{ "type": "genome", "identifier": "GCF_900110205.1", "organism": "Rhizobium tibeticum", "title": "Rhizobium tibeticum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900110205.1", "bioproject": "PRJNA224116", "biosample": "SAMN05216228", "wgs_master": "FOCV00000000.1", "refseq_category": "na", "taxid": "501024", "species_taxid": "501024", "organism_name": "Rhizobium tibeticum", "infraspecific_name": "strain=CGMCC 1.7071", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/11/17", "asm_name": "IMG-taxon 2671180023 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900110205.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/110/205/GCF_900110205.1_IMG-taxon_2671180023_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": "7065782", "genome_size_ungapped": "7063752", "gc_percent": "59.500000", "replicon_count": "0", "scaffold_count": "166", "contig_count": "166", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900110205.1-RS_2024_04_24", "annotation_date": "2024-04-24", "total_gene_count": "7036", "protein_coding_gene_count": "6466", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-11-17", "dateModified": "2016-11-17", "datePublished": "2016-11-17", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhizobium tibeticum" ], "sample_taxid": [ "501024" ], "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": "1.997 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)": "7065782", "Number of Sequences": "166", "Longest Sequences (bp)": "375657", "N50 (bp)": "152901", "Gap Ratio (%)": "0.028730", "GCcontent (%)": "59.7", "Number of CDSs": "6992", "Average Protein Length": "280.7", "Coding Ratio (%)": "83.3", "Number of rRNAs": "3", "Number of tRNAs": "47", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhizobium tibeticum", "strain": "strain=CGMCC 1.7071", "accession": "GCA_900110205.1", "taxid": 501024, "species_taxid": 501024, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2258, "total_fragments": 2267, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Rhizobium tibeticum", "strain": "", "accession": "GCA_900108425.1", "taxid": 501024, "species_taxid": 501024, "relation_to_type": "type", "validated": true, "ani": 99.9773, "matched_fragments": 2184, "total_fragments": 2267, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Rhizobium favelukesii", "strain": "strain=LPU83", "accession": "GCA_000577275.2", "taxid": 348824, "species_taxid": 348824, "relation_to_type": "type", "validated": true, "ani": 95.4501, "matched_fragments": 1875, "total_fragments": 2267, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Rhizobium altiplani", "strain": "strain=BR 10423", "accession": "GCA_001542405.1", "taxid": 1864509, "species_taxid": 1864509, "relation_to_type": "type", "validated": true, "ani": 86.2611, "matched_fragments": 1468, "total_fragments": 2267, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium grahamii", "strain": "strain=CCGE 502", "accession": "GCA_000298315.2", "taxid": 1120045, "species_taxid": 1120045, "relation_to_type": "type", "validated": true, "ani": 85.5824, "matched_fragments": 1401, "total_fragments": 2267, "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": 81.1818, "matched_fragments": 1038, "total_fragments": 2267, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium sophorae", "strain": "strain=CCBAU 03386", "accession": "GCA_013087515.1", "taxid": 1535242, "species_taxid": 1535242, "relation_to_type": "type", "validated": true, "ani": 81.1346, "matched_fragments": 1093, "total_fragments": 2267, "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": 81.0345, "matched_fragments": 1037, "total_fragments": 2267, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium changzhiense", "strain": "strain=WYCCWR 11279", "accession": "GCA_013087625.1", "taxid": 2692317, "species_taxid": 2692317, "relation_to_type": "type", "validated": true, "ani": 80.9694, "matched_fragments": 1041, "total_fragments": 2267, "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": 80.8805, "matched_fragments": 1060, "total_fragments": 2267, "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": 79.3261, "matched_fragments": 592, "total_fragments": 2267, "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": 78.9625, "matched_fragments": 612, "total_fragments": 2267, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900110205.1", "gtdb_species": "s__Rhizobium tibeticum", "ani": 100.0, "matched_fragments": 2259, "total_fragments": 2267, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.5244, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_000577275.2", "gtdb_species": "s__Rhizobium favelukesii", "ani": 95.4546, "matched_fragments": 1874, "total_fragments": 2267, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.5244, "mean_intra_species_ani": "99.59", "min_intra_species_ani": "99.23", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000799845.1", "gtdb_species": "s__Rhizobium sp000799845", "ani": 95.2651, "matched_fragments": 1760, "total_fragments": 2267, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.2724, "mean_intra_species_ani": "99.41", "min_intra_species_ani": "99.41", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000282035.1", "gtdb_species": "s__Rhizobium sp000282035", "ani": 88.9766, "matched_fragments": 1525, "total_fragments": 2267, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.51", "min_intra_species_ani": "98.50", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.87", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_002211365.1", "gtdb_species": "s__Rhizobium sp002211365", "ani": 86.6248, "matched_fragments": 1414, "total_fragments": 2267, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.54", "min_intra_species_ani": "97.07", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001542405.1", "gtdb_species": "s__Rhizobium altiplani", "ani": 86.2491, "matched_fragments": 1470, "total_fragments": 2267, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.38", "min_intra_species_ani": "95.34", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.71", "num_clustered_genomes": 19, "status": "-" }, { "accession": "GCA_900466605.1", "gtdb_species": "s__Rhizobium sp900466605", "ani": 85.9586, "matched_fragments": 1348, "total_fragments": 2267, "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_014194695.1", "gtdb_species": "s__Rhizobium sp014194695", "ani": 85.6552, "matched_fragments": 1339, "total_fragments": 2267, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.49", "min_intra_species_ani": "98.48", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.94", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000298315.2", "gtdb_species": "s__Rhizobium grahamii", "ani": 85.5808, "matched_fragments": 1401, "total_fragments": 2267, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.32", "min_intra_species_ani": "97.32", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000746265.1", "gtdb_species": "s__Rhizobium sp000746265", "ani": 85.1026, "matched_fragments": 1340, "total_fragments": 2267, "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_000746385.1", "gtdb_species": "s__Rhizobium sp000746385", "ani": 82.1997, "matched_fragments": 1035, "total_fragments": 2267, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.83", "min_intra_species_ani": "96.83", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.23, "cell_length": 0.207, "doubling_h": 0.225, "growth_tmp": 28.0, "optimum_tmp": 28.423, "optimum_ph": 6.983, "genome_size": 7065782.0, "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": 0.05, "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", "tibeticum" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }