{ "type": "genome", "identifier": "GCF_015339545.1", "organism": "Nocardioides salarius", "title": "Nocardioides salarius", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Chinese Center for Disease Control and Prevention", "publication": [ {} ], "properties": { "assembly_accession": "GCF_015339545.1", "bioproject": "PRJNA224116", "biosample": "SAMN15541901", "wgs_master": "JACDTV000000000.1", "refseq_category": "na", "taxid": "374513", "species_taxid": "374513", "organism_name": "Nocardioides salarius", "infraspecific_name": "strain=DSM 18239", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/11/10", "asm_name": "ASM1533954v1", "asm_submitter": "Chinese Center for Disease Control and Prevention", "gbrs_paired_asm": "GCA_015339545.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/015/339/545/GCF_015339545.1_ASM1533954v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4429352", "genome_size_ungapped": "4429322", "gc_percent": "73.000000", "replicon_count": "0", "scaffold_count": "44", "contig_count": "44", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_015339545.1-RS_2025_01_06", "annotation_date": "2025-01-06", "total_gene_count": "4281", "protein_coding_gene_count": "4187", "non_coding_gene_count": "59", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-11-10", "dateModified": "2020-11-10", "datePublished": "2020-11-10", "_annotation": { "sample_count": 1, "sample_organism": [ "Nocardioides salarius" ], "sample_taxid": [ "374513" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea" ], "sample_host_location_id": [], "data_size": "1.159 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)": "4429352", "Number of Sequences": "44", "Longest Sequences (bp)": "456049", "N50 (bp)": "248692", "Gap Ratio (%)": "0.000677", "GCcontent (%)": "72.9", "Number of CDSs": "4237", "Average Protein Length": "321.8", "Coding Ratio (%)": "92.3", "Number of rRNAs": "5", "Number of tRNAs": "59", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Nocardioides salarius", "strain": "strain=DSM 18239", "accession": "GCA_015339545.1", "taxid": 374513, "species_taxid": 374513, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1452, "total_fragments": 1455, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Nocardioides salarius", "strain": "strain=DSM 18239", "accession": "GCA_015070765.1", "taxid": 374513, "species_taxid": 374513, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1449, "total_fragments": 1455, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Nocardioides salarius", "strain": "strain=DSM 18239", "accession": "GCA_016907435.1", "taxid": 374513, "species_taxid": 374513, "relation_to_type": "type", "validated": true, "ani": 99.9981, "matched_fragments": 1453, "total_fragments": 1455, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Nocardioides marinisabuli", "strain": "strain=DSM 18965", "accession": "GCA_013409965.1", "taxid": 419476, "species_taxid": 419476, "relation_to_type": "type", "validated": true, "ani": 90.5385, "matched_fragments": 1151, "total_fragments": 1455, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides marinisabuli", "strain": "strain=DSM 18965", "accession": "GCA_013466785.1", "taxid": 419476, "species_taxid": 419476, "relation_to_type": "type", "validated": true, "ani": 90.471, "matched_fragments": 1162, "total_fragments": 1455, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides ferulae", "strain": "strain=SZ4R5S7", "accession": "GCA_003660455.1", "taxid": 2340821, "species_taxid": 2340821, "relation_to_type": "type", "validated": true, "ani": 81.9733, "matched_fragments": 878, "total_fragments": 1455, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides acrostichi", "strain": "strain=CBS4Y-1", "accession": "GCA_015319165.1", "taxid": 2784339, "species_taxid": 2784339, "relation_to_type": "type", "validated": true, "ani": 81.4788, "matched_fragments": 793, "total_fragments": 1455, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides lacusdianchii", "strain": "strain=JXJ CY 38", "accession": "GCA_020102855.1", "taxid": 2783664, "species_taxid": 2783664, "relation_to_type": "type", "validated": true, "ani": 81.2374, "matched_fragments": 764, "total_fragments": 1455, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides donggukensis", "strain": "strain=MJB4", "accession": "GCA_014842875.1", "taxid": 2774019, "species_taxid": 2774019, "relation_to_type": "type", "validated": true, "ani": 80.8177, "matched_fragments": 698, "total_fragments": 1455, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides ganghwensis", "strain": "strain=9920", "accession": "GCA_014779655.1", "taxid": 252230, "species_taxid": 252230, "relation_to_type": "type", "validated": true, "ani": 80.7044, "matched_fragments": 759, "total_fragments": 1455, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides carbamazepini", "strain": "strain=CBZ_1", "accession": "GCA_024614185.1", "taxid": 2854259, "species_taxid": 2854259, "relation_to_type": "type", "validated": true, "ani": 80.3232, "matched_fragments": 754, "total_fragments": 1455, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides humilatus", "strain": "strain=BN130099", "accession": "GCA_008373755.1", "taxid": 2607660, "species_taxid": 2607660, "relation_to_type": "type", "validated": true, "ani": 80.0928, "matched_fragments": 664, "total_fragments": 1455, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_016907435.1", "gtdb_species": "s__Nocardioides salarius", "ani": 99.9981, "matched_fragments": 1453, "total_fragments": 1455, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "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": 3, "status": "conclusive" }, { "accession": "GCF_013466785.1", "gtdb_species": "s__Nocardioides marinisabuli", "ani": 90.4902, "matched_fragments": 1160, "total_fragments": 1455, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "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_001653335.1", "gtdb_species": "s__Nocardioides dokdonensis", "ani": 87.4666, "matched_fragments": 1115, "total_fragments": 1455, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "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_015070375.1", "gtdb_species": "s__Nocardioides kribbensis", "ani": 83.3444, "matched_fragments": 871, "total_fragments": 1455, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.79", "min_intra_species_ani": "97.79", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_001627335.1", "gtdb_species": "s__Nocardioides sp001627335", "ani": 83.2857, "matched_fragments": 804, "total_fragments": 1455, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.38", "min_intra_species_ani": "96.50", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 12, "status": "-" }, { "accession": "GCF_013408145.1", "gtdb_species": "s__Nocardioides marinus", "ani": 83.2685, "matched_fragments": 913, "total_fragments": 1455, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.85", "min_intra_species_ani": "95.82", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.73", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_013177455.1", "gtdb_species": "s__Nocardioides sp013177455", "ani": 82.3452, "matched_fragments": 870, "total_fragments": 1455, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.28", "min_intra_species_ani": "98.92", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_013155365.1", "gtdb_species": "s__Nocardioides sp013155365", "ani": 82.1153, "matched_fragments": 819, "total_fragments": 1455, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "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_003660455.1", "gtdb_species": "s__Nocardioides ferulae", "ani": 81.9882, "matched_fragments": 876, "total_fragments": 1455, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "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_018459925.1", "gtdb_species": "s__Nocardioides aquaticus", "ani": 81.5879, "matched_fragments": 802, "total_fragments": 1455, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "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_902506435.1", "gtdb_species": "s__Nocardioides sp902506435", "ani": 81.5727, "matched_fragments": 778, "total_fragments": 1455, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "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_015319165.1", "gtdb_species": "s__Nocardioides acrostichi", "ani": 81.5017, "matched_fragments": 791, "total_fragments": 1455, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "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_003047295.1", "gtdb_species": "s__Nocardioides sediminis", "ani": 81.1727, "matched_fragments": 739, "total_fragments": 1455, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "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_001429625.1", "gtdb_species": "s__Nocardioides sp001429625", "ani": 81.0729, "matched_fragments": 789, "total_fragments": 1455, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "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_016735675.1", "gtdb_species": "s__Nocardioides sp016735675", "ani": 80.8828, "matched_fragments": 734, "total_fragments": 1455, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "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_014108865.1", "gtdb_species": "s__Nocardioides sp014108865", "ani": 79.5833, "matched_fragments": 624, "total_fragments": 1455, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "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": -0.241, "cell_length": 0.041, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 27.5, "optimum_ph": 6.5, "genome_size": 4214904.166, "gc_content": 71.317, "coding_genes": 4058.0, "rRNA16S_genes": 3.0, "tRNA_genes": 48.0, "gram_stain": 1.0, "sporulation": 0.023, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 0.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 1.0, "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": [ "Nocardioides", "salarius" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }