{ "type": "genome", "identifier": "GCF_017875645.1", "organism": "Nocardia goodfellowii", "title": "Nocardia goodfellowii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_017875645.1", "bioproject": "PRJNA224116", "biosample": "SAMN05878021", "wgs_master": "JAGGMR000000000.1", "refseq_category": "reference genome", "taxid": "882446", "species_taxid": "882446", "organism_name": "Nocardia goodfellowii", "infraspecific_name": "strain=DSM 45516", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/04/08", "asm_name": "ASM1787564v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_017875645.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/017/875/645/GCF_017875645.1_ASM1787564v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7982434", "genome_size_ungapped": "7982434", "gc_percent": "67.500000", "replicon_count": "0", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_017875645.1-RS_2024_08_29", "annotation_date": "2024-08-29", "total_gene_count": "7448", "protein_coding_gene_count": "7323", "non_coding_gene_count": "72", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-04-08", "dateModified": "2021-04-08", "datePublished": "2021-04-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Nocardia goodfellowii" ], "sample_taxid": [ "882446" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "2.185 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)": "7982434", "Number of Sequences": "2", "Longest Sequences (bp)": "7948519", "N50 (bp)": "7948519", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "67.3", "Number of CDSs": "7523", "Average Protein Length": "316.2", "Coding Ratio (%)": "89.4", "Number of rRNAs": "12", "Number of tRNAs": "63", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Nocardia goodfellowii", "strain": "strain=DSM 45516", "accession": "GCA_017875645.1", "taxid": 882446, "species_taxid": 882446, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2660, "total_fragments": 2660, "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": 81.9484, "matched_fragments": 1362, "total_fragments": 2660, "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": 81.862, "matched_fragments": 1321, "total_fragments": 2660, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia amikacinitolerans", "strain": "strain=NBRC 108937", "accession": "GCA_001612615.1", "taxid": 756689, "species_taxid": 756689, "relation_to_type": "type", "validated": true, "ani": 81.7035, "matched_fragments": 1373, "total_fragments": 2660, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia amikacinitolerans", "strain": "strain=DSM 45539", "accession": "GCA_024172045.1", "taxid": 756689, "species_taxid": 756689, "relation_to_type": "type", "validated": true, "ani": 81.6664, "matched_fragments": 1373, "total_fragments": 2660, "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": 81.575, "matched_fragments": 1335, "total_fragments": 2660, "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": 81.3734, "matched_fragments": 1154, "total_fragments": 2660, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia colli", "strain": "strain=CICC 11023", "accession": "GCA_008704205.1", "taxid": 2545717, "species_taxid": 2545717, "relation_to_type": "type", "validated": true, "ani": 81.3625, "matched_fragments": 1429, "total_fragments": 2660, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia tenerifensis", "strain": "strain=DSM 44704", "accession": "GCA_003202065.1", "taxid": 228006, "species_taxid": 228006, "relation_to_type": "type", "validated": true, "ani": 81.3542, "matched_fragments": 1405, "total_fragments": 2660, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia vulneris", "strain": "strain=NBRC 108936", "accession": "GCA_001613425.1", "taxid": 1141657, "species_taxid": 1141657, "relation_to_type": "type", "validated": true, "ani": 81.3039, "matched_fragments": 1341, "total_fragments": 2660, "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": 81.2795, "matched_fragments": 1312, "total_fragments": 2660, "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": 81.2781, "matched_fragments": 1307, "total_fragments": 2660, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia vulneris", "strain": "strain=W9851", "accession": "GCA_000811985.1", "taxid": 1141657, "species_taxid": 1141657, "relation_to_type": "type", "validated": true, "ani": 81.2492, "matched_fragments": 1344, "total_fragments": 2660, "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": 80.9928, "matched_fragments": 1319, "total_fragments": 2660, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia barduliensis", "strain": "strain=335427", "accession": "GCA_013315795.1", "taxid": 2736643, "species_taxid": 2736643, "relation_to_type": "type", "validated": true, "ani": 80.95, "matched_fragments": 1236, "total_fragments": 2660, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia gamkensis", "strain": "strain=NBRC 108242", "accession": "GCA_001612985.1", "taxid": 352869, "species_taxid": 352869, "relation_to_type": "type", "validated": true, "ani": 80.9372, "matched_fragments": 1250, "total_fragments": 2660, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia arthritidis", "strain": "strain=NBRC 100137", "accession": "GCA_001612765.1", "taxid": 228602, "species_taxid": 228602, "relation_to_type": "type", "validated": true, "ani": 80.9363, "matched_fragments": 1187, "total_fragments": 2660, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia gamkensis", "strain": "strain=DSM 44956", "accession": "GCA_012396055.1", "taxid": 352869, "species_taxid": 352869, "relation_to_type": "type", "validated": true, "ani": 80.8893, "matched_fragments": 1272, "total_fragments": 2660, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia gamkensis", "strain": "strain=NRRL B-24450", "accession": "GCA_013181665.1", "taxid": 352869, "species_taxid": 352869, "relation_to_type": "type", "validated": true, "ani": 80.8703, "matched_fragments": 1268, "total_fragments": 2660, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia anaemiae", "strain": "strain=NBRC 100462", "accession": "GCA_001612725.1", "taxid": 263910, "species_taxid": 263910, "relation_to_type": "type", "validated": true, "ani": 80.846, "matched_fragments": 1255, "total_fragments": 2660, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia aurantia", "strain": "strain=RB56", "accession": "GCA_009604425.1", "taxid": 2585199, "species_taxid": 2585199, "relation_to_type": "type", "validated": true, "ani": 79.2789, "matched_fragments": 1039, "total_fragments": 2660, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_017875645.1", "gtdb_species": "s__Nocardia goodfellowii", "ani": 100.0, "matched_fragments": 2659, "total_fragments": 2660, "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_015355755.1", "gtdb_species": "s__Nocardia sp015355755", "ani": 88.079, "matched_fragments": 1921, "total_fragments": 2660, "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_006716565.1", "gtdb_species": "s__Nocardia bhagyanarayanae", "ani": 81.9283, "matched_fragments": 1365, "total_fragments": 2660, "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": 81.8524, "matched_fragments": 1320, "total_fragments": 2660, "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_001612615.1", "gtdb_species": "s__Nocardia amikacinitolerans", "ani": 81.7094, "matched_fragments": 1372, "total_fragments": 2660, "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": "-" }, { "accession": "GCF_001613365.1", "gtdb_species": "s__Nocardia xishanensis", "ani": 81.5984, "matched_fragments": 1331, "total_fragments": 2660, "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_011801125.1", "gtdb_species": "s__Nocardia brasiliensis_C", "ani": 81.4129, "matched_fragments": 1308, "total_fragments": 2660, "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_001182745.1", "gtdb_species": "s__Nocardia farcinica", "ani": 81.3985, "matched_fragments": 1177, "total_fragments": 2660, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.16", "min_intra_species_ani": "98.59", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.88", "num_clustered_genomes": 42, "status": "-" }, { "accession": "GCF_008704205.1", "gtdb_species": "s__Nocardia colli", "ani": 81.3777, "matched_fragments": 1426, "total_fragments": 2660, "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_000250675.2", "gtdb_species": "s__Nocardia brasiliensis_B", "ani": 81.3375, "matched_fragments": 1337, "total_fragments": 2660, "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": "-" }, { "accession": "GCF_000308715.1", "gtdb_species": "s__Nocardia tenerifensis", "ani": 81.3148, "matched_fragments": 1304, "total_fragments": 2660, "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_001613425.1", "gtdb_species": "s__Nocardia vulneris", "ani": 81.3001, "matched_fragments": 1343, "total_fragments": 2660, "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": "-" }, { "accession": "GCF_001612685.1", "gtdb_species": "s__Nocardia altamirensis", "ani": 81.2697, "matched_fragments": 1309, "total_fragments": 2660, "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_001612765.1", "gtdb_species": "s__Nocardia arthritidis", "ani": 80.952, "matched_fragments": 1182, "total_fragments": 2660, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.103, "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_001612985.1", "gtdb_species": "s__Nocardia gamkensis", "ani": 80.9352, "matched_fragments": 1252, "total_fragments": 2660, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 96.7192, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "0.99", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_015477835.1", "gtdb_species": "s__Nocardia higoensis_A", "ani": 80.8498, "matched_fragments": 1010, "total_fragments": 2660, "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_001612725.1", "gtdb_species": "s__Nocardia anaemiae", "ani": 80.8381, "matched_fragments": 1259, "total_fragments": 2660, "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_000381925.1", "gtdb_species": "s__Nocardia sp000381925", "ani": 79.3738, "matched_fragments": 1060, "total_fragments": 2660, "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_009604425.1", "gtdb_species": "s__Nocardia sp009604425", "ani": 79.2732, "matched_fragments": 1039, "total_fragments": 2660, "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": 28.0, "optimum_ph": 7.0, "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": 1.0, "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": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Nocardia", "goodfellowii" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }