{ "type": "genome", "identifier": "GCF_000308795.1", "organism": "Nocardia thailandica NBRC 100428", "title": "Nocardia thailandica NBRC 100428", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Technology and Evaluation", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000308795.1", "bioproject": "PRJNA224116", "biosample": "SAMD00041779", "wgs_master": "BAGK00000000.1", "refseq_category": "reference genome", "taxid": "1206740", "species_taxid": "257275", "organism_name": "Nocardia thailandica NBRC 100428", "infraspecific_name": "strain=NBRC 100428", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2012/07/16", "asm_name": "ASM30879v1", "asm_submitter": "National Institute of Technology and Evaluation", "gbrs_paired_asm": "GCA_000308795.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/308/795/GCF_000308795.1_ASM30879v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6821826", "genome_size_ungapped": "6821826", "gc_percent": "71.500000", "replicon_count": "0", "scaffold_count": "312", "contig_count": "312", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000308795.1-RS_2024_09_02", "annotation_date": "2024-09-02", "total_gene_count": "6657", "protein_coding_gene_count": "6423", "non_coding_gene_count": "74", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2012-07-16", "dateModified": "2012-07-16", "datePublished": "2012-07-16", "_annotation": { "sample_count": 1, "sample_organism": [ "Nocardia thailandica NBRC 100428" ], "sample_taxid": [ "1206740" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not applicable" ], "sample_host_location_id": [], "data_size": "1.825 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)": "6818391", "Number of Sequences": "289", "Longest Sequences (bp)": "191597", "N50 (bp)": "47211", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "71.6", "Number of CDSs": "6354", "Average Protein Length": "302.5", "Coding Ratio (%)": "84.6", "Number of rRNAs": "2", "Number of tRNAs": "74", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Nocardia thailandica", "strain": "strain=NBRC 100428", "accession": "GCA_000308795.1", "taxid": 257275, "species_taxid": 257275, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2118, "total_fragments": 2134, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Nocardia asteroides", "strain": "strain=NBRC 15531", "accession": "GCA_000308355.2", "taxid": 1824, "species_taxid": 1824, "relation_to_type": "suspected-type", "validated": true, "ani": 84.1372, "matched_fragments": 1470, "total_fragments": 2134, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia asteroides", "strain": "strain=NCTC11293", "accession": "GCA_900637185.1", "taxid": 1824, "species_taxid": 1824, "relation_to_type": "suspected-type", "validated": true, "ani": 84.079, "matched_fragments": 1477, "total_fragments": 2134, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia asteroides", "strain": "strain=ATCC 19247", "accession": "GCA_005863255.1", "taxid": 1824, "species_taxid": 1824, "relation_to_type": "suspected-type", "validated": true, "ani": 84.0548, "matched_fragments": 1465, "total_fragments": 2134, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia asteroides", "strain": "strain=DSM 43373", "accession": "GCA_900114685.1", "taxid": 1824, "species_taxid": 1824, "relation_to_type": "suspected-type", "validated": true, "ani": 84.0508, "matched_fragments": 1488, "total_fragments": 2134, "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": 83.5914, "matched_fragments": 1383, "total_fragments": 2134, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia mangyaensis", "strain": "strain=Y48", "accession": "GCA_001886715.1", "taxid": 2213200, "species_taxid": 2213200, "relation_to_type": "type", "validated": true, "ani": 82.9573, "matched_fragments": 1286, "total_fragments": 2134, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia ignorata", "strain": "strain=NBRC 108230", "accession": "GCA_001612905.1", "taxid": 145285, "species_taxid": 145285, "relation_to_type": "type", "validated": true, "ani": 82.8527, "matched_fragments": 1285, "total_fragments": 2134, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia ignorata", "strain": "strain=DSM 44496", "accession": "GCA_004362495.1", "taxid": 145285, "species_taxid": 145285, "relation_to_type": "type", "validated": true, "ani": 82.7461, "matched_fragments": 1329, "total_fragments": 2134, "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": 81.3349, "matched_fragments": 1006, "total_fragments": 2134, "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": 81.2355, "matched_fragments": 1049, "total_fragments": 2134, "ani_threshold": 95, "status": "below_threshold" }, { "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": 80.8709, "matched_fragments": 1120, "total_fragments": 2134, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia brasiliensis", "strain": "strain=NCTC11294", "accession": "GCA_900454265.1", "taxid": 37326, "species_taxid": 37326, "relation_to_type": "suspected-type", "validated": true, "ani": 80.845, "matched_fragments": 1122, "total_fragments": 2134, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 2.78, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000308795.1", "gtdb_species": "s__Nocardia thailandica", "ani": 100.0, "matched_fragments": 2118, "total_fragments": 2134, "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_900637185.1", "gtdb_species": "s__Nocardia asteroides", "ani": 84.0898, "matched_fragments": 1474, "total_fragments": 2134, "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_003182135.1", "gtdb_species": "s__Nocardia neocaledoniensis", "ani": 83.7515, "matched_fragments": 1430, "total_fragments": 2134, "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": "GCF_014646295.1", "gtdb_species": "s__Nocardia rhizosphaerihabitans", "ani": 83.5958, "matched_fragments": 1381, "total_fragments": 2134, "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": 82.9677, "matched_fragments": 1283, "total_fragments": 2134, "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_001612825.1", "gtdb_species": "s__Nocardia caishijiensis", "ani": 82.8378, "matched_fragments": 1263, "total_fragments": 2134, "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": "GCF_001612905.1", "gtdb_species": "s__Nocardia ignorata", "ani": 82.8269, "matched_fragments": 1290, "total_fragments": 2134, "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_003315035.1", "gtdb_species": "s__Nocardia puris", "ani": 81.8797, "matched_fragments": 1207, "total_fragments": 2134, "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_000284035.1", "gtdb_species": "s__Nocardia cyriacigeorgica_B", "ani": 81.4953, "matched_fragments": 1083, "total_fragments": 2134, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.41", "min_intra_species_ani": "98.27", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_001613125.1", "gtdb_species": "s__Nocardia shimofusensis", "ani": 81.4845, "matched_fragments": 1049, "total_fragments": 2134, "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_005863245.1", "gtdb_species": "s__Nocardia cyriacigeorgica_C", "ani": 81.4031, "matched_fragments": 1102, "total_fragments": 2134, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.66", "min_intra_species_ani": "96.66", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000308555.1", "gtdb_species": "s__Nocardia cyriacigeorgica", "ani": 81.3901, "matched_fragments": 996, "total_fragments": 2134, "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_000308715.1", "gtdb_species": "s__Nocardia tenerifensis", "ani": 81.2857, "matched_fragments": 1100, "total_fragments": 2134, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "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_010858045.1", "gtdb_species": "s__Nocardia cyriacigeorgica_E", "ani": 81.1656, "matched_fragments": 1084, "total_fragments": 2134, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.94", "min_intra_species_ani": "98.91", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.91", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000308475.2", "gtdb_species": "s__Nocardia brasiliensis", "ani": 80.9198, "matched_fragments": 1111, "total_fragments": 2134, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.223, "cell_length": 0.046, "doubling_h": null, "growth_tmp": 29.0, "optimum_tmp": 30.56, "optimum_ph": 7.496, "genome_size": 6821826.0, "gc_content": 71.64, "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", "thailandica", "NBRC", "100428" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }