{ "type": "genome", "identifier": "GCF_020515525.1", "organism": "Rhodococcus yananensis", "title": "Rhodococcus yananensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Yan'an university", "publication": [ {} ], "properties": { "assembly_accession": "GCF_020515525.1", "bioproject": "PRJNA224116", "biosample": "SAMN21894551", "wgs_master": "JAIYEP000000000.1", "refseq_category": "reference genome", "taxid": "2879464", "species_taxid": "2879464", "organism_name": "Rhodococcus yananensis", "infraspecific_name": "strain=FBM22-1", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/10/17", "asm_name": "ASM2051552v1", "asm_submitter": "Yan'an university", "gbrs_paired_asm": "GCA_020515525.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/020/515/525/GCF_020515525.1_ASM2051552v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4246627", "genome_size_ungapped": "4246627", "gc_percent": "68.500000", "replicon_count": "0", "scaffold_count": "178", "contig_count": "178", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_020515525.1-RS_2024_08_29", "annotation_date": "2024-08-29", "total_gene_count": "3939", "protein_coding_gene_count": "3798", "non_coding_gene_count": "59", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-10-17", "dateModified": "2021-10-17", "datePublished": "2021-10-17", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhodococcus yananensis" ], "sample_taxid": [ "2879464" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Yan'an" ], "sample_host_location_id": [], "data_size": "1.152 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)": "4246627", "Number of Sequences": "178", "Longest Sequences (bp)": "166343", "N50 (bp)": "49062", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.7", "Number of CDSs": "3833", "Average Protein Length": "327.1", "Coding Ratio (%)": "88.6", "Number of rRNAs": "3", "Number of tRNAs": "62", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhodococcus yananensis", "strain": "strain=FBM22-1", "accession": "GCA_020515525.1", "taxid": 2879464, "species_taxid": 2879464, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1324, "total_fragments": 1328, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhodococcus rhodochrous", "strain": "strain=DSM 43241", "accession": "GCA_001646825.1", "taxid": 1829, "species_taxid": 1829, "relation_to_type": "suspected-type", "validated": true, "ani": 81.6602, "matched_fragments": 855, "total_fragments": 1328, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus rhodochrous", "strain": "strain=NCTC10210", "accession": "GCA_900187265.1", "taxid": 1829, "species_taxid": 1829, "relation_to_type": "suspected-type", "validated": true, "ani": 81.6316, "matched_fragments": 873, "total_fragments": 1328, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus rhodochrous", "strain": "strain=NBRC 16069", "accession": "GCA_001047055.1", "taxid": 1829, "species_taxid": 1829, "relation_to_type": "suspected-type", "validated": true, "ani": 81.6114, "matched_fragments": 865, "total_fragments": 1328, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus pyridinivorans", "strain": "strain=DSM 44555", "accession": "GCA_900105195.1", "taxid": 103816, "species_taxid": 103816, "relation_to_type": "type", "validated": true, "ani": 81.6023, "matched_fragments": 854, "total_fragments": 1328, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus gordoniae", "strain": "strain=DSM 44689", "accession": "GCA_001646655.1", "taxid": 223392, "species_taxid": 223392, "relation_to_type": "type", "validated": true, "ani": 81.5156, "matched_fragments": 820, "total_fragments": 1328, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus phenolicus", "strain": "strain=DSM 44812", "accession": "GCA_001646785.1", "taxid": 263849, "species_taxid": 263849, "relation_to_type": "type", "validated": true, "ani": 81.486, "matched_fragments": 845, "total_fragments": 1328, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus gordoniae", "strain": "strain=NCTC13296", "accession": "GCA_900455725.1", "taxid": 223392, "species_taxid": 223392, "relation_to_type": "type", "validated": true, "ani": 81.4773, "matched_fragments": 855, "total_fragments": 1328, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus zopfii", "strain": "strain=ATCC 51349", "accession": "GCA_022134735.1", "taxid": 43772, "species_taxid": 43772, "relation_to_type": "type", "validated": true, "ani": 81.1998, "matched_fragments": 808, "total_fragments": 1328, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus zopfii", "strain": "strain=NBRC 100606", "accession": "GCA_001895025.1", "taxid": 43772, "species_taxid": 43772, "relation_to_type": "type", "validated": true, "ani": 81.1366, "matched_fragments": 888, "total_fragments": 1328, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus ruber", "strain": "strain=DSM 43338", "accession": "GCA_001646835.1", "taxid": 1830, "species_taxid": 1830, "relation_to_type": "type", "validated": true, "ani": 80.8505, "matched_fragments": 782, "total_fragments": 1328, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus ruber", "strain": "strain=NBRC 15591", "accession": "GCA_001894945.1", "taxid": 1830, "species_taxid": 1830, "relation_to_type": "type", "validated": true, "ani": 80.8183, "matched_fragments": 802, "total_fragments": 1328, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus aetherivorans", "strain": "strain=DSM 44752", "accession": "GCA_011058165.1", "taxid": 191292, "species_taxid": 191292, "relation_to_type": "type", "validated": true, "ani": 80.8095, "matched_fragments": 839, "total_fragments": 1328, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus aetherivorans", "strain": "strain=JCM 14343", "accession": "GCA_009176285.1", "taxid": 191292, "species_taxid": 191292, "relation_to_type": "type", "validated": true, "ani": 80.782, "matched_fragments": 833, "total_fragments": 1328, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia amamiensis", "strain": "strain=NBRC 102102", "accession": "GCA_001612745.1", "taxid": 404578, "species_taxid": 404578, "relation_to_type": "type", "validated": true, "ani": 77.9658, "matched_fragments": 418, "total_fragments": 1328, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium fallax", "strain": "strain=JCM 6405", "accession": "GCA_010726955.1", "taxid": 1793, "species_taxid": 1793, "relation_to_type": "type", "validated": true, "ani": 77.7029, "matched_fragments": 364, "total_fragments": 1328, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_012729135.1", "gtdb_species": "s__Rhodococcus sp012729135", "ani": 99.402, "matched_fragments": 1060, 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"d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.98", "min_intra_species_ani": "98.16", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.93", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_004345605.1", "gtdb_species": "s__Rhodococcus sp004345605", "ani": 81.4854, "matched_fragments": 914, "total_fragments": 1328, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus", "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_001646785.1", "gtdb_species": "s__Rhodococcus phenolicus", "ani": 81.4646, "matched_fragments": 847, "total_fragments": 1328, "gtdb_taxonomy": 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