{ "type": "genome", "identifier": "GCF_000583735.1", "organism": "Rhodococcus wratislaviensis NBRC 100605", "title": "Rhodococcus wratislaviensis NBRC 100605", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Technology and Evaluation", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000583735.1", "bioproject": "PRJNA224116", "biosample": "SAMD00041784", "wgs_master": "BAWF00000000.1", "refseq_category": "na", "taxid": "1219028", "species_taxid": "44752", "organism_name": "Rhodococcus wratislaviensis NBRC 100605", "infraspecific_name": "strain=NBRC 100605", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/02/28", "asm_name": "ASM58373v1", "asm_submitter": "National Institute of Technology and Evaluation", "gbrs_paired_asm": "GCA_000583735.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/583/735/GCF_000583735.1_ASM58373v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "10403277", "genome_size_ungapped": "10403277", "gc_percent": "67.000000", "replicon_count": "0", "scaffold_count": "151", "contig_count": "151", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000583735.1-RS_2024_12_23", "annotation_date": "2024-12-23", "total_gene_count": "9557", "protein_coding_gene_count": "9158", "non_coding_gene_count": "59", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-02-28", "dateModified": "2014-02-28", "datePublished": "2014-02-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhodococcus wratislaviensis NBRC 100605" ], "sample_taxid": [ "1219028" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not applicable" ], "sample_host_location_id": [], "data_size": "2.862 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)": "10403277", "Number of Sequences": "151", "Longest Sequences (bp)": "484788", "N50 (bp)": "179070", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "66.8", "Number of CDSs": "9515", "Average Protein Length": "317.6", "Coding Ratio (%)": "87.2", "Number of rRNAs": "5", "Number of tRNAs": "60", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhodococcus wratislaviensis", "strain": "strain=NBRC 100605", "accession": "GCA_000583735.1", "taxid": 44752, "species_taxid": 44752, "relation_to_type": "suspected-type", "validated": true, "ani": 100.0, "matched_fragments": 3398, "total_fragments": 3402, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhodococcus wratislaviensis", "strain": "strain=NCTC13229", "accession": "GCA_900455735.1", "taxid": 44752, "species_taxid": 44752, "relation_to_type": "suspected-type", "validated": true, "ani": 98.8972, "matched_fragments": 2410, "total_fragments": 3402, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhodococcus opacus", "strain": "strain=ATCC 51881", "accession": "GCA_012396235.1", "taxid": 37919, "species_taxid": 37919, "relation_to_type": "type", "validated": true, "ani": 94.0937, "matched_fragments": 2159, "total_fragments": 3402, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus opacus", "strain": "strain=DSM 43205", "accession": "GCA_001646735.1", "taxid": 37919, "species_taxid": 37919, "relation_to_type": "type", "validated": true, "ani": 93.9512, "matched_fragments": 2082, "total_fragments": 3402, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus koreensis", "strain": "strain=NBRC 100607", "accession": "GCA_001894845.1", "taxid": 99653, "species_taxid": 99653, "relation_to_type": "type", "validated": true, "ani": 90.6958, "matched_fragments": 2274, "total_fragments": 3402, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus pseudokoreensis", "strain": "strain=R79", "accession": "GCA_017068395.1", "taxid": 2811421, "species_taxid": 2811421, "relation_to_type": "type", "validated": true, "ani": 90.5346, "matched_fragments": 2193, "total_fragments": 3402, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus jostii", "strain": "strain=DSM 44719", "accession": "GCA_900105375.1", "taxid": 132919, "species_taxid": 132919, "relation_to_type": "type", "validated": true, "ani": 90.2478, "matched_fragments": 2434, "total_fragments": 3402, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus jostii", "strain": "strain=NBRC 16295", "accession": "GCA_001894825.1", "taxid": 132919, "species_taxid": 132919, "relation_to_type": "type", "validated": true, "ani": 90.2358, "matched_fragments": 2343, "total_fragments": 3402, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prescottella defluvii", "strain": "strain=Ca11", "accession": "GCA_000738775.1", "taxid": 1323361, "species_taxid": 1323361, "relation_to_type": "type", "validated": true, "ani": 80.0071, "matched_fragments": 822, "total_fragments": 3402, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900455735.1", "gtdb_species": "s__Rhodococcus wratislaviensis", "ani": 98.8972, "matched_fragments": 2410, "total_fragments": 3402, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.31", "min_intra_species_ani": "98.94", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.93", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_012396235.1", "gtdb_species": "s__Rhodococcus opacus", "ani": 94.0915, "matched_fragments": 2160, "total_fragments": 3402, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.04", "min_intra_species_ani": "95.98", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.77", "num_clustered_genomes": 23, "status": "-" }, { "accession": "GCF_000014565.1", "gtdb_species": "s__Rhodococcus jostii_A", "ani": 93.7407, "matched_fragments": 2290, "total_fragments": 3402, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.76", "min_intra_species_ani": "95.96", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.77", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000010805.1", "gtdb_species": "s__Rhodococcus opacus_C", "ani": 90.8754, "matched_fragments": 2162, "total_fragments": 3402, "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_900105905.1", "gtdb_species": "s__Rhodococcus koreensis", "ani": 90.6743, "matched_fragments": 2311, "total_fragments": 3402, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.00", "min_intra_species_ani": "98.46", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.80", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_017068395.1", "gtdb_species": "s__Rhodococcus sp002165735", "ani": 90.5229, "matched_fragments": 2195, "total_fragments": 3402, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.37", "min_intra_species_ani": "95.32", "mean_intra_species_af": "0.78", "min_intra_species_af": "0.69", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_001894825.1", "gtdb_species": "s__Rhodococcus jostii", "ani": 90.2528, "matched_fragments": 2341, "total_fragments": 3402, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000738775.1", "gtdb_species": "s__Rhodococcus defluvii", "ani": 80.0373, "matched_fragments": 819, "total_fragments": 3402, "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_004011865.1", "gtdb_species": "s__Rhodococcus agglutinans", "ani": 79.9627, "matched_fragments": 918, "total_fragments": 3402, "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_006704125.1", "gtdb_species": "s__Rhodococcus sp006704125", "ani": 79.6312, "matched_fragments": 845, "total_fragments": 3402, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.123, "cell_length": 0.518, "doubling_h": 0.724, "growth_tmp": 28.0, "optimum_tmp": 27.0, "optimum_ph": 7.305, "genome_size": 10164733.0, "gc_content": 66.8, "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": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Rhodococcus", "wratislaviensis", "NBRC", "100605" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }