{ "type": "genome", "identifier": "GCF_027158485.1", "organism": "Oxalobacter formigenes", "title": "Oxalobacter formigenes", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Western Ontario", "publication": [ {} ], "properties": { "assembly_accession": "GCF_027158485.1", "bioproject": "PRJNA224116", "biosample": "SAMN28572146", "wgs_master": "JAMKYJ000000000.1", "refseq_category": "na", "taxid": "847", "species_taxid": "847", "organism_name": "Oxalobacter formigenes", "infraspecific_name": "strain=OxB", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/12/20", "asm_name": "ASM2715848v1", "asm_submitter": "University of Western Ontario", "gbrs_paired_asm": "GCA_027158485.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/027/158/485/GCF_027158485.1_ASM2715848v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2407303", "genome_size_ungapped": "2407303", "gc_percent": "49.500000", "replicon_count": "0", "scaffold_count": "48", "contig_count": "48", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-02-10", "total_gene_count": "2253", "protein_coding_gene_count": "2179", "non_coding_gene_count": "52", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-12-20", "dateModified": "2022-12-20", "datePublished": "2022-12-20", "_annotation": { "sample_count": 1, "sample_organism": [ "Oxalobacter formigenes" ], "sample_taxid": [ "847" ], "sample_host_organism": [ "Ovis aries" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Canada:London" ], "sample_host_location_id": [], "data_size": "0.681 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)": "2407303", "Number of Sequences": "48", "Longest Sequences (bp)": "313515", "N50 (bp)": "148325", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "49.6", "Number of CDSs": "2173", "Average Protein Length": "319.5", "Coding Ratio (%)": "86.5", "Number of rRNAs": "3", "Number of tRNAs": "45", "Number of CRISPRs": "4" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Oxalicibacterium faecigallinarum", "strain": "strain=CCM 2767", "accession": "GCA_014635705.1", "taxid": 573741, "species_taxid": 573741, "relation_to_type": "type", "validated": true, "ani": 77.0764, "matched_fragments": 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"below_threshold" }, { "organism_name": "Janthinobacterium agaricidamnosum", "strain": "strain=DSM 9628", "accession": "GCA_000723165.1", "taxid": 55508, "species_taxid": 55508, "relation_to_type": "type", "validated": true, "ani": 76.8002, "matched_fragments": 55, "total_fragments": 785, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Collimonas pratensis", "strain": "strain=Ter91", "accession": "GCA_001584185.1", "taxid": 279113, "species_taxid": 279113, "relation_to_type": "type", "validated": true, "ani": 76.6616, "matched_fragments": 53, "total_fragments": 785, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Janthinobacterium agaricidamnosum", "strain": "strain=NBRC 102515", "accession": "GCA_001571185.1", "taxid": 55508, "species_taxid": 55508, "relation_to_type": "type", "validated": true, "ani": 76.6315, "matched_fragments": 54, "total_fragments": 785, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Noviherbaspirillum saxi", "strain": "strain=K1R23-30", "accession": "GCA_003591035.1", "taxid": 2320863, "species_taxid": 2320863, "relation_to_type": "type", "validated": true, "ani": 76.5393, "matched_fragments": 62, "total_fragments": 785, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oxalicibacterium flavum", "strain": "strain=CCM 7086", "accession": "GCA_014635065.1", "taxid": 179467, "species_taxid": 179467, "relation_to_type": "type", "validated": true, "ani": 76.5376, "matched_fragments": 51, "total_fragments": 785, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbaspirillum rubrisubalbicans", "strain": "strain=NBRC 102523", "accession": "GCA_001591225.1", "taxid": 80842, "species_taxid": 80842, "relation_to_type": "type", "validated": true, "ani": 76.4583, "matched_fragments": 51, "total_fragments": 785, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbaspirillum chlorophenolicum", "strain": 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"mean_intra_species_af": "0.99", "min_intra_species_af": "0.98", "num_clustered_genomes": 6, "status": "conclusive" }, { "accession": "GCA_905202055.1", "gtdb_species": "s__Oxalobacter sp905202055", "ani": 88.8358, "matched_fragments": 591, "total_fragments": 785, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalobacter", "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_000158475.2", "gtdb_species": "s__Oxalobacter formigenes_B", "ani": 78.9637, "matched_fragments": 348, "total_fragments": 785, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.93", "min_intra_species_ani": "99.93", 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"status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.398, "cell_length": 0.079, "doubling_h": null, "growth_tmp": 29.0, "optimum_tmp": 37.0, "optimum_ph": null, "genome_size": 2463878.833, "gc_content": 50.375, "coding_genes": 2217.667, "rRNA16S_genes": 1.5, "tRNA_genes": 47.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": null, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "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": [ "Oxalobacter", "formigenes" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }