{ "type": "genome", "identifier": "GCF_900455725.1", "organism": "Rhodococcus gordoniae", "title": "Rhodococcus gordoniae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "SC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900455725.1", "bioproject": "PRJNA224116", "biosample": "SAMEA4412658", "wgs_master": "UGVI00000000.1", "refseq_category": "reference genome", "taxid": "223392", "species_taxid": "223392", "organism_name": "Rhodococcus gordoniae", "infraspecific_name": "strain=NCTC13296", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/08/01", "asm_name": "50477_H01", "asm_submitter": "SC", "gbrs_paired_asm": "GCA_900455725.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/455/725/GCF_900455725.1_50477_H01", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4871915", "genome_size_ungapped": "4871915", "gc_percent": "68.000000", "replicon_count": "0", "scaffold_count": "3", "contig_count": "3", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900455725.1-RS_2024_05_04", "annotation_date": "2024-05-04", "total_gene_count": "4468", "protein_coding_gene_count": "4345", "non_coding_gene_count": "69", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-08-01", "dateModified": "2018-08-01", "datePublished": "2018-08-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhodococcus gordoniae" ], "sample_taxid": [ "223392" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [ "disease" ], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.318 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)": "4871915", "Number of Sequences": "3", "Longest Sequences (bp)": "4524654", "N50 (bp)": "4524654", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "67.9", "Number of CDSs": "4462", "Average Protein Length": "329.7", "Coding Ratio (%)": "90.6", "Number of rRNAs": "12", "Number of tRNAs": "61", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhodococcus gordoniae", "strain": "strain=NCTC13296", "accession": "GCA_900455725.1", "taxid": 223392, "species_taxid": 223392, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1620, "total_fragments": 1623, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhodococcus gordoniae", "strain": "strain=DSM 44689", "accession": "GCA_001646655.1", "taxid": 223392, "species_taxid": 223392, "relation_to_type": "type", "validated": true, "ani": 99.9641, "matched_fragments": 1547, "total_fragments": 1623, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhodococcus pyridinivorans", "strain": "strain=DSM 44555", "accession": "GCA_900105195.1", "taxid": 103816, "species_taxid": 103816, "relation_to_type": "type", "validated": true, "ani": 91.7616, "matched_fragments": 1367, "total_fragments": 1623, "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": 91.1549, "matched_fragments": 1348, "total_fragments": 1623, "ani_threshold": 95, "status": "below_threshold" }, { "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": 91.1502, "matched_fragments": 1311, "total_fragments": 1623, "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": 91.1264, "matched_fragments": 1324, "total_fragments": 1623, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001646655.1", "gtdb_species": "s__Rhodococcus gordoniae", "ani": 99.9641, "matched_fragments": 1547, "total_fragments": 1623, "gtdb_taxonomy": "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": "conclusive" }, { "accession": "GCF_013602415.1", "gtdb_species": "s__Rhodococcus sp013602415", "ani": 93.1578, "matched_fragments": 1422, "total_fragments": 1623, "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_900105195.1", "gtdb_species": "s__Rhodococcus pyridinivorans", "ani": 91.758, "matched_fragments": 1366, "total_fragments": 1623, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.16", "min_intra_species_ani": "95.17", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.84", "num_clustered_genomes": 21, "status": "-" }, { "accession": "GCF_900187265.1", "gtdb_species": "s__Rhodococcus rhodochrous", "ani": 91.1593, "matched_fragments": 1348, "total_fragments": 1623, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.52", "min_intra_species_ani": "95.51", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.84", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCF_015865005.1", "gtdb_species": "s__Rhodococcus sp015865005", "ani": 81.5717, "matched_fragments": 925, "total_fragments": 1623, "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_001895025.1", "gtdb_species": "s__Rhodococcus zopfii", "ani": 81.5601, "matched_fragments": 948, "total_fragments": 1623, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.81", "min_intra_species_ani": "97.81", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001646785.1", "gtdb_species": "s__Rhodococcus phenolicus", "ani": 81.5567, "matched_fragments": 966, "total_fragments": 1623, "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": "GCA_012729135.1", "gtdb_species": "s__Rhodococcus sp012729135", "ani": 81.3861, "matched_fragments": 770, "total_fragments": 1623, "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_012844225.1", "gtdb_species": "s__Rhodococcus sp012844225", "ani": 81.3591, "matched_fragments": 887, "total_fragments": 1623, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.09", "min_intra_species_ani": "99.02", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.123, "cell_length": 0.518, "doubling_h": 0.724, "growth_tmp": 31.0, "optimum_tmp": 28.738, "optimum_ph": 7.305, "genome_size": 4816904.0, "gc_content": 66.845, "coding_genes": 5562.836, "rRNA16S_genes": 4.1, "tRNA_genes": 52.6, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 0.0, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 0.95, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.05, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 1.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Rhodococcus", "gordoniae" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }