{ "type": "genome", "identifier": "GCF_001612905.1", "organism": "Nocardia ignorata NBRC 108230", "title": "Nocardia ignorata NBRC 108230", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Technology and Evaluation", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001612905.1", "bioproject": "PRJNA224116", "biosample": "SAMD00040654", "wgs_master": "BDBI00000000.1", "refseq_category": "na", "taxid": "1210075", "species_taxid": "145285", "organism_name": "Nocardia ignorata NBRC 108230", "infraspecific_name": "strain=NBRC 108230", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/04/01", "asm_name": "ASM161290v1", "asm_submitter": "National Institute of Technology and Evaluation", "gbrs_paired_asm": "GCA_001612905.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/612/905/GCF_001612905.1_ASM161290v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7013162", "genome_size_ungapped": "7013162", "gc_percent": "67.500000", "replicon_count": "0", "scaffold_count": "69", "contig_count": "69", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001612905.1-RS_2024_08_26", "annotation_date": "2024-08-26", "total_gene_count": "6715", "protein_coding_gene_count": "6543", "non_coding_gene_count": "68", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-04-01", "dateModified": "2016-04-01", "datePublished": "2016-04-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Nocardia ignorata NBRC 108230" ], "sample_taxid": [ "1210075" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.915 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 2.78, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "7013162", "Number of Sequences": "69", "Longest Sequences (bp)": "730220", "N50 (bp)": "230637", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "67.7", "Number of CDSs": "6668", "Average Protein Length": "313.4", "Coding Ratio (%)": "89.4", "Number of rRNAs": "5", "Number of tRNAs": "68", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Nocardia ignorata", "strain": "strain=NBRC 108230", "accession": "GCA_001612905.1", "taxid": 145285, "species_taxid": 145285, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2297, "total_fragments": 2301, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Nocardia ignorata", "strain": "strain=DSM 44496", "accession": "GCA_004362495.1", "taxid": 145285, "species_taxid": 145285, "relation_to_type": "type", "validated": true, "ani": 99.999, "matched_fragments": 2297, "total_fragments": 2301, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Nocardia coubleae", "strain": "strain=DSM 44960", "accession": "GCA_012395945.1", "taxid": 356147, "species_taxid": 356147, "relation_to_type": "type", "validated": true, "ani": 96.9913, "matched_fragments": 1926, "total_fragments": 2301, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Nocardia coubleae", "strain": "strain=NBRC 108252", "accession": "GCA_001612805.1", "taxid": 356147, "species_taxid": 356147, "relation_to_type": "type", "validated": true, "ani": 96.9719, "matched_fragments": 1923, "total_fragments": 2301, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Nocardia rosealba", "strain": "strain=NEAU-G4", "accession": "GCA_020216065.1", "taxid": 2878563, "species_taxid": 2878563, "relation_to_type": "type", "validated": true, "ani": 95.527, "matched_fragments": 1835, "total_fragments": 2301, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Nocardia caishijiensis", "strain": "strain=NBRC 108228", "accession": "GCA_001612825.1", "taxid": 184756, "species_taxid": 184756, "relation_to_type": "type", "validated": true, "ani": 91.6459, "matched_fragments": 1728, "total_fragments": 2301, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia caishijiensis", "strain": "strain=DSM 44831", "accession": "GCA_009858255.1", "taxid": 184756, "species_taxid": 184756, "relation_to_type": "type", "validated": true, "ani": 91.597, "matched_fragments": 1765, "total_fragments": 2301, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia thailandica", "strain": "strain=NBRC 100428", "accession": "GCA_000308795.1", "taxid": 257275, "species_taxid": 257275, "relation_to_type": "type", "validated": true, "ani": 82.7165, "matched_fragments": 1300, "total_fragments": 2301, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 2.78, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001612905.1", "gtdb_species": "s__Nocardia ignorata", "ani": 100.0, "matched_fragments": 2297, "total_fragments": 2301, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 96.9719, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "inconclusive" }, { "accession": "GCF_001612805.1", "gtdb_species": "s__Nocardia coubleae", "ani": 96.9719, "matched_fragments": 1923, "total_fragments": 2301, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 96.9719, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "inconclusive" }, { "accession": "GCF_013839555.1", "gtdb_species": "s__Nocardia sp013839555", "ani": 95.2815, "matched_fragments": 1437, "total_fragments": 2301, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.2705, "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": "inconclusive" }, { "accession": "GCF_001612825.1", "gtdb_species": "s__Nocardia caishijiensis", "ani": 91.6498, "matched_fragments": 1728, "total_fragments": 2301, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014646295.1", "gtdb_species": "s__Nocardia rhizosphaerihabitans", "ani": 85.6653, "matched_fragments": 1556, "total_fragments": 2301, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "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_001886715.1", "gtdb_species": "s__Nocardia mangyaensis", "ani": 85.1093, "matched_fragments": 1486, "total_fragments": 2301, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "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_001613085.1", "gtdb_species": "s__Nocardia salmonicida", "ani": 84.9002, "matched_fragments": 1586, "total_fragments": 2301, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.01", "min_intra_species_ani": "95.63", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.85", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000308795.1", "gtdb_species": "s__Nocardia thailandica", "ani": 82.6952, "matched_fragments": 1304, "total_fragments": 2301, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "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_000308715.1", "gtdb_species": "s__Nocardia tenerifensis", "ani": 81.018, "matched_fragments": 1038, "total_fragments": 2301, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "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_008704205.1", "gtdb_species": "s__Nocardia colli", "ani": 80.8506, "matched_fragments": 1104, "total_fragments": 2301, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "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": -0.223, "cell_length": 0.046, "doubling_h": null, "growth_tmp": 29.0, "optimum_tmp": 28.0, "optimum_ph": 7.496, "genome_size": 7012465.5, "gc_content": 67.71, "coding_genes": 6908.619, "rRNA16S_genes": 3.166, "tRNA_genes": 53.5, "gram_stain": 1.0, "sporulation": 0.833, "motility": 0.0, "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": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 1.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Nocardia", "ignorata", "NBRC", "108230" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }