{ "type": "genome", "identifier": "GCF_001552535.1", "organism": "Nocardioides jensenii JCM 1364 = NBRC 14755", "title": "Nocardioides jensenii JCM 1364 = NBRC 14755", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Technology and Evaluation", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001552535.1", "bioproject": "PRJNA224116", "biosample": "SAMD00046513", "wgs_master": "BCRJ00000000.1", "refseq_category": "reference genome", "taxid": "1303683", "species_taxid": "1843", "organism_name": "Nocardioides jensenii JCM 1364 = NBRC 14755", "infraspecific_name": "strain=NBRC 14755", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/02/06", "asm_name": "ASM155253v1", "asm_submitter": "National Institute of Technology and Evaluation", "gbrs_paired_asm": "GCA_001552535.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/552/535/GCF_001552535.1_ASM155253v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5102139", "genome_size_ungapped": "5102139", "gc_percent": "69.000000", "replicon_count": "0", "scaffold_count": "187", "contig_count": "187", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001552535.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "5071", "protein_coding_gene_count": "4964", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-02-06", "dateModified": "2016-02-06", "datePublished": "2016-02-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Nocardioides jensenii JCM 1364 = NBRC 14755" ], "sample_taxid": [ "1303683" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.385 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)": "5102139", "Number of Sequences": "187", "Longest Sequences (bp)": "269216", "N50 (bp)": "51818", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.9", "Number of CDSs": "4861", "Average Protein Length": "312.1", "Coding Ratio (%)": "89.2", "Number of rRNAs": "3", "Number of tRNAs": "52", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Nocardioides jensenii", "strain": "strain=NBRC 14755", "accession": "GCA_001552535.1", "taxid": 1843, "species_taxid": 1843, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1596, "total_fragments": 1607, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Nocardioides daedukensis", "strain": "strain=DSM 23819", "accession": "GCA_013408415.1", "taxid": 634462, "species_taxid": 634462, "relation_to_type": "type", "validated": true, "ani": 81.9003, "matched_fragments": 781, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides guangzhouensis", "strain": "strain=130", "accession": "GCA_004519545.1", "taxid": 2497878, "species_taxid": 2497878, "relation_to_type": "type", "validated": true, "ani": 80.8268, "matched_fragments": 726, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides ginsengisegetis", "strain": "strain=DSM 21349", "accession": "GCA_014138045.1", "taxid": 661491, "species_taxid": 661491, "relation_to_type": "type", "validated": true, "ani": 80.6975, "matched_fragments": 679, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides donggukensis", "strain": "strain=MJB4", "accession": "GCA_014842875.1", "taxid": 2774019, "species_taxid": 2774019, "relation_to_type": "type", "validated": true, "ani": 80.5086, "matched_fragments": 655, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides marinisabuli", "strain": "strain=DSM 18965", "accession": "GCA_013466785.1", "taxid": 419476, "species_taxid": 419476, "relation_to_type": "type", "validated": true, "ani": 80.3914, "matched_fragments": 658, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides ungokensis", "strain": "strain=LMG 28591", "accession": "GCA_013466985.1", "taxid": 1643322, "species_taxid": 1643322, "relation_to_type": "type", "validated": true, "ani": 80.3912, "matched_fragments": 650, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides luti", "strain": "strain=KIGAM211", "accession": "GCA_014212315.1", "taxid": 2761101, "species_taxid": 2761101, "relation_to_type": "type", "validated": true, "ani": 80.3628, "matched_fragments": 698, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides szechwanensis", "strain": "strain=CGMCC 1.11147", "accession": "GCA_900103935.1", "taxid": 1005944, "species_taxid": 1005944, "relation_to_type": "type", "validated": true, "ani": 80.2879, "matched_fragments": 643, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides szechwanensis", "strain": "strain=NBRC 108562", "accession": "GCA_007992395.1", "taxid": 1005944, "species_taxid": 1005944, "relation_to_type": "type", "validated": true, "ani": 80.201, "matched_fragments": 653, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides lacusdianchii", "strain": "strain=JXJ CY 38", "accession": "GCA_020102855.1", "taxid": 2783664, "species_taxid": 2783664, "relation_to_type": "type", "validated": true, "ani": 80.1739, "matched_fragments": 626, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides cavernaquae", "strain": "strain=K1W22B-1", "accession": "GCA_003600895.1", "taxid": 2321396, "species_taxid": 2321396, "relation_to_type": "type", "validated": true, "ani": 80.17, "matched_fragments": 528, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides lijunqiniae", "strain": "strain=S-531", "accession": "GCA_015024225.1", "taxid": 2760832, "species_taxid": 2760832, "relation_to_type": "type", "validated": true, "ani": 80.1037, "matched_fragments": 661, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides kribbensis", "strain": "strain=DSM 16314", "accession": "GCA_015070375.1", "taxid": 305517, "species_taxid": 305517, "relation_to_type": "type", "validated": true, "ani": 80.0811, "matched_fragments": 652, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides psychrotolerans", "strain": "strain=NBRC 108563", "accession": "GCA_007992415.1", "taxid": 1005945, "species_taxid": 1005945, "relation_to_type": "type", "validated": true, "ani": 80.0147, "matched_fragments": 645, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides alcanivorans", "strain": "strain=NGK65", "accession": "GCA_021555175.1", "taxid": 2897352, "species_taxid": 2897352, "relation_to_type": "type", "validated": true, "ani": 79.9866, "matched_fragments": 643, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides deserti", "strain": "strain=SC8A-24", "accession": "GCA_014266025.1", "taxid": 1588644, "species_taxid": 1588644, "relation_to_type": "type", "validated": true, "ani": 79.9792, "matched_fragments": 645, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides psychrotolerans", "strain": "strain=CGMCC 1.11156", "accession": "GCA_900113685.1", "taxid": 1005945, "species_taxid": 1005945, "relation_to_type": "type", "validated": true, "ani": 79.9789, "matched_fragments": 651, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides deserti", "strain": "strain=CGMCC 4.7183", "accession": "GCA_014646035.1", "taxid": 1588644, "species_taxid": 1588644, "relation_to_type": "type", "validated": true, "ani": 79.9601, "matched_fragments": 635, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides okcheonensis", "strain": "strain=MMS20-HV4-12", "accession": "GCA_020991065.1", "taxid": 2894081, "species_taxid": 2894081, "relation_to_type": "type", "validated": true, "ani": 79.9492, "matched_fragments": 648, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides jejuensis", "strain": "strain=18JY15-6", "accession": "GCA_004337475.1", "taxid": 2502782, "species_taxid": 2502782, "relation_to_type": "type", "validated": true, "ani": 79.7013, "matched_fragments": 489, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides speluncae", "strain": "strain=YIM ART13", "accession": "GCA_003121585.1", "taxid": 2670337, "species_taxid": 2670337, "relation_to_type": "type", "validated": true, "ani": 79.6948, "matched_fragments": 698, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides alkalitolerans", "strain": "strain=DSM 16699", "accession": "GCA_000426525.1", "taxid": 281714, "species_taxid": 281714, "relation_to_type": "type", "validated": true, "ani": 79.689, "matched_fragments": 585, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides panacis", "strain": "strain=G188", "accession": "GCA_019039255.1", "taxid": 2849501, "species_taxid": 2849501, "relation_to_type": "type", "validated": true, "ani": 79.488, "matched_fragments": 595, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001552535.1", "gtdb_species": "s__Nocardioides jensenii", "ani": 100.0, "matched_fragments": 1596, "total_fragments": 1607, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "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_001426745.1", "gtdb_species": "s__Nocardioides sp001426745", "ani": 87.1019, "matched_fragments": 1163, "total_fragments": 1607, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.99", "min_intra_species_ani": "98.75", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.95", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_012272695.1", "gtdb_species": "s__Nocardioides sp012272695", "ani": 83.6714, "matched_fragments": 929, "total_fragments": 1607, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "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": "GCA_001429555.1", "gtdb_species": "s__Nocardioides sp001429555", "ani": 83.5962, "matched_fragments": 980, "total_fragments": 1607, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "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_013408415.1", "gtdb_species": "s__Nocardioides daedukensis", "ani": 81.9003, "matched_fragments": 781, "total_fragments": 1607, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "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_014842875.1", "gtdb_species": "s__Nocardioides sp014842875", "ani": 80.5267, "matched_fragments": 653, "total_fragments": 1607, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "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": "GCA_902805925.1", "gtdb_species": "s__Nocardioides sp902805925", "ani": 80.2971, "matched_fragments": 512, "total_fragments": 1607, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "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_900103935.1", "gtdb_species": "s__Nocardioides szechwanensis", "ani": 80.2965, "matched_fragments": 642, "total_fragments": 1607, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.222, "cell_length": 0.301, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 28.172, "optimum_ph": 7.323, "genome_size": 5095531.0, "gc_content": 71.317, "coding_genes": 4058.0, "rRNA16S_genes": 3.0, "tRNA_genes": 48.0, "gram_stain": 1.0, "sporulation": 0.023, "motility": 0.217, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 0.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 1.0, "bacillus_cell_shape": 0.893, "coccus_cell_shape": 0.021, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.085, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Nocardioides", "jensenii", "JCM", "1364", "=", "NBRC", "14755" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }