{ "type": "genome", "identifier": "GCF_001895045.1", "organism": "Rhodococcus coprophilus NBRC 100603", "title": "Rhodococcus coprophilus NBRC 100603", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Technology and Evaluation", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001895045.1", "bioproject": "PRJNA224116", "biosample": "SAMD00046763", "wgs_master": "BDAM00000000.1", "refseq_category": "na", "taxid": "1219011", "species_taxid": "38310", "organism_name": "Rhodococcus coprophilus NBRC 100603", "infraspecific_name": "strain=NBRC 100603", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/12/05", "asm_name": "ASM189504v1", "asm_submitter": "National Institute of Technology and Evaluation", "gbrs_paired_asm": "GCA_001895045.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/895/045/GCF_001895045.1_ASM189504v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4549097", "genome_size_ungapped": "4549097", "gc_percent": "67.000000", "replicon_count": "0", "scaffold_count": "30", "contig_count": "30", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001895045.1-RS_2024_08_26", "annotation_date": "2024-08-26", "total_gene_count": "4247", "protein_coding_gene_count": "4141", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-12-05", "dateModified": "2016-12-05", "datePublished": "2016-12-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhodococcus coprophilus NBRC 100603" ], "sample_taxid": [ "1219011" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.246 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)": "4549097", "Number of Sequences": "30", "Longest Sequences (bp)": "959485", "N50 (bp)": "438482", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "66.9", "Number of CDSs": "4200", "Average Protein Length": "326.2", "Coding Ratio (%)": "90.3", "Number of rRNAs": "3", "Number of tRNAs": "58", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhodococcus coprophilus", "strain": "strain=NBRC 100603", "accession": "GCA_001895045.1", "taxid": 38310, "species_taxid": 38310, 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882, "total_fragments": 1502, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodococcus pyridinivorans", "strain": "strain=NBRC 100608", "accession": "GCA_001894905.1", "taxid": 103816, "species_taxid": 103816, "relation_to_type": "type", "validated": true, "ani": 81.302, "matched_fragments": 918, "total_fragments": 1502, "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": 80.708, "matched_fragments": 822, "total_fragments": 1502, "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": 80.6618, "matched_fragments": 846, "total_fragments": 1502, "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": 80.2334, "matched_fragments": 798, "total_fragments": 1502, "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": 80.2185, "matched_fragments": 809, "total_fragments": 1502, "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": 79.3689, "matched_fragments": 611, "total_fragments": 1502, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001895045.1", "gtdb_species": "s__Rhodococcus coprophilus", "ani": 100.0, "matched_fragments": 1501, "total_fragments": 1502, "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": 3, "status": "conclusive" }, { "accession": "GCF_012844225.1", "gtdb_species": "s__Rhodococcus sp012844225", "ani": 87.7361, "matched_fragments": 1257, "total_fragments": 1502, "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": "-" }, { "accession": "GCF_900187265.1", "gtdb_species": "s__Rhodococcus rhodochrous", "ani": 81.4615, "matched_fragments": 972, "total_fragments": 1502, "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_001646655.1", "gtdb_species": "s__Rhodococcus gordoniae", "ani": 81.3648, "matched_fragments": 863, "total_fragments": 1502, "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": 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