96", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_014196765.1", "gtdb_species": "s__Mycoplana azooxidifex", "ani": 83.9352, "matched_fragments": 1207, "total_fragments": 2152, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana", "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_003046475.1", "gtdb_species": "s__Mycoplana dimorpha", "ani": 82.5836, "matched_fragments": 959, "total_fragments": 2152, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana", "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_014851675.1", "gtdb_species": "s__Mycoplana sp014851675", "ani": 81.9333, "matched_fragments": 969, "total_fragments": 2152, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana", "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_009826855.1", "gtdb_species": "s__Shinella zoogloeoides", "ani": 81.727, "matched_fragments": 918, "total_fragments": 2152, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella", "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_003574625.1", "gtdb_species": "s__Shinella zoogloeoides_A", "ani": 81.5982, "matched_fragments": 924, "total_fragments": 2152, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella", "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_004514435.1", "gtdb_species": "s__Shinella sp004514435", "ani": 81.2344, "matched_fragments": 876, "total_fragments": 2152, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.21", "min_intra_species_ani": "98.45", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001262505.1", "gtdb_species": "s__Shinella sp001262505", "ani": 81.1629, "matched_fragments": 1024, "total_fragments": 2152, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.95", "min_intra_species_ani": "98.39", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.87", "num_clustered_genomes": 4, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.046, "cell_length": 0.544, "doubling_h": 0.225, "growth_tmp": 25.0, "optimum_tmp": 25.0, "optimum_ph": 7.0, "genome_size": 6579265.5, "gc_content": 60.147, "coding_genes": 6587.615, "rRNA16S_genes": 3.0, "tRNA_genes": 51.725, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.0, "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", "subbaraonis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }