{ "type": "genome", "identifier": "GCF_001625085.1", "organism": "Nocardia acidivorans NBRC 108247", "title": "Nocardia acidivorans NBRC 108247", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Technology and Evaluation", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001625085.1", "bioproject": "PRJNA224116", "biosample": "SAMD00040643", "wgs_master": "BDAW00000000.1", "refseq_category": "reference genome", "taxid": "1210062", "species_taxid": "404580", "organism_name": "Nocardia acidivorans NBRC 108247", "infraspecific_name": "strain=NBRC 108247", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/04/01", "asm_name": "ASM162508v1", "asm_submitter": "National Institute of Technology and Evaluation", "gbrs_paired_asm": "GCA_001625085.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/625/085/GCF_001625085.1_ASM162508v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7571893", "genome_size_ungapped": "7571893", "gc_percent": "67.000000", "replicon_count": "0", "scaffold_count": "161", "contig_count": "161", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001625085.1-RS_2024_09_09", "annotation_date": "2024-09-09", "total_gene_count": "7237", "protein_coding_gene_count": "7006", "non_coding_gene_count": "71", "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 acidivorans NBRC 108247" ], "sample_taxid": [ "1210062" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Italy:island Stromboli" ], "sample_host_location_id": [], "data_size": "2.085 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "7571893", "Number of Sequences": "161", "Longest Sequences (bp)": "295680", "N50 (bp)": "93005", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "66.9", "Number of CDSs": "7075", "Average Protein Length": "306.0", "Coding Ratio (%)": "85.8", "Number of rRNAs": "4", "Number of tRNAs": "73", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Nocardia acidivorans", "strain": "strain=NBRC 108247", "accession": "GCA_001625085.1", "taxid": 404580, "species_taxid": 404580, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2439, "total_fragments": 2445, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Nocardia crassostreae", "strain": "strain=NBRC 100342", "accession": "GCA_001613405.1", "taxid": 53428, "species_taxid": 53428, "relation_to_type": "type", "validated": true, "ani": 82.9815, "matched_fragments": 1491, "total_fragments": 2445, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia inohanensis", "strain": "strain=NBRC 100128", "accession": "GCA_001612945.1", "taxid": 209246, "species_taxid": 209246, "relation_to_type": "type", "validated": true, "ani": 82.7362, "matched_fragments": 1575, "total_fragments": 2445, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia seriolae", "strain": "strain=NBRC 15557", "accession": "GCA_007990715.1", "taxid": 37332, "species_taxid": 37332, "relation_to_type": "type", "validated": true, "ani": 82.7256, "matched_fragments": 1430, "total_fragments": 2445, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia yamanashiensis", "strain": "strain=NBRC 100130", "accession": "GCA_001613325.1", "taxid": 209247, "species_taxid": 209247, "relation_to_type": "type", "validated": true, "ani": 82.6965, "matched_fragments": 1592, "total_fragments": 2445, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia jejuensis", "strain": "strain=NBRC 103114", "accession": "GCA_001613145.1", "taxid": 328049, "species_taxid": 328049, "relation_to_type": "type", "validated": true, "ani": 82.6879, "matched_fragments": 1599, "total_fragments": 2445, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia concava", "strain": "strain=NBRC 100430", "accession": "GCA_000308815.1", "taxid": 257281, "species_taxid": 257281, "relation_to_type": "type", "validated": true, "ani": 82.646, "matched_fragments": 1568, "total_fragments": 2445, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia yunnanensis", "strain": "strain=CFH S0054", "accession": "GCA_003626895.1", "taxid": 2382165, "species_taxid": 2382165, "relation_to_type": "type", "validated": true, "ani": 82.5287, "matched_fragments": 1569, "total_fragments": 2445, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia tengchongensis", "strain": "strain=CFH S0057", "accession": "GCA_018362975.1", "taxid": 2055889, "species_taxid": 2055889, "relation_to_type": "type", "validated": true, "ani": 82.458, "matched_fragments": 1472, "total_fragments": 2445, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia terrae", "strain": "strain=ET3-3", "accession": "GCA_009760405.1", "taxid": 2675851, "species_taxid": 2675851, "relation_to_type": "type", "validated": true, "ani": 82.3836, "matched_fragments": 1584, "total_fragments": 2445, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia niigatensis", "strain": "strain=NBRC 100131", "accession": "GCA_000308655.1", "taxid": 209249, "species_taxid": 209249, "relation_to_type": "type", "validated": true, "ani": 82.3832, "matched_fragments": 1449, "total_fragments": 2445, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia otitidiscaviarum", "strain": "strain=NCTC1934", "accession": "GCA_900454305.1", "taxid": 1823, "species_taxid": 1823, "relation_to_type": "type", "validated": true, "ani": 81.7229, "matched_fragments": 1360, "total_fragments": 2445, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia otitidiscaviarum", "strain": "strain=NBRC 14405", "accession": "GCA_000308635.1", "taxid": 1823, "species_taxid": 1823, "relation_to_type": "type", "validated": true, "ani": 81.6953, "matched_fragments": 1333, "total_fragments": 2445, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001625085.1", "gtdb_species": "s__Nocardia acidivorans", "ani": 100.0, "matched_fragments": 2439, "total_fragments": 2445, "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": "conclusive" }, { "accession": "GCF_009649815.1", "gtdb_species": "s__Nocardia sp009649815", "ani": 88.4956, "matched_fragments": 1876, "total_fragments": 2445, "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, 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