{ "type": "genome", "identifier": "GCF_001613085.1", "organism": "Nocardia salmonicida NBRC 13393", "title": "Nocardia salmonicida NBRC 13393", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Technology and Evaluation", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001613085.1", "bioproject": "PRJNA224116", "biosample": "SAMD00018771", "wgs_master": "BDBR00000000.1", "refseq_category": "na", "taxid": "1210085", "species_taxid": "53431", "organism_name": "Nocardia salmonicida NBRC 13393", "infraspecific_name": "strain=NBRC 13393", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/04/01", "asm_name": "ASM161308v1", "asm_submitter": "National Institute of Technology and Evaluation", "gbrs_paired_asm": "GCA_001613085.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/613/085/GCF_001613085.1_ASM161308v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "8253158", "genome_size_ungapped": "8253158", "gc_percent": "67.000000", "replicon_count": "0", "scaffold_count": "99", "contig_count": "99", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001613085.1-RS_2024_09_09", "annotation_date": "2024-09-09", "total_gene_count": "7848", "protein_coding_gene_count": "7642", "non_coding_gene_count": "59", "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 salmonicida NBRC 13393" ], "sample_taxid": [ "1210085" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "NA" ], "sample_host_location_id": [], "data_size": "2.264 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)": "8253158", "Number of Sequences": "99", "Longest Sequences (bp)": "595514", "N50 (bp)": "169848", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "67.0", "Number of CDSs": "7761", "Average Protein Length": "310.9", "Coding Ratio (%)": "87.7", "Number of rRNAs": "2", "Number of tRNAs": "59", "Number of CRISPRs": "4" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Nocardia salmonicida", "strain": "strain=NBRC 13393", "accession": "GCA_001613085.1", "taxid": 53431, "species_taxid": 53431, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2699, "total_fragments": 2704, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Nocardia salmonicida subsp. cummidelens", "strain": "strain=NBRC 100378", "accession": "GCA_001612865.1", "taxid": 2800120, "species_taxid": 53431, "relation_to_type": "type", "validated": true, "ani": 97.4063, "matched_fragments": 2202, "total_fragments": 2704, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Nocardia fluminea", "strain": "strain=DSM 44489", "accession": "GCA_002846365.1", "taxid": 134984, "species_taxid": 134984, "relation_to_type": "type", "validated": true, "ani": 90.9552, "matched_fragments": 2094, "total_fragments": 2704, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia alba", "strain": "strain=DSM 44684", "accession": "GCA_004339125.1", "taxid": 225051, "species_taxid": 225051, "relation_to_type": "type", "validated": true, "ani": 89.8971, "matched_fragments": 1883, "total_fragments": 2704, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia alba", "strain": "strain=NBRC 108234", "accession": "GCA_001612665.1", "taxid": 225051, "species_taxid": 225051, "relation_to_type": "type", "validated": true, "ani": 89.8762, "matched_fragments": 1892, "total_fragments": 2704, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia rhizosphaerihabitans", "strain": "strain=CGMCC 4.7329", "accession": "GCA_014646295.1", "taxid": 1691570, "species_taxid": 1691570, "relation_to_type": "type", "validated": true, "ani": 85.9837, "matched_fragments": 1732, "total_fragments": 2704, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia rosealba", "strain": "strain=NEAU-G4", "accession": "GCA_020216065.1", "taxid": 2878563, "species_taxid": 2878563, "relation_to_type": "type", "validated": true, "ani": 84.5657, "matched_fragments": 1565, "total_fragments": 2704, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia shimofusensis", "strain": "strain=NBRC 100134", "accession": "GCA_001613125.1", "taxid": 228596, "species_taxid": 228596, "relation_to_type": "type", "validated": true, "ani": 80.5687, "matched_fragments": 1030, "total_fragments": 2704, "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": 80.463, "matched_fragments": 1018, "total_fragments": 2704, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia iowensis", "strain": "strain=NRRL 5646", "accession": "GCA_019222765.1", "taxid": 204891, "species_taxid": 204891, "relation_to_type": "type", "validated": true, "ani": 80.2413, "matched_fragments": 1143, "total_fragments": 2704, "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": 80.2091, "matched_fragments": 1110, "total_fragments": 2704, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 2.78, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001613085.1", "gtdb_species": "s__Nocardia salmonicida", "ani": 100.0, "matched_fragments": 2699, "total_fragments": 2704, "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": "conclusive" }, { "accession": "GCF_002846365.1", "gtdb_species": "s__Nocardia fluminea", "ani": 90.9716, "matched_fragments": 2092, "total_fragments": 2704, "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_001612665.1", "gtdb_species": "s__Nocardia alba", "ani": 89.895, "matched_fragments": 1890, "total_fragments": 2704, "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": "GCA_014360565.1", "gtdb_species": "s__Nocardia sp014360565", "ani": 89.282, "matched_fragments": 1566, "total_fragments": 2704, "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_014646295.1", "gtdb_species": "s__Nocardia rhizosphaerihabitans", "ani": 85.9623, "matched_fragments": 1735, "total_fragments": 2704, "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": 85.8316, "matched_fragments": 1679, "total_fragments": 2704, "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_001612905.1", "gtdb_species": "s__Nocardia ignorata", "ani": 84.7727, "matched_fragments": 1594, "total_fragments": 2704, "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": "-" }, { "accession": "GCF_001612805.1", "gtdb_species": "s__Nocardia coubleae", "ani": 84.7468, "matched_fragments": 1559, "total_fragments": 2704, "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": "-" }, { "accession": "GCF_013839555.1", "gtdb_species": "s__Nocardia sp013839555", "ani": 84.323, "matched_fragments": 1220, "total_fragments": 2704, "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": "-" }, { "accession": "GCF_001613125.1", "gtdb_species": "s__Nocardia shimofusensis", "ani": 80.6025, "matched_fragments": 1026, "total_fragments": 2704, "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_000308595.1", "gtdb_species": "s__Nocardia higoensis", "ani": 80.4603, "matched_fragments": 1019, "total_fragments": 2704, "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_019222765.1", "gtdb_species": "s__Nocardia iowensis", "ani": 80.2448, "matched_fragments": 1142, "total_fragments": 2704, "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": 27.0, "optimum_tmp": 30.56, "optimum_ph": 7.496, "genome_size": 8251840.5, "gc_content": 67.02, "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", "salmonicida", "NBRC", "13393" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }