{ "type": "genome", "identifier": "GCF_002155975.1", "organism": "Amycolatopsis kentuckyensis", "title": "Amycolatopsis kentuckyensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "USDA/ARS/NCAUR", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002155975.1", "bioproject": "PRJNA224116", "biosample": "SAMN06294975", "wgs_master": "MUMI00000000.1", "refseq_category": "reference genome", "taxid": "218823", "species_taxid": "218823", "organism_name": "Amycolatopsis kentuckyensis", "infraspecific_name": "strain=NRRL B-24129", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/05/22", "asm_name": "ASM215597v1", "asm_submitter": "USDA/ARS/NCAUR", "gbrs_paired_asm": "GCA_002155975.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/155/975/GCF_002155975.1_ASM215597v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "10183912", "genome_size_ungapped": "10182227", "gc_percent": "71.500000", "replicon_count": "0", "scaffold_count": "916", "contig_count": "916", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002155975.1-RS_2024_06_30", "annotation_date": "2024-06-30", "total_gene_count": "9932", "protein_coding_gene_count": "9479", "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 kentuckyensis" ], "sample_taxid": [ "218823" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA:Lexington, Kentucky" ], "sample_host_location_id": [], "data_size": "2.728 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 2.78, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "10183912", "Number of Sequences": "916", "Longest Sequences (bp)": "99724", "N50 (bp)": "19672", "Gap Ratio (%)": "0.017714", "GCcontent (%)": "71.7", "Number of CDSs": "8729", "Average Protein Length": "312.8", "Coding Ratio (%)": "80.4", "Number of rRNAs": "2", "Number of tRNAs": "71", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "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": 100.0, "matched_fragments": 2898, "total_fragments": 2941, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Amycolatopsis mediterranei", "strain": "strain=S699", "accession": "GCA_000220945.1", "taxid": 33910, "species_taxid": 33910, "relation_to_type": "type", "validated": true, "ani": 92.1316, "matched_fragments": 2325, "total_fragments": 2941, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis rifamycinica", "strain": "strain=DSM 46095", "accession": "GCA_000695625.1", "taxid": 287986, "species_taxid": 287986, "relation_to_type": "type", "validated": true, "ani": 91.9135, "matched_fragments": 2250, "total_fragments": 2941, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis tolypomycina", "strain": "strain=DSM 44544", "accession": "GCA_900105945.1", "taxid": 208445, "species_taxid": 208445, "relation_to_type": "type", "validated": true, "ani": 91.8516, "matched_fragments": 2364, "total_fragments": 2941, "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": 90.8289, "matched_fragments": 1939, "total_fragments": 2941, "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": 90.822, "matched_fragments": 2285, "total_fragments": 2941, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis vastitatis", "strain": "strain=H5", "accession": "GCA_002234595.1", "taxid": 1905142, "species_taxid": 1905142, "relation_to_type": "type", "validated": true, "ani": 89.9861, "matched_fragments": 2160, "total_fragments": 2941, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis balhimycina", "strain": "strain=DSM 44591", "accession": "GCA_000384295.1", "taxid": 208443, "species_taxid": 208443, "relation_to_type": "type", "validated": true, "ani": 89.529, "matched_fragments": 2195, "total_fragments": 2941, "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": 88.9507, "matched_fragments": 2265, "total_fragments": 2941, "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": 88.9117, "matched_fragments": 2018, "total_fragments": 2941, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis pretoriensis", "strain": "strain=DSM 44654", "accession": "GCA_900107925.1", "taxid": 218821, "species_taxid": 218821, "relation_to_type": "type", "validated": true, "ani": 88.5982, "matched_fragments": 2135, "total_fragments": 2941, "ani_threshold": 95, "status": "below_threshold" }, { "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": 88.4956, "matched_fragments": 1974, "total_fragments": 2941, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis camponoti", "strain": "strain=A23", "accession": "GCA_902497555.1", "taxid": 2606593, "species_taxid": 2606593, "relation_to_type": "type", "validated": true, "ani": 88.4299, "matched_fragments": 2227, "total_fragments": 2941, "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": 80.1514, "matched_fragments": 1145, "total_fragments": 2941, "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": 78.9495, "matched_fragments": 1013, "total_fragments": 2941, "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": 78.6394, "matched_fragments": 993, "total_fragments": 2941, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinokineospora globicatena", "strain": "strain=DSM 44256", "accession": "GCA_024171945.1", "taxid": 103729, "species_taxid": 103729, "relation_to_type": "type", "validated": true, "ani": 78.0157, "matched_fragments": 875, "total_fragments": 2941, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 2.78, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002155975.1", "gtdb_species": "s__Amycolatopsis kentuckyensis", "ani": 100.0, "matched_fragments": 2898, "total_fragments": 2941, "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": "conclusive" }, { "accession": "GCF_014654205.1", "gtdb_species": "s__Amycolatopsis bullii", "ani": 92.1748, "matched_fragments": 2242, "total_fragments": 2941, "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": 92.1501, "matched_fragments": 2323, "total_fragments": 2941, "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": "0.99", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_002904335.1", "gtdb_species": "s__Amycolatopsis sp002904335", "ani": 92.1341, "matched_fragments": 2276, "total_fragments": 2941, "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_000695625.1", "gtdb_species": "s__Amycolatopsis rifamycinica", "ani": 91.903, "matched_fragments": 2251, "total_fragments": 2941, "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_900105945.1", "gtdb_species": "s__Amycolatopsis tolypomycina", "ani": 91.8284, "matched_fragments": 2366, "total_fragments": 2941, "gtdb_taxonomy": 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0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Amycolatopsis", "kentuckyensis" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }