{ "type": "genome", "identifier": "GCF_900113515.1", "organism": "Amycolatopsis regifaucium", "title": "Amycolatopsis regifaucium", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900113515.1", "bioproject": "PRJNA224116", "biosample": "SAMN04489731", "wgs_master": "FOPQ00000000.1", "refseq_category": "reference genome", "taxid": "546365", "species_taxid": "546365", "organism_name": "Amycolatopsis regifaucium", "infraspecific_name": "strain=DSM 45072", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/11/05", "asm_name": "IMG-taxon 2634166327 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900113515.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/113/515/GCF_900113515.1_IMG-taxon_2634166327_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": "8287612", "genome_size_ungapped": "8287612", "gc_percent": "68.500000", "replicon_count": "0", "scaffold_count": "49", "contig_count": "49", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900113515.1-RS_2024_04_27", "annotation_date": "2024-04-27", "total_gene_count": "7762", "protein_coding_gene_count": "7579", "non_coding_gene_count": "66", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-11-05", "dateModified": "2016-11-05", "datePublished": "2016-11-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Amycolatopsis regifaucium" ], "sample_taxid": [ "546365" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "2.253 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)": "8287612", "Number of Sequences": "49", "Longest Sequences (bp)": "959305", "N50 (bp)": "439505", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.5", "Number of CDSs": "7788", "Average Protein Length": "319.7", "Coding Ratio (%)": "90.1", "Number of rRNAs": "4", "Number of tRNAs": "63", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Amycolatopsis regifaucium", "strain": "strain=DSM 45072", "accession": "GCA_900113515.1", "taxid": 546365, "species_taxid": 546365, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2730, "total_fragments": 2739, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Amycolatopsis regifaucium", "strain": "strain=GY080", "accession": "GCA_001558125.2", "taxid": 546365, "species_taxid": 546365, "relation_to_type": "type", "validated": true, "ani": 99.9892, "matched_fragments": 2704, "total_fragments": 2739, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Amycolatopsis regifaucium", "strain": "strain=GY080", "accession": "GCA_001613935.1", "taxid": 546365, "species_taxid": 546365, "relation_to_type": "type", "validated": true, "ani": 99.9892, "matched_fragments": 2712, "total_fragments": 2739, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Amycolatopsis orientalis", "strain": "strain=KCTC 9412", "accession": "GCA_000478275.1", "taxid": 31958, "species_taxid": 31958, "relation_to_type": "type", "validated": true, "ani": 91.5605, "matched_fragments": 2220, "total_fragments": 2739, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis umgeniensis", "strain": "strain=DSM 45272", "accession": "GCA_014205155.1", "taxid": 336628, "species_taxid": 336628, "relation_to_type": "type", "validated": true, "ani": 90.1808, "matched_fragments": 2182, "total_fragments": 2739, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis azurea", "strain": "strain=DSM 43854", "accession": "GCA_000340415.1", "taxid": 36819, "species_taxid": 36819, "relation_to_type": "type", "validated": true, "ani": 90.0218, "matched_fragments": 2108, "total_fragments": 2739, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis coloradensis", "strain": "strain=DSM 44225", "accession": "GCA_001953865.1", "taxid": 76021, "species_taxid": 76021, "relation_to_type": "type", "validated": true, "ani": 89.9954, "matched_fragments": 2118, "total_fragments": 2739, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis roodepoortensis", "strain": "strain=DSM 46661", "accession": "GCA_014873915.1", "taxid": 700274, "species_taxid": 700274, "relation_to_type": "type", "validated": true, "ani": 89.8308, "matched_fragments": 2148, "total_fragments": 2739, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis keratiniphila subsp. nogabecina", "strain": "strain=FH 1893", "accession": "GCA_001953855.1", "taxid": 208442, "species_taxid": 129921, "relation_to_type": "type", "validated": true, "ani": 89.7098, "matched_fragments": 2176, "total_fragments": 2739, "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": 81.4762, "matched_fragments": 1546, "total_fragments": 2739, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis panacis", "strain": "strain=YIM PH21725", "accession": "GCA_003600245.1", "taxid": 2340917, "species_taxid": 2340917, "relation_to_type": "type", "validated": true, "ani": 80.3126, "matched_fragments": 1025, "total_fragments": 2739, "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": 79.6421, "matched_fragments": 1072, "total_fragments": 2739, "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": 79.0121, "matched_fragments": 930, "total_fragments": 2739, "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": 78.7512, "matched_fragments": 940, "total_fragments": 2739, "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": 77.9057, "matched_fragments": 790, "total_fragments": 2739, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 2.78, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001613935.1", "gtdb_species": "s__Amycolatopsis regifaucium", "ani": 99.9892, "matched_fragments": 2712, "total_fragments": 2739, "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": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_000478275.1", "gtdb_species": "s__Amycolatopsis orientalis", "ani": 91.54, "matched_fragments": 2223, "total_fragments": 2739, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.64", "min_intra_species_ani": "96.64", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002849735.1", "gtdb_species": "s__Amycolatopsis sp002849735", "ani": 90.3033, "matched_fragments": 2134, "total_fragments": 2739, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "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": 2, "status": "-" }, { "accession": "GCF_003947415.1", "gtdb_species": "s__Amycolatopsis sp003947415", "ani": 90.2635, "matched_fragments": 2161, "total_fragments": 2739, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.38", "min_intra_species_ani": "96.38", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_014205155.1", "gtdb_species": "s__Amycolatopsis umgeniensis", "ani": 90.1717, "matched_fragments": 2183, "total_fragments": 2739, "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_000342005.1", "gtdb_species": "s__Amycolatopsis decaplanina", "ani": 90.0786, "matched_fragments": 2135, "total_fragments": 2739, "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_001995215.1", "gtdb_species": "s__Amycolatopsis azurea", "ani": 90.0387, "matched_fragments": 2128, "total_fragments": 2739, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000384215.1", "gtdb_species": "s__Amycolatopsis alba", "ani": 90.0274, "matched_fragments": 2157, "total_fragments": 2739, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "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": 2, "status": "-" }, { "accession": "GCF_001953865.1", "gtdb_species": "s__Amycolatopsis coloradensis", "ani": 89.9774, "matched_fragments": 2120, "total_fragments": 2739, "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_014873915.1", "gtdb_species": "s__Amycolatopsis roodepoortensis", "ani": 89.8183, "matched_fragments": 2150, "total_fragments": 2739, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.45", "min_intra_species_ani": "96.45", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002234405.1", "gtdb_species": "s__Amycolatopsis thailandensis", "ani": 89.7506, "matched_fragments": 2038, "total_fragments": 2739, "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_013870525.1", "gtdb_species": "s__Amycolatopsis pittospori", "ani": 89.6429, "matched_fragments": 2047, "total_fragments": 2739, "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_900105055.1", "gtdb_species": "s__Amycolatopsis lurida", "ani": 89.6265, "matched_fragments": 2224, "total_fragments": 2739, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.56", "min_intra_species_ani": "95.13", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.304, "cell_length": 0.239, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 32.5, "optimum_ph": 7.0, "genome_size": 8290721.0, "gc_content": 70.207, "coding_genes": 8151.527, "rRNA16S_genes": 3.75, "tRNA_genes": 51.4, "gram_stain": 1.0, "sporulation": 1.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 0.909, "thermophilic_range_tmp": 0.09, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Amycolatopsis", "regifaucium" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }