{ "type": "genome", "identifier": "GCF_000732925.1", "organism": "Amycolatopsis japonica", "title": "Amycolatopsis japonica", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Bielefeld University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000732925.1", "bioproject": "PRJNA224116", "biosample": "SAMN02836828", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "208439", "species_taxid": "208439", "organism_name": "Amycolatopsis japonica", "infraspecific_name": "strain=DSM 44213", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/07/24", "asm_name": "ASM73292v1", "asm_submitter": "Bielefeld University", "gbrs_paired_asm": "GCA_000732925.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/732/925/GCF_000732925.1_ASM73292v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "9053857", "genome_size_ungapped": "9053857", "gc_percent": "69.000000", "replicon_count": "2", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000732925.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "8607", "protein_coding_gene_count": "8475", "non_coding_gene_count": "71", "pubmed_id": "25193710" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-07-24", "dateModified": "2014-07-24", "datePublished": "2014-07-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Amycolatopsis japonica" ], "sample_taxid": [ "208439" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan" ], "sample_host_location_id": [], "data_size": "2.447 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)": "9053857", "Number of Sequences": "2", "Longest Sequences (bp)": "8961318", "N50 (bp)": "8961318", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.9", "Number of CDSs": "8658", "Average Protein Length": "319.1", "Coding Ratio (%)": "91.5", "Number of rRNAs": "12", "Number of tRNAs": "63", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Amycolatopsis japonica", "strain": "strain=MG417-CF17", "accession": "GCA_000732925.1", "taxid": 208439, "species_taxid": 208439, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 3016, "total_fragments": 3017, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Amycolatopsis keratiniphila subsp. keratiniphila", "strain": "strain=DSM 44409", "accession": "GCA_001620365.2", "taxid": 227715, "species_taxid": 129921, "relation_to_type": "type", "validated": true, "ani": 95.0074, "matched_fragments": 2558, "total_fragments": 3017, "ani_threshold": 95, "status": "inconclusive" }, { "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": 94.9623, "matched_fragments": 2625, "total_fragments": 3017, "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": 92.4732, "matched_fragments": 2481, "total_fragments": 3017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis lurida", "strain": "strain=DSM 43134", "accession": "GCA_900105055.1", "taxid": 31959, "species_taxid": 31959, "relation_to_type": "type", "validated": true, "ani": 92.2187, "matched_fragments": 2455, "total_fragments": 3017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis azurea", "strain": "strain=DSM 43854", "accession": "GCA_001995215.1", "taxid": 36819, "species_taxid": 36819, "relation_to_type": "type", "validated": true, "ani": 91.3428, "matched_fragments": 2427, "total_fragments": 3017, "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": 91.3371, "matched_fragments": 2392, "total_fragments": 3017, "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": 91.0772, "matched_fragments": 2195, "total_fragments": 3017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis alba", "strain": "strain=DSM 44262", "accession": "GCA_002234385.1", "taxid": 76020, "species_taxid": 76020, "relation_to_type": "type", "validated": true, "ani": 90.9835, "matched_fragments": 2214, "total_fragments": 3017, "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": 90.8503, "matched_fragments": 2428, "total_fragments": 3017, "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": 81.6938, "matched_fragments": 1700, "total_fragments": 3017, "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": 79.8998, "matched_fragments": 1135, "total_fragments": 3017, "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": 79.02, "matched_fragments": 1043, "total_fragments": 3017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis aidingensis", "strain": "strain=YIM 96748", "accession": "GCA_018885265.1", "taxid": 2842453, 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"96.67", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.88", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_001620365.2", "gtdb_species": "s__Amycolatopsis keratiniphila", "ani": 94.9913, "matched_fragments": 2560, "total_fragments": 3017, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.78", "min_intra_species_ani": "96.67", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.86", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000342005.1", "gtdb_species": "s__Amycolatopsis decaplanina", "ani": 92.7011, "matched_fragments": 2294, "total_fragments": 3017, "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": 92.4735, "matched_fragments": 2479, "total_fragments": 3017, "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_900105055.1", "gtdb_species": "s__Amycolatopsis lurida", "ani": 92.2006, "matched_fragments": 2458, "total_fragments": 3017, "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": "-" }, { "accession": "GCF_014654365.1", "gtdb_species": "s__Amycolatopsis oliviviridis", "ani": 91.3841, "matched_fragments": 2448, "total_fragments": 3017, "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": 91.356, "matched_fragments": 2425, "total_fragments": 3017, "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_002234405.1", "gtdb_species": "s__Amycolatopsis thailandensis", "ani": 91.0914, "matched_fragments": 2193, "total_fragments": 3017, "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_000384215.1", "gtdb_species": "s__Amycolatopsis alba", "ani": 90.9978, "matched_fragments": 2388, "total_fragments": 3017, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.304, "cell_length": 0.239, "doubling_h": null, "growth_tmp": 28.5, "optimum_tmp": 28.0, "optimum_ph": 7.391, "genome_size": 9053857.6, "gc_content": 68.672, "coding_genes": 8358.0, "rRNA16S_genes": 4.0, "tRNA_genes": 54.0, "gram_stain": 1.0, "sporulation": 0.0, "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", "japonica" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }