{ "type": "genome", "identifier": "GCF_001612965.1", "organism": "Nocardia kruczakiae NBRC 101016", "title": "Nocardia kruczakiae NBRC 101016", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Technology and Evaluation", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001612965.1", "bioproject": "PRJNA224116", "biosample": "SAMD00040657", "wgs_master": "BDBL00000000.1", "refseq_category": "reference genome", "taxid": "1210078", "species_taxid": "261477", "organism_name": "Nocardia kruczakiae NBRC 101016", "infraspecific_name": "strain=NBRC 101016", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/04/01", "asm_name": "ASM161296v1", "asm_submitter": "National Institute of Technology and Evaluation", "gbrs_paired_asm": "GCA_001612965.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/612/965/GCF_001612965.1_ASM161296v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7324382", "genome_size_ungapped": "7324382", "gc_percent": "68.000000", "replicon_count": "0", "scaffold_count": "103", "contig_count": "103", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001612965.1-RS_2024_08_12", "annotation_date": "2024-08-12", "total_gene_count": "6750", "protein_coding_gene_count": "6595", "non_coding_gene_count": "55", "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 kruczakiae NBRC 101016" ], "sample_taxid": [ "1210078" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA:Bethesda, Maryland" ], "sample_host_location_id": [], "data_size": "2.000 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 2.78, "strain_heterogeneity": 28.57, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "7324382", "Number of Sequences": "103", "Longest Sequences (bp)": "387552", "N50 (bp)": "146771", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.0", "Number of CDSs": "6664", "Average Protein Length": "321.2", "Coding Ratio (%)": "87.7", "Number of rRNAs": "3", "Number of tRNAs": "63", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Nocardia kruczakiae", "strain": "strain=NBRC 101016", "accession": "GCA_001612965.1", "taxid": 261477, "species_taxid": 261477, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2378, "total_fragments": 2388, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Nocardia aobensis", "strain": "strain=NBRC 100429", "accession": "GCA_000308375.1", "taxid": 257277, "species_taxid": 257277, "relation_to_type": "type", "validated": true, "ani": 95.7004, "matched_fragments": 1997, "total_fragments": 2388, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Nocardia cerradoensis", "strain": "strain=NBRC 101014", "accession": "GCA_000308535.1", "taxid": 85688, "species_taxid": 85688, "relation_to_type": "type", "validated": true, "ani": 94.8376, "matched_fragments": 1945, "total_fragments": 2388, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia mikamii", "strain": "strain=NBRC 108933", "accession": "GCA_001613505.1", "taxid": 508464, "species_taxid": 508464, "relation_to_type": "type", "validated": true, "ani": 94.7431, "matched_fragments": 2152, "total_fragments": 2388, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia africana", "strain": "strain=NBRC 100379", "accession": "GCA_001612635.1", "taxid": 134964, "species_taxid": 134964, "relation_to_type": "type", "validated": true, "ani": 92.2899, "matched_fragments": 1947, "total_fragments": 2388, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia africana", "strain": "strain=FDAARGOS_1597", "accession": "GCA_020731565.1", "taxid": 134964, "species_taxid": 134964, "relation_to_type": "type", "validated": true, "ani": 92.2437, "matched_fragments": 1957, "total_fragments": 2388, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia nova", "strain": "strain=NBRC 15556", "accession": "GCA_001613005.1", "taxid": 37330, "species_taxid": 37330, "relation_to_type": "type", "validated": true, "ani": 92.2125, "matched_fragments": 1946, "total_fragments": 2388, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia elegans", "strain": "strain=NBRC 108235", "accession": "GCA_001612845.1", "taxid": 300029, "species_taxid": 300029, "relation_to_type": "type", "validated": true, "ani": 92.1494, "matched_fragments": 1970, "total_fragments": 2388, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia coffeae", "strain": "strain=CA2R105", "accession": "GCA_019890715.1", "taxid": 2873381, "species_taxid": 2873381, "relation_to_type": "type", "validated": true, "ani": 80.9813, "matched_fragments": 1286, "total_fragments": 2388, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia jiangxiensis", "strain": "strain=NBRC 101359", "accession": "GCA_000308615.1", "taxid": 282685, "species_taxid": 282685, "relation_to_type": "type", "validated": true, "ani": 80.9167, "matched_fragments": 1239, "total_fragments": 2388, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia miyunensis", "strain": "strain=NBRC 108239", "accession": "GCA_001613065.1", "taxid": 282684, "species_taxid": 282684, "relation_to_type": "type", "validated": true, "ani": 80.8655, "matched_fragments": 1229, "total_fragments": 2388, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia otitidiscaviarum", "strain": "strain=NBRC 14405", "accession": "GCA_000308635.1", "taxid": 1823, "species_taxid": 1823, "relation_to_type": "type", "validated": true, "ani": 80.2277, "matched_fragments": 1061, "total_fragments": 2388, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia otitidiscaviarum", "strain": "strain=NCTC1934", "accession": "GCA_900454305.1", "taxid": 1823, "species_taxid": 1823, "relation_to_type": "type", "validated": true, "ani": 80.2146, "matched_fragments": 1085, "total_fragments": 2388, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia bhagyanarayanae", "strain": "strain=DSM 103495", "accession": "GCA_006716565.1", "taxid": 1215925, "species_taxid": 1215925, "relation_to_type": "type", "validated": true, "ani": 80.0975, "matched_fragments": 1092, "total_fragments": 2388, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 2.78, "strain_heterogeneity": 28.57 }, "gtdb_result": [ { "accession": "GCF_001612965.1", "gtdb_species": "s__Nocardia kruczakiae", "ani": 100.0, "matched_fragments": 2378, "total_fragments": 2388, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.6988, "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_000308375.1", "gtdb_species": "s__Nocardia aobensis", "ani": 95.711, "matched_fragments": 1996, "total_fragments": 2388, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.6988, "mean_intra_species_ani": "98.11", "min_intra_species_ani": "97.03", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "inconclusive" }, { "accession": "GCF_000308535.1", "gtdb_species": "s__Nocardia cerradoensis", "ani": 94.8376, "matched_fragments": 1945, "total_fragments": 2388, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.0231, "mean_intra_species_ani": "99.71", "min_intra_species_ani": "99.43", "mean_intra_species_af": "1.00", "min_intra_species_af": "0.99", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001613505.1", "gtdb_species": "s__Nocardia mikamii", "ani": 94.7451, "matched_fragments": 2151, "total_fragments": 2388, "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_015354405.1", "gtdb_species": "s__Nocardia sp015354405", "ani": 94.6768, "matched_fragments": 1992, "total_fragments": 2388, "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_001612635.1", "gtdb_species": "s__Nocardia africana", "ani": 92.2946, "matched_fragments": 1946, "total_fragments": 2388, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.93", "min_intra_species_ani": "99.93", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001612845.1", "gtdb_species": "s__Nocardia elegans", "ani": 92.165, "matched_fragments": 1968, "total_fragments": 2388, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 96.9334, "mean_intra_species_ani": "99.79", "min_intra_species_ani": "99.59", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002933465.1", "gtdb_species": "s__Nocardia nova_B", "ani": 91.4765, "matched_fragments": 1761, "total_fragments": 2388, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.92", "min_intra_species_ani": "99.92", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000308615.1", "gtdb_species": "s__Nocardia jiangxiensis", "ani": 80.9193, "matched_fragments": 1238, "total_fragments": 2388, "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_000308635.1", "gtdb_species": "s__Nocardia otitidiscaviarum", "ani": 80.2193, "matched_fragments": 1063, "total_fragments": 2388, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.88", "min_intra_species_ani": "97.41", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_006716565.1", "gtdb_species": "s__Nocardia bhagyanarayanae", "ani": 80.0964, "matched_fragments": 1092, "total_fragments": 2388, "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_001613045.1", "gtdb_species": "s__Nocardia lijiangensis", "ani": 80.0337, "matched_fragments": 1059, "total_fragments": 2388, "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": 30.56, "optimum_ph": 7.496, "genome_size": 7322393.0, "gc_content": 68.04, "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", "kruczakiae", "NBRC", "101016" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }