{ "type": "genome", "identifier": "GCF_003937945.1", "organism": "Amycolatopsis eburnea", "title": "Amycolatopsis eburnea", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Chiang Mai University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003937945.1", "bioproject": "PRJNA224116", "biosample": "SAMN10496485", "wgs_master": "RSEC00000000.1", "refseq_category": "reference genome", "taxid": "2267691", "species_taxid": "2267691", "organism_name": "Amycolatopsis eburnea", "infraspecific_name": "strain=GLM-1", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/12/11", "asm_name": "ASM393794v1", "asm_submitter": "Chiang Mai University", "gbrs_paired_asm": "GCA_003937945.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/937/945/GCF_003937945.1_ASM393794v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "10230128", "genome_size_ungapped": "10229923", "gc_percent": "72.000000", "replicon_count": "0", "scaffold_count": "74", "contig_count": "74", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003937945.1-RS_2024_11_18", "annotation_date": "2024-11-18", "total_gene_count": "9531", "protein_coding_gene_count": "9383", "non_coding_gene_count": "78", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-12-11", "dateModified": "2018-12-11", "datePublished": "2018-12-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Amycolatopsis eburnea" ], "sample_taxid": [ "2267691" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Thailand: Chiang Mai" ], "sample_host_location_id": [], "data_size": "2.707 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)": "10230128", "Number of Sequences": "74", "Longest Sequences (bp)": "1461667", "N50 (bp)": "573040", "Gap Ratio (%)": "0.002004", "GCcontent (%)": "71.8", "Number of CDSs": "9527", "Average Protein Length": "330.9", "Coding Ratio (%)": "92.5", "Number of rRNAs": "0", "Number of tRNAs": "74", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Amycolatopsis eburnea", "strain": "strain=GLM-1", "accession": "GCA_003937945.1", "taxid": 2267691, "species_taxid": 2267691, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 3389, "total_fragments": 3390, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Amycolatopsis lexingtonensis", "strain": "strain=DSM 44653", "accession": "GCA_014873755.1", "taxid": 218822, "species_taxid": 218822, "relation_to_type": "type", "validated": true, "ani": 94.4602, "matched_fragments": 2909, "total_fragments": 3390, "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": 94.2165, "matched_fragments": 2531, "total_fragments": 3390, "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": 89.547, "matched_fragments": 2558, "total_fragments": 3390, "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": 89.4263, "matched_fragments": 2332, "total_fragments": 3390, "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": 89.3468, "matched_fragments": 2060, "total_fragments": 3390, "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": 89.3001, "matched_fragments": 2473, "total_fragments": 3390, "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": 89.2365, "matched_fragments": 2573, "total_fragments": 3390, "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": 89.093, "matched_fragments": 2142, "total_fragments": 3390, "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": 88.9151, "matched_fragments": 2392, "total_fragments": 3390, "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": 88.8711, "matched_fragments": 2442, "total_fragments": 3390, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis jejuensis", "strain": "strain=NRRL B-24427", "accession": "GCA_000717335.1", "taxid": 330084, "species_taxid": 330084, "relation_to_type": "type", "validated": true, "ani": 80.8856, "matched_fragments": 1508, "total_fragments": 3390, "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": 80.3493, "matched_fragments": 1341, "total_fragments": 3390, "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": 79.1961, "matched_fragments": 1160, "total_fragments": 3390, "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": 78.6618, "matched_fragments": 1151, "total_fragments": 3390, "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": 78.2479, "matched_fragments": 1003, "total_fragments": 3390, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 2.78, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003937945.1", "gtdb_species": "s__Amycolatopsis eburnea", "ani": 100.0, "matched_fragments": 3389, "total_fragments": 3390, "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_014873755.1", "gtdb_species": "s__Amycolatopsis lexingtonensis", "ani": 94.4731, "matched_fragments": 2908, "total_fragments": 3390, "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_900107925.1", "gtdb_species": "s__Amycolatopsis pretoriensis", "ani": 89.5381, "matched_fragments": 2559, "total_fragments": 3390, "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": 89.2838, "matched_fragments": 2475, "total_fragments": 3390, "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_902497555.1", "gtdb_species": "s__Amycolatopsis sp902497555", "ani": 89.2653, "matched_fragments": 2568, "total_fragments": 3390, "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_014654205.1", "gtdb_species": "s__Amycolatopsis bullii", "ani": 89.0739, "matched_fragments": 2356, "total_fragments": 3390, "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_002234595.1", "gtdb_species": "s__Amycolatopsis vastitatis", 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"matched_fragments": 1622, "total_fragments": 3390, "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_000717335.1", "gtdb_species": "s__Amycolatopsis jejuensis", "ani": 80.861, "matched_fragments": 1514, "total_fragments": 3390, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.304, "cell_length": 0.239, "doubling_h": null, "growth_tmp": 28.508, "optimum_tmp": 29.166, "optimum_ph": 7.391, "genome_size": 9093664.233, "gc_content": 70.207, "coding_genes": 8151.527, "rRNA16S_genes": 3.75, "tRNA_genes": 51.4, "gram_stain": 1.0, "sporulation": 0.88, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.022, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.977, "mesophilic_range_tmp": 0.909, "thermophilic_range_tmp": 0.09, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.586, "coccus_cell_shape": 0.068, "filament_cell_shape": 0.344, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Amycolatopsis", "eburnea" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }