{ "type": "genome", "identifier": "GCF_000384215.1", "organism": "Amycolatopsis alba DSM 44262", "title": "Amycolatopsis alba DSM 44262", "description": "na", "data type": "Genome sequencing and assembly", "organization": "JGI", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000384215.1", "bioproject": "PRJNA224116", "biosample": "SAMN02261260", "wgs_master": "ARAF00000000.1", "refseq_category": "reference genome", "taxid": "1125972", "species_taxid": "76020", "organism_name": "Amycolatopsis alba DSM 44262", "infraspecific_name": "strain=DSM 44262", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/04/26", "asm_name": "ASM38421v1", "asm_submitter": "JGI", "gbrs_paired_asm": "GCA_000384215.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/384/215/GCF_000384215.1_ASM38421v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "9811274", "genome_size_ungapped": "9811174", "gc_percent": "68.500000", "replicon_count": "0", "scaffold_count": "1", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000384215.1-RS_2024_04_28", "annotation_date": "2024-04-28", "total_gene_count": "8988", "protein_coding_gene_count": "8855", "non_coding_gene_count": "66", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-04-26", "dateModified": "2013-04-26", "datePublished": "2013-04-26", "_annotation": { "sample_count": 1, "sample_organism": [ "Amycolatopsis alba DSM 44262" ], "sample_taxid": [ "1125972" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [ "None" ], "sample_host_disease_id": [], "sample_host_location": [ "India" ], "sample_host_location_id": [], "data_size": "2.655 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)": "9811274", "Number of Sequences": "1", "Longest Sequences (bp)": "9811274", "N50 (bp)": "9811274", "Gap Ratio (%)": "0.001060", "GCcontent (%)": "68.7", "Number of CDSs": "9076", "Average Protein Length": "326.7", "Coding Ratio (%)": "90.7", "Number of rRNAs": "12", "Number of tRNAs": "63", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Amycolatopsis alba", "strain": "strain=DSM 44262", "accession": "GCA_000384215.1", "taxid": 76020, "species_taxid": 76020, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 3269, "total_fragments": 3270, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Amycolatopsis alba", "strain": "strain=DSM 44262", "accession": "GCA_002234385.1", "taxid": 76020, "species_taxid": 76020, "relation_to_type": "type", "validated": true, "ani": 99.9409, "matched_fragments": 3038, "total_fragments": 3270, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Amycolatopsis azurea", "strain": "strain=DSM 43854", "accession": "GCA_001995215.1", "taxid": 36819, "species_taxid": 36819, "relation_to_type": "type", "validated": true, "ani": 92.8152, "matched_fragments": 2515, "total_fragments": 3270, "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": 92.8148, "matched_fragments": 2477, "total_fragments": 3270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis thailandensis", "strain": "strain=JCM 16380", "accession": "GCA_002234405.1", "taxid": 589330, "species_taxid": 589330, "relation_to_type": "type", "validated": true, "ani": 92.4654, "matched_fragments": 2333, "total_fragments": 3270, "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": 91.5753, "matched_fragments": 2477, "total_fragments": 3270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis japonica", "strain": "strain=MG417-CF17", "accession": "GCA_000732925.1", "taxid": 208439, "species_taxid": 208439, "relation_to_type": "type", "validated": true, "ani": 91.0428, "matched_fragments": 2391, "total_fragments": 3270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis orientalis", "strain": "strain=KCTC 9412", "accession": "GCA_000478275.1", "taxid": 31958, "species_taxid": 31958, "relation_to_type": "type", "validated": true, "ani": 90.249, "matched_fragments": 2274, "total_fragments": 3270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis regifaucium", "strain": "strain=GY080", "accession": "GCA_001613935.1", "taxid": 546365, "species_taxid": 546365, "relation_to_type": "type", "validated": true, "ani": 89.8765, "matched_fragments": 2183, "total_fragments": 3270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis pittospori", "strain": "strain=PIP199", "accession": "GCA_013870525.1", "taxid": 2749434, "species_taxid": 2749434, "relation_to_type": "type", "validated": true, "ani": 89.8037, "matched_fragments": 2183, "total_fragments": 3270, "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": 81.4302, "matched_fragments": 1722, "total_fragments": 3270, "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": 79.7173, "matched_fragments": 1129, "total_fragments": 3270, "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": 78.9265, "matched_fragments": 1025, "total_fragments": 3270, "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", 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"min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_001995215.1", "gtdb_species": "s__Amycolatopsis azurea", "ani": 92.827, "matched_fragments": 2513, "total_fragments": 3270, "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_014654365.1", "gtdb_species": "s__Amycolatopsis oliviviridis", "ani": 92.7869, "matched_fragments": 2507, "total_fragments": 3270, "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_002234405.1", "gtdb_species": "s__Amycolatopsis thailandensis", "ani": 92.4491, "matched_fragments": 2336, "total_fragments": 3270, "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": 91.7288, "matched_fragments": 2269, "total_fragments": 3270, "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": 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1, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.304, "cell_length": 0.239, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 26.0, "optimum_ph": 7.391, "genome_size": 9811224.0, "gc_content": 68.7, "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": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 1.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Amycolatopsis", "alba", "DSM", "44262" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }