{ "type": "genome", "identifier": "GCF_016894385.1", "organism": "Cupriavidus oxalaticus", "title": "Cupriavidus oxalaticus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Los Alamos National Laboratory", "publication": [ {} ], "properties": { "assembly_accession": "GCF_016894385.1", "bioproject": "PRJNA224116", "biosample": "SAMN17610838", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "96344", "species_taxid": "96344", "organism_name": "Cupriavidus oxalaticus", "infraspecific_name": "strain=Ox1", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/02/16", "asm_name": "ASM1689438v1", "asm_submitter": "Los Alamos National Laboratory", "gbrs_paired_asm": "GCA_016894385.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/016/894/385/GCF_016894385.1_ASM1689438v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6694750", "genome_size_ungapped": "6694750", "gc_percent": "67.000000", "replicon_count": "2", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_016894385.1-RS_2024_08_21", "annotation_date": "2024-08-21", "total_gene_count": "6095", "protein_coding_gene_count": "5934", "non_coding_gene_count": "84", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-02-16", "dateModified": "2021-02-16", "datePublished": "2021-02-16", "_annotation": { "sample_count": 1, "sample_organism": [ "Cupriavidus oxalaticus" ], "sample_taxid": [ "96344" ], "sample_host_organism": [ "Pheretima sp." ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "India" ], "sample_host_location_id": [], "data_size": "1.825 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "6694750", "Number of Sequences": "2", "Longest Sequences (bp)": "3885446", "N50 (bp)": "3885446", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "66.9", "Number of CDSs": "6020", "Average Protein Length": "326.4", "Coding Ratio (%)": "88.1", "Number of rRNAs": "15", "Number of tRNAs": "73", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Cupriavidus oxalaticus", "strain": "strain=Ox1", "accession": "GCA_016894385.1", "taxid": 96344, "species_taxid": 96344, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2231, "total_fragments": 2231, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Cupriavidus oxalaticus", "strain": "strain=NBRC 13593", "accession": "GCA_001592245.1", "taxid": 96344, "species_taxid": 96344, "relation_to_type": "type", "validated": true, "ani": 99.9716, "matched_fragments": 2184, "total_fragments": 2231, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Cupriavidus nantongensis", "strain": "strain=X1", "accession": "GCA_001598055.1", "taxid": 1796606, "species_taxid": 1796606, "relation_to_type": "type", "validated": true, "ani": 88.8841, "matched_fragments": 1482, "total_fragments": 2231, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cupriavidus alkaliphilus", "strain": "strain=ASC-732", "accession": "GCA_900094595.1", "taxid": 942866, "species_taxid": 942866, "relation_to_type": "type", "validated": true, "ani": 88.8583, "matched_fragments": 1506, "total_fragments": 2231, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cupriavidus taiwanensis", "strain": "strain=LMG 19424", "accession": "GCA_000069785.1", "taxid": 164546, "species_taxid": 164546, "relation_to_type": "suspected-type", "validated": true, "ani": 88.7775, "matched_fragments": 1535, "total_fragments": 2231, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cupriavidus neocaledonicus", "strain": "strain=STM6070", "accession": "GCA_000372525.1", "taxid": 1040979, "species_taxid": 1040979, "relation_to_type": "type", "validated": true, "ani": 88.7125, "matched_fragments": 1512, "total_fragments": 2231, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cupriavidus lacunae", "strain": "strain=S23", "accession": "GCA_003353055.1", "taxid": 2666307, "species_taxid": 2666307, "relation_to_type": "type", "validated": true, "ani": 88.219, "matched_fragments": 1546, "total_fragments": 2231, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cupriavidus numazuensis", "strain": "strain=LMG 26411", "accession": "GCA_905397435.1", "taxid": 221992, "species_taxid": 221992, "relation_to_type": "type", "validated": true, "ani": 84.7798, "matched_fragments": 1466, "total_fragments": 2231, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Burkholderia perseverans", "strain": "strain=INN12", "accession": "GCA_022870505.1", "taxid": 2615214, "species_taxid": 2615214, "relation_to_type": "type", "validated": true, "ani": 78.6431, "matched_fragments": 795, "total_fragments": 2231, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Massilia solisilvae", "strain": "strain=JCM 31607", "accession": "GCA_024753215.1", "taxid": 1811225, "species_taxid": 1811225, "relation_to_type": "type", "validated": true, "ani": 78.6185, "matched_fragments": 562, "total_fragments": 2231, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia pallida", "strain": "strain=7MH5", "accession": "GCA_004524855.1", "taxid": 2547399, "species_taxid": 2547399, "relation_to_type": "type", "validated": true, "ani": 78.5529, "matched_fragments": 686, "total_fragments": 2231, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia podalyriae", "strain": "strain=WC7.3b", "accession": "GCA_014397785.1", "taxid": 1938811, "species_taxid": 1938811, "relation_to_type": "type", "validated": true, "ani": 77.9542, "matched_fragments": 597, "total_fragments": 2231, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_016894385.1", "gtdb_species": "s__Cupriavidus oxalaticus", "ani": 100.0, "matched_fragments": 2231, "total_fragments": 2231, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.73", "min_intra_species_ani": "98.93", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.92", "num_clustered_genomes": 5, "status": "conclusive" }, { "accession": "GCF_004768545.1", "gtdb_species": "s__Cupriavidus oxalaticus_A", "ani": 94.0585, "matched_fragments": 1773, "total_fragments": 2231, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.89", "min_intra_species_ani": "98.53", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.85", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000426345.1", "gtdb_species": "s__Cupriavidus sp000426345", "ani": 93.9516, "matched_fragments": 1688, "total_fragments": 2231, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.93", "min_intra_species_ani": "98.88", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_017814975.1", "gtdb_species": "s__Cupriavidus sp017814975", "ani": 93.4616, "matched_fragments": 1703, "total_fragments": 2231, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus", "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_003402535.1", "gtdb_species": "s__Cupriavidus sp003402535", "ani": 92.835, "matched_fragments": 1794, "total_fragments": 2231, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus", "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_900250075.1", "gtdb_species": "s__Cupriavidus taiwanensis_C", "ani": 88.9045, "matched_fragments": 1582, "total_fragments": 2231, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.42", "min_intra_species_ani": "95.79", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.85", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_000744095.1", "gtdb_species": "s__Cupriavidus necator_A", "ani": 88.8488, "matched_fragments": 1641, "total_fragments": 2231, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus", "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": -0.237, "cell_length": 0.035, "doubling_h": null, "growth_tmp": 29.5, "optimum_tmp": 32.5, "optimum_ph": 7.516, "genome_size": 6642072.5, "gc_content": 66.94, "coding_genes": 6270.277, "rRNA16S_genes": 5.2, "tRNA_genes": 64.4, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.0, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "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": [ "Cupriavidus", "oxalaticus" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }