{ "type": "genome", "identifier": "GCF_001310275.1", "organism": "Nocardia arizonensis", "title": "Nocardia arizonensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DSMZ", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001310275.1", "bioproject": "PRJNA224116", "biosample": "SAMN03944864", "wgs_master": "LGYZ00000000.1", "refseq_category": "na", "taxid": "1141647", "species_taxid": "1141647", "organism_name": "Nocardia arizonensis", "infraspecific_name": "strain=W9405", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/10/13", "asm_name": "ASM131027v1", "asm_submitter": "DSMZ", "gbrs_paired_asm": "GCA_001310275.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/310/275/GCF_001310275.1_ASM131027v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7198456", "genome_size_ungapped": "7198456", "gc_percent": "68.000000", "replicon_count": "0", "scaffold_count": "133", "contig_count": "133", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001310275.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "6664", "protein_coding_gene_count": "6447", "non_coding_gene_count": "56", "pubmed_id": "26427857" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-10-13", "dateModified": "2015-10-13", "datePublished": "2015-10-13", "_annotation": { "sample_count": 1, "sample_organism": [ "Nocardia arizonensis" ], "sample_taxid": [ "1141647" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Arizona" ], "sample_host_location_id": [], "data_size": "1.967 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 1.39, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "7198456", "Number of Sequences": "133", "Longest Sequences (bp)": "471248", "N50 (bp)": "141802", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "67.9", "Number of CDSs": "6601", "Average Protein Length": "314.5", "Coding Ratio (%)": "86.5", "Number of rRNAs": "2", "Number of tRNAs": "56", "Number of CRISPRs": "4" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Nocardia arizonensis", "strain": "strain=W9405", "accession": "GCA_001310275.1", "taxid": 1141647, "species_taxid": 1141647, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2339, "total_fragments": 2340, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Nocardia arizonensis", "strain": "strain=NBRC 108935", "accession": "GCA_001618405.1", "taxid": 1141647, "species_taxid": 1141647, "relation_to_type": "type", "validated": true, "ani": 99.9826, "matched_fragments": 2306, "total_fragments": 2340, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Nocardia takedensis", "strain": "strain=NBRC 100417", "accession": "GCA_000308695.1", "taxid": 259390, "species_taxid": 259390, "relation_to_type": "type", "validated": true, "ani": 84.5896, "matched_fragments": 1471, "total_fragments": 2340, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia bovistercoris", "strain": "strain=NEAU-351", "accession": "GCA_015674855.1", "taxid": 2785916, "species_taxid": 2785916, "relation_to_type": "type", "validated": true, "ani": 84.3953, "matched_fragments": 1525, "total_fragments": 2340, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia noduli", "strain": "strain=ncl1", "accession": "GCA_019038455.1", "taxid": 2815722, "species_taxid": 2815722, "relation_to_type": "type", "validated": true, "ani": 82.7983, "matched_fragments": 1393, "total_fragments": 2340, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia aurea", "strain": "strain=SYSU K10002", "accession": "GCA_003123685.1", "taxid": 2144174, "species_taxid": 2144174, "relation_to_type": "type", "validated": true, "ani": 82.5061, "matched_fragments": 1441, "total_fragments": 2340, "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": 81.8598, "matched_fragments": 1238, "total_fragments": 2340, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia amikacinitolerans", "strain": "strain=NBRC 108937", "accession": "GCA_001612615.1", "taxid": 756689, "species_taxid": 756689, "relation_to_type": "type", "validated": true, "ani": 81.8421, "matched_fragments": 1231, "total_fragments": 2340, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia amikacinitolerans", "strain": "strain=DSM 45539", "accession": "GCA_024172045.1", "taxid": 756689, "species_taxid": 756689, "relation_to_type": "type", "validated": true, "ani": 81.8382, "matched_fragments": 1243, "total_fragments": 2340, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia lijiangensis", "strain": "strain=NBRC 108240", "accession": "GCA_001613045.1", "taxid": 299618, "species_taxid": 299618, "relation_to_type": "type", "validated": true, "ani": 81.7499, "matched_fragments": 1219, "total_fragments": 2340, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia beijingensis", "strain": "strain=NBRC 16342", "accession": "GCA_001612785.1", "taxid": 95162, "species_taxid": 95162, "relation_to_type": "type", "validated": true, "ani": 81.1421, "matched_fragments": 1168, "total_fragments": 2340, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia higoensis", "strain": "strain=NBRC 100133", "accession": "GCA_000308595.1", "taxid": 228599, "species_taxid": 228599, "relation_to_type": "type", "validated": true, "ani": 81.1087, "matched_fragments": 1100, "total_fragments": 2340, "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": 79.5757, "matched_fragments": 981, "total_fragments": 2340, "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": 79.5439, "matched_fragments": 974, "total_fragments": 2340, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia veterana", "strain": "strain=NBRC 100344", "accession": "GCA_000308855.1", "taxid": 132249, "species_taxid": 132249, "relation_to_type": "type", "validated": true, "ani": 79.3316, "matched_fragments": 894, "total_fragments": 2340, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinokineospora diospyrosa", "strain": "strain=DSM 44255", "accession": "GCA_024171925.1", "taxid": 103728, "species_taxid": 103728, "relation_to_type": "type", "validated": true, "ani": 76.4575, "matched_fragments": 438, "total_fragments": 2340, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 1.39, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001310275.1", "gtdb_species": "s__Nocardia arizonensis", "ani": 100.0, "matched_fragments": 2339, "total_fragments": 2340, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_000308695.1", "gtdb_species": "s__Nocardia takedensis", "ani": 84.5771, "matched_fragments": 1472, "total_fragments": 2340, "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_015674855.1", "gtdb_species": "s__Nocardia bovistercoris", "ani": 84.4073, "matched_fragments": 1524, "total_fragments": 2340, "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_003123685.1", "gtdb_species": "s__Nocardia aurea", "ani": 82.5043, "matched_fragments": 1441, "total_fragments": 2340, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.19", "min_intra_species_ani": "95.19", "mean_intra_species_af": "0.76", "min_intra_species_af": "0.76", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_006716565.1", "gtdb_species": "s__Nocardia bhagyanarayanae", "ani": 81.8718, "matched_fragments": 1237, "total_fragments": 2340, "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_001612615.1", "gtdb_species": "s__Nocardia amikacinitolerans", "ani": 81.8501, "matched_fragments": 1228, "total_fragments": 2340, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.80", "min_intra_species_ani": "97.80", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001613045.1", "gtdb_species": "s__Nocardia lijiangensis", "ani": 81.7613, "matched_fragments": 1218, "total_fragments": 2340, "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_001182745.1", "gtdb_species": "s__Nocardia farcinica", "ani": 81.7315, "matched_fragments": 1126, "total_fragments": 2340, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.16", "min_intra_species_ani": "98.59", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.88", "num_clustered_genomes": 42, "status": "-" }, { "accession": "GCF_001613365.1", "gtdb_species": "s__Nocardia xishanensis", "ani": 81.6737, "matched_fragments": 1228, "total_fragments": 2340, "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_000308555.1", "gtdb_species": "s__Nocardia cyriacigeorgica", "ani": 81.2752, "matched_fragments": 1000, "total_fragments": 2340, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.94", "min_intra_species_ani": "96.19", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 19, "status": "-" }, { "accession": "GCF_000308435.1", "gtdb_species": "s__Nocardia araoensis", "ani": 81.1481, "matched_fragments": 1112, "total_fragments": 2340, "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_001612785.1", "gtdb_species": "s__Nocardia beijingensis", "ani": 81.1295, "matched_fragments": 1169, "total_fragments": 2340, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.03", "min_intra_species_ani": "98.03", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000308595.1", "gtdb_species": "s__Nocardia higoensis", "ani": 81.1009, "matched_fragments": 1098, "total_fragments": 2340, "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_008704205.1", "gtdb_species": "s__Nocardia colli", "ani": 80.6804, "matched_fragments": 1168, "total_fragments": 2340, "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": 79.5226, "matched_fragments": 978, "total_fragments": 2340, "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_000308855.1", "gtdb_species": "s__Nocardia veterana", "ani": 79.3694, "matched_fragments": 888, "total_fragments": 2340, "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_009604425.1", "gtdb_species": "s__Nocardia sp009604425", "ani": 79.3381, "matched_fragments": 939, "total_fragments": 2340, "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_016464305.1", "gtdb_species": "s__REN6 sp016464305", "ani": 76.3529, "matched_fragments": 443, "total_fragments": 2340, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__REN6", "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": 29.192, "optimum_tmp": 30.56, "optimum_ph": 7.496, "genome_size": 7189788.5, "gc_content": 68.006, "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": 0.098, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.882, "coccobacillus_cell_shape": 0.019, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Nocardia", "arizonensis" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }