{ "type": "genome", "identifier": "GCF_001938945.1", "organism": "Xaviernesmea rhizosphaerae", "title": "Xaviernesmea rhizosphaerae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Chinese Academy of Agricultural Sciences", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001938945.1", "bioproject": "PRJNA224116", "biosample": "SAMN05832038", "wgs_master": "MKIO00000000.1", "refseq_category": "na", "taxid": "1672749", "species_taxid": "1672749", "organism_name": "Xaviernesmea rhizosphaerae", "infraspecific_name": "strain=MH17", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/01/06", "asm_name": "ASM193894v1", "asm_submitter": "Chinese Academy of Agricultural Sciences", "gbrs_paired_asm": "GCA_001938945.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/938/945/GCF_001938945.1_ASM193894v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5537226", "genome_size_ungapped": "5536630", "gc_percent": "64.500000", "replicon_count": "0", "scaffold_count": "48", "contig_count": "48", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001938945.1-RS_2024_04_30", "annotation_date": "2024-04-30", "total_gene_count": "4979", "protein_coding_gene_count": "4824", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-01-06", "dateModified": "2017-01-06", "datePublished": "2017-01-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhizobium rhizosphaerae" ], "sample_taxid": [ "1672749" ], "sample_host_organism": [ "rice" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.525 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)": "5537226", "Number of Sequences": "48", "Longest Sequences (bp)": "560723", "N50 (bp)": "237867", "Gap Ratio (%)": "0.010944", "GCcontent (%)": "64.5", "Number of CDSs": "4968", "Average Protein Length": "313.5", "Coding Ratio (%)": "84.4", "Number of rRNAs": "3", "Number of tRNAs": "56", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Shinella pollutisoli", "strain": "strain=KCTC 52677", "accession": "GCA_024609765.1", "taxid": 2250594, "species_taxid": 2250594, "relation_to_type": "type", "validated": true, "ani": 80.4527, "matched_fragments": 744, "total_fragments": 1823, "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": 80.4164, "matched_fragments": 804, "total_fragments": 1823, "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": 80.3842, "matched_fragments": 761, "total_fragments": 1823, "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": 80.2531, "matched_fragments": 852, "total_fragments": 1823, "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": 80.0836, "matched_fragments": 729, "total_fragments": 1823, "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": 80.0291, "matched_fragments": 730, "total_fragments": 1823, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella curvata", "strain": "strain=C3", "accession": "GCA_022899935.1", "taxid": 1817964, "species_taxid": 1817964, "relation_to_type": "type", "validated": true, "ani": 79.989, "matched_fragments": 734, "total_fragments": 1823, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium giardinii", "strain": "strain=H152", "accession": "GCA_000379605.1", "taxid": 56731, "species_taxid": 56731, "relation_to_type": "type", "validated": true, "ani": 79.9086, "matched_fragments": 805, "total_fragments": 1823, "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": 79.8829, "matched_fragments": 734, "total_fragments": 1823, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella kummerowiae", "strain": "strain=CCBAU 25048", "accession": "GCA_009827055.1", "taxid": 417745, "species_taxid": 417745, "relation_to_type": "type", "validated": true, "ani": 79.8061, "matched_fragments": 742, "total_fragments": 1823, "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": 79.7322, "matched_fragments": 725, "total_fragments": 1823, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium chutanense", "strain": "strain=C5", "accession": "GCA_002531935.1", "taxid": 2035448, "species_taxid": 2035448, "relation_to_type": "type", "validated": true, "ani": 79.7016, "matched_fragments": 751, "total_fragments": 1823, "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": 79.4733, "matched_fragments": 729, "total_fragments": 1823, "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": 79.4437, "matched_fragments": 701, "total_fragments": 1823, "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": 79.4153, "matched_fragments": 594, "total_fragments": 1823, "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": 79.4033, "matched_fragments": 715, "total_fragments": 1823, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ensifer sojae", "strain": "strain=CCBAU 05684", "accession": "GCA_002288525.1", "taxid": 716925, "species_taxid": 716925, "relation_to_type": "type", "validated": true, "ani": 79.2692, "matched_fragments": 644, "total_fragments": 1823, "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": 79.1979, "matched_fragments": 637, "total_fragments": 1823, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neorhizobium alkalisoli", "strain": "strain=DSM 21826", "accession": "GCA_002968635.1", "taxid": 528178, "species_taxid": 528178, "relation_to_type": "type", "validated": true, "ani": 78.9963, "matched_fragments": 556, "total_fragments": 1823, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agrobacterium salinitolerans", "strain": "strain=YIC 5082", "accession": "GCA_002008225.1", "taxid": 1183413, "species_taxid": 1183413, "relation_to_type": "type", "validated": true, "ani": 78.866, "matched_fragments": 576, "total_fragments": 1823, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001938945.1", "gtdb_species": "s__Pararhizobium rhizosphaerae", "ani": 100.0, "matched_fragments": 1819, "total_fragments": 1823, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.96", "min_intra_species_ani": "97.96", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_900109605.1", "gtdb_species": "s__Pararhizobium oryzae", "ani": 84.3732, "matched_fragments": 1271, "total_fragments": 1823, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium", "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_001424045.1", "gtdb_species": "s__Pararhizobium sp001424045", "ani": 80.6514, "matched_fragments": 840, "total_fragments": 1823, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.68", "min_intra_species_ani": "97.68", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900467185.1", "gtdb_species": "s__Pararhizobium sp900467185", "ani": 80.5928, "matched_fragments": 853, "total_fragments": 1823, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium", "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_001424985.1", "gtdb_species": "s__Pararhizobium sp001424985", "ani": 80.4114, "matched_fragments": 795, "total_fragments": 1823, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium", "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_016839145.1", "gtdb_species": "s__Shinella sp016839145", "ani": 80.3847, "matched_fragments": 776, "total_fragments": 1823, "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_014203155.1", "gtdb_species": "s__Shinella fusca", "ani": 80.3691, "matched_fragments": 761, "total_fragments": 1823, "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": 80.1013, "matched_fragments": 722, "total_fragments": 1823, "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": "GCA_900469965.1", "gtdb_species": "s__Mycoplana sp900469965", "ani": 79.9745, "matched_fragments": 747, "total_fragments": 1823, "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_018760785.1", "gtdb_species": "s__Rhizobium_A sp018760785", "ani": 79.9446, "matched_fragments": 746, "total_fragments": 1823, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A", "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_000379605.1", "gtdb_species": "s__Pararhizobium giardinii", "ani": 79.9004, "matched_fragments": 807, "total_fragments": 1823, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.65", "min_intra_species_ani": "96.17", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.82", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_002007205.1", "gtdb_species": "s__Ensifer adhaerens_D", "ani": 79.8759, "matched_fragments": 769, "total_fragments": 1823, "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": "-" }, { "accession": "GCF_009827055.1", "gtdb_species": "s__Shinella kummerowiae", "ani": 79.8413, "matched_fragments": 737, "total_fragments": 1823, "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_001424065.1", "gtdb_species": "s__Pararhizobium sp001424065", "ani": 79.6726, "matched_fragments": 716, "total_fragments": 1823, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.05", "min_intra_species_ani": "98.24", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900492205.1", "gtdb_species": "s__Allorhizobium naphthalenivorans_A", "ani": 79.6087, "matched_fragments": 642, "total_fragments": 1823, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.27", "min_intra_species_ani": "95.27", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014197145.1", "gtdb_species": "s__Gellertiella hungarica", "ani": 79.1214, "matched_fragments": 556, "total_fragments": 1823, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Gellertiella", "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_002968635.1", "gtdb_species": "s__Neorhizobium alkalisoli", "ani": 78.9967, "matched_fragments": 555, "total_fragments": 1823, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium", "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": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Xaviernesmea", "rhizosphaerae" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }