{ "type": "genome", "identifier": "GCF_003130705.1", "organism": "Rhodococcus oxybenzonivorans", "title": "Rhodococcus oxybenzonivorans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Chung-Ang university", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003130705.1", "bioproject": "PRJNA224116", "biosample": "SAMN07126182", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "1990687", "species_taxid": "1990687", "organism_name": "Rhodococcus oxybenzonivorans", "infraspecific_name": "strain=S2-17", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/05/17", "asm_name": "ASM313070v1", "asm_submitter": "Chung-Ang university", "gbrs_paired_asm": "GCA_003130705.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/130/705/GCF_003130705.1_ASM313070v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "8014224", "genome_size_ungapped": "8014224", "gc_percent": "65.500000", "replicon_count": "4", "scaffold_count": "4", "contig_count": "4", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-03-05", "total_gene_count": "7515", "protein_coding_gene_count": "7068", "non_coding_gene_count": "64", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-05-17", "dateModified": "2018-05-17", "datePublished": "2018-05-17", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhodococcus oxybenzonivorans" ], "sample_taxid": [ "1990687" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea: Incheon" ], "sample_host_location_id": [], "data_size": "2.212 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)": "8014224", "Number of Sequences": "4", "Longest Sequences (bp)": "6611769", "N50 (bp)": "6611769", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "65.6", "Number of CDSs": "7549", "Average Protein Length": "311.1", "Coding Ratio (%)": "87.9", "Number of rRNAs": "12", "Number of tRNAs": "54", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhodococcus oxybenzonivorans", "strain": "strain=S2-17", "accession": "GCA_003130705.1", "taxid": 1990687, "species_taxid": 1990687, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2668, "total_fragments": 2669, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhodococcus opacus", "strain": "strain=DSM 43205", "accession": "GCA_001646735.1", "taxid": 37919, "species_taxid": 37919, "relation_to_type": "type", "validated": true, "ani": 84.3218, "matched_fragments": 1529, "total_fragments": 2669, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus opacus", "strain": "strain=ATCC 51881", "accession": "GCA_012396235.1", "taxid": 37919, "species_taxid": 37919, "relation_to_type": "type", "validated": true, "ani": 84.0937, "matched_fragments": 1544, "total_fragments": 2669, "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": 84.0284, "matched_fragments": 1657, "total_fragments": 2669, "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": 83.9134, "matched_fragments": 1634, "total_fragments": 2669, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus wratislaviensis", "strain": "strain=NCTC13229", "accession": "GCA_900455735.1", "taxid": 44752, "species_taxid": 44752, "relation_to_type": "suspected-type", "validated": true, "ani": 83.8795, "matched_fragments": 1464, "total_fragments": 2669, "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": 83.8425, "matched_fragments": 1608, "total_fragments": 2669, "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": 83.6793, "matched_fragments": 1600, "total_fragments": 2669, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus qingshengii", "strain": "strain=djl-6", "accession": "GCA_023221595.1", "taxid": 334542, "species_taxid": 334542, "relation_to_type": "type", "validated": true, "ani": 79.0164, "matched_fragments": 656, "total_fragments": 2669, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prescottella agglutinans", "strain": "strain=CCTCC AB2014297", "accession": "GCA_004011865.1", "taxid": 1644129, "species_taxid": 1644129, "relation_to_type": "type", "validated": true, "ani": 78.9246, "matched_fragments": 714, "total_fragments": 2669, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus erythropolis", "strain": "strain=JCM 3201", "accession": "GCA_003990875.1", "taxid": 1833, "species_taxid": 1833, "relation_to_type": "type", "validated": true, "ani": 78.8486, "matched_fragments": 650, "total_fragments": 2669, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus erythropolis", "strain": "strain=DSM 43066", "accession": "GCA_022134675.1", "taxid": 1833, "species_taxid": 1833, "relation_to_type": "type", "validated": true, "ani": 78.7252, "matched_fragments": 651, "total_fragments": 2669, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003130705.1", "gtdb_species": "s__Rhodococcus sp003130705", "ani": 100.0, "matched_fragments": 2668, "total_fragments": 2669, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus", "ani_circumscription_radius": 95.0, 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"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_012396235.1", "gtdb_species": "s__Rhodococcus opacus", "ani": 84.089, "matched_fragments": 1546, "total_fragments": 2669, "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_017068395.1", "gtdb_species": "s__Rhodococcus sp002165735", "ani": 83.9066, "matched_fragments": 1637, "total_fragments": 2669, "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": 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"0.80", "num_clustered_genomes": 38, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.123, "cell_length": 0.518, "doubling_h": 0.724, "growth_tmp": 28.385, "optimum_tmp": 28.738, "optimum_ph": 7.305, "genome_size": 6175685.754, "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": 0.421, "coccus_cell_shape": 0.421, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.157, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Rhodococcus", "oxybenzonivorans" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }