{ "type": "genome", "identifier": "GCF_008704205.1", "organism": "Nocardia colli", "title": "Nocardia colli", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Second Affiliated Hospital of Kunming Medical University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_008704205.1", "bioproject": "PRJNA224116", "biosample": "SAMN12784532", "wgs_master": "VXLC00000000.1", "refseq_category": "reference genome", "taxid": "2545717", "species_taxid": "2545717", "organism_name": "Nocardia colli", "infraspecific_name": "strain=CICC 11023", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/09/25", "asm_name": "ASM870420v1", "asm_submitter": "Second Affiliated Hospital of Kunming Medical University", "gbrs_paired_asm": "GCA_008704205.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/008/704/205/GCF_008704205.1_ASM870420v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "10032764", "genome_size_ungapped": "10032764", "gc_percent": "67.500000", "replicon_count": "0", "scaffold_count": "80", "contig_count": "80", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_008704205.1-RS_2024_11_06", "annotation_date": "2024-11-06", "total_gene_count": "9216", "protein_coding_gene_count": "9071", "non_coding_gene_count": "68", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-09-25", "dateModified": "2019-09-25", "datePublished": "2019-09-25", "_annotation": { "sample_count": 1, "sample_organism": [ "Nocardia colli" ], "sample_taxid": [ "2545717" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Kunming, Yunnan" ], "sample_host_location_id": [], "data_size": "2.743 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 6.48, "strain_heterogeneity": 33.33, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "10032764", "Number of Sequences": "80", "Longest Sequences (bp)": "1411492", "N50 (bp)": "419347", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "67.4", "Number of CDSs": "9240", "Average Protein Length": "317.1", "Coding Ratio (%)": "87.6", "Number of rRNAs": "3", "Number of tRNAs": "71", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Nocardia colli", "strain": "strain=CICC 11023", "accession": "GCA_008704205.1", "taxid": 2545717, "species_taxid": 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"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": 85.1024, "matched_fragments": 2149, "total_fragments": 3307, "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": 82.1881, "matched_fragments": 1418, "total_fragments": 3307, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia caishijiensis", "strain": "strain=DSM 44831", "accession": "GCA_009858255.1", "taxid": 184756, "species_taxid": 184756, "relation_to_type": "type", "validated": true, "ani": 80.6897, "matched_fragments": 1118, "total_fragments": 3307, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 6.48, "strain_heterogeneity": 33.33 }, "gtdb_result": [ { "accession": "GCF_008704205.1", "gtdb_species": "s__Nocardia colli", "ani": 100.0, "matched_fragments": 3304, "total_fragments": 3307, "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_900269665.1", "gtdb_species": "s__Nocardia suismassiliense", "ani": 87.3729, "matched_fragments": 2259, "total_fragments": 3307, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.20", "min_intra_species_ani": "95.20", "mean_intra_species_af": "0.87", 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"num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_019222765.1", "gtdb_species": "s__Nocardia iowensis", "ani": 86.519, "matched_fragments": 2061, "total_fragments": 3307, "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_001613425.1", "gtdb_species": "s__Nocardia vulneris", "ani": 85.0963, "matched_fragments": 2150, "total_fragments": 3307, "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": "-" }, { 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