{ "type": "genome", "identifier": "GCF_001613425.1", "organism": "Nocardia vulneris", "title": "Nocardia vulneris", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Technology and Evaluation", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001613425.1", "bioproject": "PRJNA224116", "biosample": "SAMD00040670", "wgs_master": "BDCI00000000.1", "refseq_category": "reference genome", "taxid": "1141657", "species_taxid": "1141657", "organism_name": "Nocardia vulneris", "infraspecific_name": "strain=NBRC 108936", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/04/01", "asm_name": "ASM161342v1", "asm_submitter": "National Institute of Technology and Evaluation", "gbrs_paired_asm": "GCA_001613425.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/613/425/GCF_001613425.1_ASM161342v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "9377610", "genome_size_ungapped": "9377610", "gc_percent": "68.000000", "replicon_count": "0", "scaffold_count": "74", "contig_count": "74", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001613425.1-RS_2024_09_09", "annotation_date": "2024-09-09", "total_gene_count": "8590", "protein_coding_gene_count": "8453", "non_coding_gene_count": "64", "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 vulneris" ], "sample_taxid": [ "1141657" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA:Illinois" ], "sample_host_location_id": [], "data_size": "2.556 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 10.65, "strain_heterogeneity": 42.86, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "9377610", "Number of Sequences": "74", "Longest Sequences (bp)": "642386", "N50 (bp)": "310852", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.1", "Number of CDSs": "8610", "Average Protein Length": "320.2", "Coding Ratio (%)": "88.2", "Number of rRNAs": "3", "Number of tRNAs": "71", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Nocardia vulneris", "strain": "strain=NBRC 108936", "accession": "GCA_001613425.1", "taxid": 1141657, "species_taxid": 1141657, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 3091, "total_fragments": 3092, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Nocardia vulneris", "strain": "strain=W9851", "accession": "GCA_000811985.1", "taxid": 1141657, "species_taxid": 1141657, "relation_to_type": "type", "validated": true, "ani": 99.9755, "matched_fragments": 3016, "total_fragments": 3092, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Nocardia brasiliensis", "strain": "strain=NCTC11294", "accession": "GCA_900454265.1", "taxid": 37326, "species_taxid": 37326, "relation_to_type": "suspected-type", "validated": true, "ani": 95.7982, "matched_fragments": 2751, "total_fragments": 3092, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Nocardia brasiliensis", "strain": "strain=NBRC 14402", "accession": "GCA_000308475.2", "taxid": 37326, "species_taxid": 37326, "relation_to_type": "suspected-type", "validated": true, "ani": 95.7627, "matched_fragments": 2695, "total_fragments": 3092, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Nocardia colli", "strain": "strain=CICC 11023", "accession": "GCA_008704205.1", "taxid": 2545717, "species_taxid": 2545717, "relation_to_type": "type", "validated": true, "ani": 85.1097, "matched_fragments": 2142, "total_fragments": 3092, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia ninae", "strain": "strain=NBRC 108245", "accession": "GCA_007990755.1", "taxid": 356145, "species_taxid": 356145, "relation_to_type": "type", "validated": true, "ani": 84.9279, "matched_fragments": 2015, "total_fragments": 3092, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia tenerifensis", "strain": "strain=NBRC 101015", "accession": "GCA_000308715.1", "taxid": 228006, "species_taxid": 228006, "relation_to_type": "type", "validated": true, "ani": 84.7288, "matched_fragments": 1855, "total_fragments": 3092, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia altamirensis", "strain": "strain=NBRC 108246", "accession": "GCA_001612685.1", "taxid": 472158, "species_taxid": 472158, "relation_to_type": "type", "validated": true, "ani": 84.396, "matched_fragments": 1924, "total_fragments": 3092, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia abscessus", "strain": "strain=FDAARGOS_1596", "accession": "GCA_020731305.1", "taxid": 120957, "species_taxid": 120957, "relation_to_type": "suspected-type", "validated": true, "ani": 82.499, "matched_fragments": 1446, "total_fragments": 3092, "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": 82.166, "matched_fragments": 1423, "total_fragments": 3092, "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": 82.095, "matched_fragments": 1370, "total_fragments": 3092, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia farcinica", "strain": "strain=DSM 43257", "accession": "GCA_900156775.1", "taxid": 37329, "species_taxid": 37329, "relation_to_type": "type", "validated": true, "ani": 81.5775, "matched_fragments": 1189, "total_fragments": 3092, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 10.65, "strain_heterogeneity": 42.86 }, "gtdb_result": [ { "accession": "GCF_001613425.1", "gtdb_species": "s__Nocardia vulneris", "ani": 100.0, "matched_fragments": 3091, "total_fragments": 3092, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.8238, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_000308475.2", "gtdb_species": "s__Nocardia brasiliensis", "ani": 95.7627, "matched_fragments": 2695, "total_fragments": 3092, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.8238, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000250675.2", "gtdb_species": "s__Nocardia brasiliensis_B", "ani": 95.2192, "matched_fragments": 2798, "total_fragments": 3092, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.2192, "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": "conclusive" }, { "accession": "GCF_000710915.1", "gtdb_species": "s__Nocardia brasiliensis_A", "ani": 94.7315, "matched_fragments": 2600, "total_fragments": 3092, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.2054, "mean_intra_species_ani": "98.35", "min_intra_species_ani": "98.32", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_011801125.1", "gtdb_species": "s__Nocardia brasiliensis_C", "ani": 89.6836, "matched_fragments": 2266, "total_fragments": 3092, "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_001612685.1", "gtdb_species": "s__Nocardia altamirensis", "ani": 84.3975, "matched_fragments": 1924, "total_fragments": 3092, "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": 82.1058, "matched_fragments": 1370, "total_fragments": 3092, "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": 28.0, "optimum_tmp": 30.56, "optimum_ph": 7.496, "genome_size": 9364285.0, "gc_content": 68.14, "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", "vulneris" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }