{ "type": "genome", "identifier": "GCF_024172045.1", "organism": "Nocardia amikacinitolerans", "title": "Nocardia amikacinitolerans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_024172045.1", "bioproject": "PRJNA224116", "biosample": "SAMN04244555", "wgs_master": "JAMTCX000000000.1", "refseq_category": "na", "taxid": "756689", "species_taxid": "756689", "organism_name": "Nocardia amikacinitolerans", "infraspecific_name": "strain=DSM 45539", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/07/06", "asm_name": "ASM2417204v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_024172045.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/024/172/045/GCF_024172045.1_ASM2417204v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7663905", "genome_size_ungapped": "7655457", "gc_percent": "68.500000", "replicon_count": "0", "scaffold_count": "57", "contig_count": "57", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_024172045.1-RS_2024_08_29", "annotation_date": "2024-08-29", "total_gene_count": "6911", "protein_coding_gene_count": "6709", "non_coding_gene_count": "68", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-07-06", "dateModified": "2022-07-06", "datePublished": "2022-07-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Nocardia amikacinitolerans" ], "sample_taxid": [ "756689" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "2.082 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)": "7663905", "Number of Sequences": "57", "Longest Sequences (bp)": "838779", "N50 (bp)": "514191", "Gap Ratio (%)": "0.110231", "GCcontent (%)": "68.5", "Number of CDSs": "6864", "Average Protein Length": "322.4", "Coding Ratio (%)": "86.6", "Number of rRNAs": "1", "Number of tRNAs": "65", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Nocardia amikacinitolerans", "strain": "strain=DSM 45539", "accession": "GCA_024172045.1", "taxid": 756689, "species_taxid": 756689, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2521, "total_fragments": 2527, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Nocardia amikacinitolerans", "strain": "strain=NBRC 108937", "accession": "GCA_001612615.1", "taxid": 756689, "species_taxid": 756689, "relation_to_type": "type", "validated": true, "ani": 99.9758, "matched_fragments": 2478, "total_fragments": 2527, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Nocardia bhagyanarayanae", "strain": "strain=DSM 103495", "accession": "GCA_006716565.1", "taxid": 1215925, "species_taxid": 1215925, "relation_to_type": "type", "validated": true, "ani": 93.3539, "matched_fragments": 2062, "total_fragments": 2527, "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": 89.6885, "matched_fragments": 1869, "total_fragments": 2527, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia xishanensis", "strain": "strain=NBRC 101358", "accession": "GCA_001613365.1", "taxid": 238964, "species_taxid": 238964, "relation_to_type": "type", "validated": true, "ani": 89.0107, "matched_fragments": 1874, "total_fragments": 2527, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia puris", "strain": "strain=DSM 44599", "accession": "GCA_003315035.1", "taxid": 208602, "species_taxid": 208602, "relation_to_type": "type", "validated": true, "ani": 83.7218, "matched_fragments": 1538, "total_fragments": 2527, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia cyriacigeorgica", "strain": "strain=NBRC 100375", "accession": "GCA_000308555.1", "taxid": 135487, "species_taxid": 135487, "relation_to_type": "type", "validated": true, "ani": 81.9321, "matched_fragments": 1124, "total_fragments": 2527, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia cyriacigeorgica", "strain": "strain=DSM 44484", "accession": "GCA_005863225.1", "taxid": 135487, "species_taxid": 135487, "relation_to_type": "type", "validated": true, "ani": 81.9095, "matched_fragments": 1186, "total_fragments": 2527, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001612615.1", "gtdb_species": "s__Nocardia amikacinitolerans", "ani": 99.9758, "matched_fragments": 2478, "total_fragments": 2527, "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": "conclusive" }, { "accession": "GCF_006716565.1", "gtdb_species": "s__Nocardia bhagyanarayanae", "ani": 93.3449, "matched_fragments": 2063, "total_fragments": 2527, "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": 89.6711, "matched_fragments": 1873, "total_fragments": 2527, "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_001613365.1", "gtdb_species": "s__Nocardia xishanensis", "ani": 89.012, "matched_fragments": 1874, "total_fragments": 2527, "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_003315035.1", "gtdb_species": "s__Nocardia puris", "ani": 83.7241, "matched_fragments": 1538, "total_fragments": 2527, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.66", "min_intra_species_ani": "99.46", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_011801125.1", "gtdb_species": "s__Nocardia brasiliensis_C", "ani": 82.4388, "matched_fragments": 1406, "total_fragments": 2527, "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_009829325.1", "gtdb_species": "s__Nocardia sp009829325", "ani": 82.3778, "matched_fragments": 1387, "total_fragments": 2527, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.48", "min_intra_species_ani": "96.48", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000710915.1", "gtdb_species": "s__Nocardia brasiliensis_A", "ani": 82.2079, "matched_fragments": 1331, "total_fragments": 2527, "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_000308555.1", "gtdb_species": "s__Nocardia cyriacigeorgica", "ani": 81.9405, "matched_fragments": 1121, "total_fragments": 2527, "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_900637185.1", "gtdb_species": "s__Nocardia asteroides", "ani": 81.8114, "matched_fragments": 1314, "total_fragments": 2527, "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": 5, "status": "-" }, { "accession": "GCF_015674855.1", "gtdb_species": "s__Nocardia bovistercoris", "ani": 81.7246, "matched_fragments": 1322, "total_fragments": 2527, "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": 29.192, "optimum_tmp": 30.56, "optimum_ph": 7.496, "genome_size": 7903167.49, "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", "amikacinitolerans" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }