{ "type": "genome", "identifier": "GCF_002156025.1", "organism": "Amycolatopsis pretoriensis", "title": "Amycolatopsis pretoriensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "USDA/ARS/NCAUR", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002156025.1", "bioproject": "PRJNA224116", "biosample": "SAMN06294977", "wgs_master": "MUMK00000000.1", "refseq_category": "na", "taxid": "218821", "species_taxid": "218821", "organism_name": "Amycolatopsis pretoriensis", "infraspecific_name": "strain=NRRL B-24133", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/05/22", "asm_name": "ASM215602v1", "asm_submitter": "USDA/ARS/NCAUR", "gbrs_paired_asm": "GCA_002156025.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/156/025/GCF_002156025.1_ASM215602v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "10112372", "genome_size_ungapped": "10110615", "gc_percent": "71.000000", "replicon_count": "0", "scaffold_count": "558", "contig_count": "558", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002156025.1-RS_2024_05_17", "annotation_date": "2024-05-17", "total_gene_count": "10057", "protein_coding_gene_count": "9691", "non_coding_gene_count": "60", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-05-22", "dateModified": "2017-05-22", "datePublished": "2017-05-22", "_annotation": { "sample_count": 1, "sample_organism": [ "Amycolatopsis pretoriensis" ], "sample_taxid": [ "218821" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Africa:Pretoria" ], "sample_host_location_id": [], "data_size": "2.722 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 2.78, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "10112372", "Number of Sequences": "558", "Longest Sequences (bp)": "191941", "N50 (bp)": "36356", "Gap Ratio (%)": "0.019115", "GCcontent (%)": "71.1", "Number of CDSs": "9399", "Average Protein Length": "309.8", "Coding Ratio (%)": "86.4", "Number of rRNAs": "2", "Number of tRNAs": "72", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Amycolatopsis pretoriensis", "strain": "strain=NRRL B-24133", "accession": "GCA_002156025.1", "taxid": 218821, "species_taxid": 218821, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 3080, "total_fragments": 3110, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Amycolatopsis pretoriensis", "strain": "strain=DSM 44654", "accession": "GCA_900107925.1", "taxid": 218821, "species_taxid": 218821, "relation_to_type": "type", "validated": true, "ani": 99.9903, "matched_fragments": 3095, "total_fragments": 3110, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Amycolatopsis camponoti", "strain": "strain=A23", "accession": "GCA_902497555.1", "taxid": 2606593, "species_taxid": 2606593, "relation_to_type": "type", "validated": true, "ani": 91.0043, "matched_fragments": 2473, "total_fragments": 3110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis eburnea", "strain": "strain=GLM-1", "accession": "GCA_003937945.1", "taxid": 2267691, "species_taxid": 2267691, "relation_to_type": "type", "validated": true, "ani": 89.4128, "matched_fragments": 2355, "total_fragments": 3110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis lexingtonensis", "strain": "strain=DSM 44653", "accession": "GCA_014873755.1", "taxid": 218822, "species_taxid": 218822, "relation_to_type": "type", "validated": true, "ani": 89.349, "matched_fragments": 2389, "total_fragments": 3110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis lexingtonensis", "strain": "strain=NRRL B-24131", "accession": "GCA_002156005.1", "taxid": 218822, "species_taxid": 218822, "relation_to_type": "type", "validated": true, "ani": 89.3121, "matched_fragments": 2127, "total_fragments": 3110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis vancoresmycina", "strain": "strain=DSM 44592", "accession": "GCA_000388135.1", "taxid": 208444, "species_taxid": 208444, "relation_to_type": "type", "validated": true, "ani": 88.9097, "matched_fragments": 1892, "total_fragments": 3110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis vancoresmycina", "strain": "strain=NRRL B-24208", "accession": "GCA_000716785.1", "taxid": 208444, "species_taxid": 208444, "relation_to_type": "type", "validated": true, "ani": 88.8649, "matched_fragments": 2265, "total_fragments": 3110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis kentuckyensis", "strain": "strain=NRRL B-24129", "accession": "GCA_002155975.1", "taxid": 218823, "species_taxid": 218823, "relation_to_type": "type", "validated": true, "ani": 88.6339, "matched_fragments": 1957, "total_fragments": 3110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis mediterranei", "strain": "strain=S699", "accession": "GCA_000220945.1", "taxid": 33910, "species_taxid": 33910, "relation_to_type": "type", "validated": true, "ani": 88.6317, "matched_fragments": 2253, "total_fragments": 3110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis thermalba", "strain": "strain=NRRL B-24845", "accession": "GCA_003385215.1", "taxid": 944492, "species_taxid": 944492, "relation_to_type": "type", "validated": true, "ani": 80.1732, "matched_fragments": 1224, "total_fragments": 3110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prauserella cavernicola", "strain": "strain=ASG 168", "accession": "GCA_016595675.1", "taxid": 2800127, "species_taxid": 2800127, "relation_to_type": "type", "validated": true, "ani": 79.0467, "matched_fragments": 1057, "total_fragments": 3110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prauserella isguenensis", "strain": "strain=CECT 8577", "accession": "GCA_014191605.1", "taxid": 1470180, "species_taxid": 1470180, "relation_to_type": "type", "validated": true, "ani": 78.74, "matched_fragments": 771, "total_fragments": 3110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis aidingensis", "strain": "strain=YIM 96748", "accession": "GCA_018885265.1", "taxid": 2842453, "species_taxid": 2842453, "relation_to_type": "type", "validated": true, "ani": 78.6861, "matched_fragments": 987, "total_fragments": 3110, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 2.78, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900107925.1", "gtdb_species": "s__Amycolatopsis pretoriensis", "ani": 99.9903, "matched_fragments": 3095, "total_fragments": 3110, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "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": "conclusive" }, { "accession": "GCF_902497555.1", "gtdb_species": "s__Amycolatopsis sp902497555", "ani": 90.9738, "matched_fragments": 2478, "total_fragments": 3110, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "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_003937945.1", "gtdb_species": "s__Amycolatopsis eburnea", "ani": 89.3942, "matched_fragments": 2358, "total_fragments": 3110, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "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_014873755.1", "gtdb_species": "s__Amycolatopsis lexingtonensis", "ani": 89.3303, "matched_fragments": 2392, "total_fragments": 3110, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "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_000716785.1", "gtdb_species": "s__Amycolatopsis vancoresmycina", "ani": 88.8839, "matched_fragments": 2261, "total_fragments": 3110, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014654205.1", "gtdb_species": "s__Amycolatopsis bullii", "ani": 88.682, "matched_fragments": 2179, "total_fragments": 3110, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "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_002904295.1", "gtdb_species": "s__Amycolatopsis sp002904295", "ani": 88.6411, "matched_fragments": 2251, "total_fragments": 3110, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "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_000220945.1", "gtdb_species": "s__Amycolatopsis mediterranei", "ani": 88.639, "matched_fragments": 2252, "total_fragments": 3110, "gtdb_taxonomy": 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0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Amycolatopsis", "pretoriensis" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }