{ "type": "genome", "identifier": "GCF_900188125.1", "organism": "Rhodococcoides kyotonense", "title": "Rhodococcoides kyotonense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900188125.1", "bioproject": "PRJNA224116", "biosample": "SAMN05421642", "wgs_master": "FZOW00000000.1", "refseq_category": "reference genome", "taxid": "398843", "species_taxid": "398843", "organism_name": "Rhodococcoides kyotonense", "infraspecific_name": "strain=JCM 23211", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/07/16", "asm_name": "IMG-taxon 2675903021 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900188125.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/188/125/GCF_900188125.1_IMG-taxon_2675903021_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6311006", "genome_size_ungapped": "6309908", "gc_percent": "64.000000", "replicon_count": "0", "scaffold_count": "50", "contig_count": "50", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900188125.1-RS_2024_08_25", "annotation_date": "2024-08-25", "total_gene_count": "5901", "protein_coding_gene_count": "5802", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-07-16", "dateModified": "2017-07-16", "datePublished": "2017-07-16", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhodococcoides kyotonense" ], "sample_taxid": [ "398843" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.743 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)": "6311006", "Number of Sequences": "50", "Longest Sequences (bp)": "619719", "N50 (bp)": "295026", "Gap Ratio (%)": "0.017398", "GCcontent (%)": "64.2", "Number of CDSs": "5848", "Average Protein Length": "327.5", "Coding Ratio (%)": "91.0", "Number of rRNAs": "3", "Number of tRNAs": "56", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhodococcus kyotonensis", "strain": "strain=JCM 23211", "accession": "GCA_900188125.1", "taxid": 398843, "species_taxid": 398843, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2077, "total_fragments": 2078, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhodococcus yunnanensis", "strain": "strain=NBRC 103083", "accession": "GCA_001895005.1", "taxid": 278209, "species_taxid": 278209, "relation_to_type": "type", "validated": true, "ani": 82.0263, "matched_fragments": 1240, "total_fragments": 2078, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus fascians", "strain": "strain=NBRC 12155", "accession": "GCA_001894785.1", "taxid": 1828, "species_taxid": 1828, "relation_to_type": "type", "validated": true, "ani": 79.8425, "matched_fragments": 817, "total_fragments": 2078, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus fascians", "strain": "strain=LMG 3623", "accession": "GCA_000761055.1", "taxid": 1828, "species_taxid": 1828, "relation_to_type": "type", "validated": true, "ani": 79.7984, "matched_fragments": 813, "total_fragments": 2078, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus kroppenstedtii", "strain": "strain=DSM 44908", "accession": "GCA_001646725.1", "taxid": 293050, "species_taxid": 293050, "relation_to_type": "type", "validated": true, "ani": 78.7707, "matched_fragments": 488, "total_fragments": 2078, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus kroppenstedtii", "strain": "strain=DSM 44908", "accession": "GCA_900111805.1", "taxid": 293050, "species_taxid": 293050, "relation_to_type": "type", "validated": true, "ani": 78.7433, "matched_fragments": 507, "total_fragments": 2078, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prescottella equi", "strain": "strain=NBRC 101255", "accession": "GCA_001552575.1", "taxid": 43767, "species_taxid": 43767, "relation_to_type": "type", "validated": true, "ani": 78.6853, "matched_fragments": 527, "total_fragments": 2078, "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": 78.6666, "matched_fragments": 524, "total_fragments": 2078, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prescottella equi", "strain": "strain=NCTC1621", "accession": "GCA_900455845.1", "taxid": 43767, "species_taxid": 43767, "relation_to_type": "type", "validated": true, "ani": 78.5984, "matched_fragments": 540, "total_fragments": 2078, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus spelaei", "strain": "strain=C9-5", "accession": "GCA_006704125.1", "taxid": 2546320, "species_taxid": 2546320, "relation_to_type": "type", "validated": true, "ani": 78.5968, "matched_fragments": 524, "total_fragments": 2078, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prescottella equi", "strain": "strain=DSM 20307", "accession": "GCA_002094305.1", "taxid": 43767, "species_taxid": 43767, "relation_to_type": "type", "validated": true, "ani": 78.5287, "matched_fragments": 547, "total_fragments": 2078, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus koreensis", "strain": "strain=DSM 44498", "accession": "GCA_900105905.1", "taxid": 99653, "species_taxid": 99653, "relation_to_type": "type", "validated": true, "ani": 78.4406, "matched_fragments": 717, "total_fragments": 2078, "ani_threshold": 95, "status": "below_threshold" }, { "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": 78.4289, "matched_fragments": 697, "total_fragments": 2078, "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": 78.4272, "matched_fragments": 705, "total_fragments": 2078, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ornithinicoccus halotolerans", "strain": "strain=EGI 80423", "accession": "GCA_009602535.1", "taxid": 1748220, "species_taxid": 1748220, "relation_to_type": "type", "validated": true, "ani": 76.4001, "matched_fragments": 104, "total_fragments": 2078, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium pseudoresistens", "strain": "strain=DSM 22185", "accession": "GCA_013409745.1", "taxid": 640634, "species_taxid": 640634, "relation_to_type": "type", "validated": true, "ani": 75.9115, "matched_fragments": 110, "total_fragments": 2078, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Humibacter albus", "strain": "strain=DSM 18994", "accession": "GCA_000421825.1", "taxid": 427754, "species_taxid": 427754, "relation_to_type": "type", "validated": true, "ani": 75.9089, "matched_fragments": 110, "total_fragments": 2078, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora purpureochromogenes", "strain": "strain=DSM 43821", "accession": "GCA_900091515.1", "taxid": 47872, "species_taxid": 47872, "relation_to_type": "type", "validated": true, "ani": 75.8301, "matched_fragments": 163, "total_fragments": 2078, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900188125.1", "gtdb_species": "s__Rhodococcus_B kyotonensis", "ani": 100.0, "matched_fragments": 2077, "total_fragments": 2078, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B", "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_001645385.1", "gtdb_species": "s__Rhodococcus_B kyotonensis_B", "ani": 84.47, "matched_fragments": 1397, "total_fragments": 2078, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.37", "min_intra_species_ani": "97.70", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001895005.1", "gtdb_species": "s__Rhodococcus_B yunnanensis", "ani": 82.0167, "matched_fragments": 1241, "total_fragments": 2078, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B", "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_002259415.1", "gtdb_species": "s__Rhodococcus_B sp002259415", "ani": 81.1169, "matched_fragments": 1028, "total_fragments": 2078, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.80", "min_intra_species_ani": "98.78", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000760735.1", "gtdb_species": "s__Rhodococcus_B fascians_E", "ani": 81.1095, "matched_fragments": 1066, "total_fragments": 2078, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.84", "min_intra_species_ani": "98.47", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.82", "num_clustered_genomes": 19, "status": "-" }, { "accession": "GCF_003641205.1", "gtdb_species": "s__Rhodococcus_B sp003641205", "ani": 80.6176, "matched_fragments": 979, "total_fragments": 2078, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B", "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_001647195.1", "gtdb_species": "s__Rhodococcus_B sp001647195", "ani": 80.5582, "matched_fragments": 797, "total_fragments": 2078, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B", "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_002258315.1", "gtdb_species": "s__Rhodococcus_B sp002258315", "ani": 80.1409, "matched_fragments": 847, "total_fragments": 2078, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002091985.1", "gtdb_species": "s__Rhodococcus_B sp002091985", "ani": 79.7648, "matched_fragments": 745, "total_fragments": 2078, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B", "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_002091955.1", "gtdb_species": "s__Rhodococcus_B sp002091955", "ani": 79.7146, "matched_fragments": 717, "total_fragments": 2078, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B", "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_014281965.1", "gtdb_species": "s__Rhodococcus_B sp014281965", "ani": 79.619, "matched_fragments": 748, "total_fragments": 2078, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B", "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_002929295.1", "gtdb_species": "s__Arthrobacter_D sp002929295", "ani": 76.5412, "matched_fragments": 109, "total_fragments": 2078, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D", "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_009602535.1", "gtdb_species": "s__Ornithinicoccus_A halotolerans", "ani": 76.4194, "matched_fragments": 103, "total_fragments": 2078, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus_A", "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_000421825.1", "gtdb_species": "s__Humibacter albus", "ani": 75.8822, "matched_fragments": 112, "total_fragments": 2078, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Humibacter", "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_003664255.1", "gtdb_species": "s__Micromonospora sp003664255", "ani": 75.8733, "matched_fragments": 173, "total_fragments": 2078, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora", "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Rhodococcoides", "kyotonense" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }