{ "type": "genome", "identifier": "GCF_013407145.1", "organism": "Nitrosopumilus cobalaminigenes", "title": "Nitrosopumilus cobalaminigenes", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Washington", "publication": [ {} ], "properties": { "assembly_accession": "GCF_013407145.1", "bioproject": "PRJNA224116", "biosample": "SAMN08535023", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "1470066", "species_taxid": "1470066", "organism_name": "Nitrosopumilus cobalaminigenes", "infraspecific_name": "strain=HCA1", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/07/13", "asm_name": "ASM1340714v1", "asm_submitter": "University of Washington", "gbrs_paired_asm": "GCA_013407145.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/407/145/GCF_013407145.1_ASM1340714v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "archaea", "genome_size": "1563356", "genome_size_ungapped": "1563356", "gc_percent": "33.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_013407145.1-RS_2024_05_05", "annotation_date": "2024-05-05", "total_gene_count": "1950", "protein_coding_gene_count": "1896", "non_coding_gene_count": "48", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-07-13", "dateModified": "2020-07-13", "datePublished": "2020-07-13", "_annotation": { "sample_count": 1, "sample_organism": [ "Nitrosopumilus cobalaminigenes" ], "sample_taxid": [ "1470066" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA" ], "sample_host_location_id": [], "data_size": "0.428 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.45, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "1563356", "Number of Sequences": "1", "Longest Sequences (bp)": "1563356", "N50 (bp)": "1563356", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "33.0", "Number of CDSs": "1858", "Average Protein Length": "253.7", "Coding Ratio (%)": "90.5", "Number of rRNAs": "3", "Number of tRNAs": "38", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Nitrosopumilus cobalaminigenes", "strain": "strain=HCA1", "accession": "GCA_013407145.1", "taxid": 1470066, "species_taxid": 1470066, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 521, "total_fragments": 521, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Nitrosopumilus oxyclinae", "strain": "strain=HCE1", "accession": "GCA_013407165.1", "taxid": 1959104, "species_taxid": 1959104, "relation_to_type": "type", "validated": true, "ani": 85.1359, "matched_fragments": 424, "total_fragments": 521, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nitrosopumilus adriaticus", "strain": "strain=NF5", "accession": "GCA_000956175.1", "taxid": 1580092, "species_taxid": 1580092, "relation_to_type": "type", "validated": true, "ani": 81.7948, "matched_fragments": 370, "total_fragments": 521, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.45, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_013407145.1", "gtdb_species": "s__Nitrosopumilus cobalaminigenes", "ani": 100.0, "matched_fragments": 521, "total_fragments": 521, "gtdb_taxonomy": "d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus", "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": "GCA_013043295.1", "gtdb_species": "s__Nitrosopumilus sp013043295", "ani": 84.7254, "matched_fragments": 277, "total_fragments": 521, "gtdb_taxonomy": "d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_013203245.1", "gtdb_species": "s__Nitrosopumilus sp013203245", "ani": 84.2935, "matched_fragments": 304, "total_fragments": 521, "gtdb_taxonomy": "d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus", "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_014078525.1", "gtdb_species": "s__Nitrosopumilus sp014078525", "ani": 81.926, "matched_fragments": 353, "total_fragments": 521, "gtdb_taxonomy": "d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus", "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_000956175.1", "gtdb_species": "s__Nitrosopumilus adriaticus", "ani": 81.8149, "matched_fragments": 369, "total_fragments": 521, "gtdb_taxonomy": "d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus", "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": -0.741, "cell_length": -0.254, "doubling_h": 1.462, "growth_tmp": null, "optimum_tmp": 29.666, "optimum_ph": null, "genome_size": 1735691.5, "gc_content": 33.605, "coding_genes": 2066.333, "rRNA16S_genes": 1.0, "tRNA_genes": 42.0, "gram_stain": 0.0, "sporulation": null, "motility": 1.0, "range_salinity": 1.0, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "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": [ "Nitrosopumilus", "cobalaminigenes" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }