{ "type": "genome", "identifier": "GCF_018362975.1", "organism": "Nocardia tengchongensis", "title": "Nocardia tengchongensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "West China Hospital, Sichuan University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_018362975.1", "bioproject": "PRJNA224116", "biosample": "SAMN19031525", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2055889", "species_taxid": "2055889", "organism_name": "Nocardia tengchongensis", "infraspecific_name": "strain=CFH S0057", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/05/16", "asm_name": "ASM1836297v1", "asm_submitter": "West China Hospital, Sichuan University", "gbrs_paired_asm": "GCA_018362975.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/362/975/GCF_018362975.1_ASM1836297v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "8006012", "genome_size_ungapped": "8006012", "gc_percent": "68.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_018362975.1-RS_2024_05_06", "annotation_date": "2024-05-06", "total_gene_count": "7769", "protein_coding_gene_count": "7180", "non_coding_gene_count": "79", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-05-16", "dateModified": "2021-05-16", "datePublished": "2021-05-16", "_annotation": { "sample_count": 1, "sample_organism": [ "Nocardia tengchongensis" ], "sample_taxid": [ "2055889" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Chengdu" ], "sample_host_location_id": [], "data_size": "2.179 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "8006012", "Number of Sequences": "1", "Longest Sequences (bp)": "8006012", "N50 (bp)": "8006012", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.3", "Number of CDSs": "7996", "Average Protein Length": "294.7", "Coding Ratio (%)": "88.3", "Number of rRNAs": "9", "Number of tRNAs": "76", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Nocardia tengchongensis", "strain": "strain=CFH S0057", "accession": "GCA_018362975.1", "taxid": 2055889, "species_taxid": 2055889, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2667, "total_fragments": 2668, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Nocardia niigatensis", "strain": "strain=NBRC 100131", "accession": "GCA_000308655.1", "taxid": 209249, "species_taxid": 209249, "relation_to_type": "type", "validated": true, "ani": 87.2099, "matched_fragments": 1949, "total_fragments": 2668, "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": 86.6052, "matched_fragments": 1743, "total_fragments": 2668, "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": 86.5082, "matched_fragments": 1886, "total_fragments": 2668, "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": 86.4519, "matched_fragments": 1872, "total_fragments": 2668, "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": 86.2385, "matched_fragments": 1809, "total_fragments": 2668, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia huaxiensis", "strain": "strain=WCH-YHL-001", "accession": "GCA_013744875.1", "taxid": 2755382, "species_taxid": 2755382, "relation_to_type": "type", "validated": true, "ani": 83.2128, "matched_fragments": 1575, "total_fragments": 2668, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia crassostreae", "strain": "strain=NBRC 100342", "accession": "GCA_001613405.1", "taxid": 53428, "species_taxid": 53428, "relation_to_type": "type", "validated": true, "ani": 82.9202, "matched_fragments": 1471, "total_fragments": 2668, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_018362975.1", "gtdb_species": "s__Nocardia tengchongensis", "ani": 100.0, "matched_fragments": 2667, "total_fragments": 2668, "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_000308655.1", "gtdb_species": "s__Nocardia niigatensis", "ani": 87.2116, "matched_fragments": 1949, "total_fragments": 2668, "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_009708175.1", "gtdb_species": "s__Nocardia sp009708175", "ani": 86.7903, "matched_fragments": 1806, "total_fragments": 2668, "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_007990715.1", "gtdb_species": "s__Nocardia seriolae", "ani": 86.6359, "matched_fragments": 1738, "total_fragments": 2668, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.94", "min_intra_species_ani": "99.87", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.93", "num_clustered_genomes": 20, "status": "-" }, { "accession": "GCF_009760405.1", "gtdb_species": "s__Nocardia terrae", "ani": 86.5212, "matched_fragments": 1885, "total_fragments": 2668, "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_000308815.1", "gtdb_species": "s__Nocardia concava", "ani": 86.4459, "matched_fragments": 1871, "total_fragments": 2668, "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_003626895.1", "gtdb_species": "s__Nocardia yunnanensis", "ani": 86.2552, "matched_fragments": 1806, "total_fragments": 2668, "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_013744875.1", "gtdb_species": "s__Nocardia sp013744875", "ani": 83.2151, "matched_fragments": 1575, "total_fragments": 2668, "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_001613405.1", "gtdb_species": "s__Nocardia crassostreae", "ani": 82.9262, "matched_fragments": 1471, "total_fragments": 2668, "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", "tengchongensis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }