{ "type": "genome", "identifier": "GCF_002234405.1", "organism": "Amycolatopsis thailandensis", "title": "Amycolatopsis thailandensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Institute of Microbial Technology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002234405.1", "bioproject": "PRJNA224116", "biosample": "SAMN07313357", "wgs_master": "NMQT00000000.1", "refseq_category": "na", "taxid": "589330", "species_taxid": "589330", "organism_name": "Amycolatopsis thailandensis", "infraspecific_name": "strain=JCM 16380", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/07/27", "asm_name": "ASM223440v1", "asm_submitter": "Institute of Microbial Technology", "gbrs_paired_asm": "GCA_002234405.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/234/405/GCF_002234405.1_ASM223440v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "9348263", "genome_size_ungapped": "9348263", "gc_percent": "69.000000", "replicon_count": "0", "scaffold_count": "421", "contig_count": "421", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002234405.1-RS_2024_04_22", "annotation_date": "2024-04-22", "total_gene_count": "8733", "protein_coding_gene_count": "8455", "non_coding_gene_count": "74", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-07-27", "dateModified": "2017-07-27", "datePublished": "2017-07-27", "_annotation": { "sample_count": 1, "sample_organism": [ "Amycolatopsis thailandensis" ], "sample_taxid": [ "589330" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Thailand" ], "sample_host_location_id": [], "data_size": "2.554 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 85.42, "contamination": 2.78, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "9348263", "Number of Sequences": "421", "Longest Sequences (bp)": "199375", "N50 (bp)": "71736", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.8", "Number of CDSs": "8456", "Average Protein Length": "319.7", "Coding Ratio (%)": "86.7", "Number of rRNAs": "4", "Number of tRNAs": "78", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Amycolatopsis thailandensis", "strain": "strain=JCM 16380", "accession": "GCA_002234405.1", "taxid": 589330, "species_taxid": 589330, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2944, "total_fragments": 2953, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Amycolatopsis azurea", "strain": "strain=DSM 43854", "accession": "GCA_000340415.1", "taxid": 36819, "species_taxid": 36819, "relation_to_type": "type", "validated": true, "ani": 93.6058, "matched_fragments": 2309, "total_fragments": 2953, "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": 93.5235, "matched_fragments": 2352, "total_fragments": 2953, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis alba", "strain": "strain=DSM 44262", "accession": "GCA_000384215.1", "taxid": 76020, "species_taxid": 76020, "relation_to_type": "type", "validated": true, "ani": 92.4511, "matched_fragments": 2335, "total_fragments": 2953, "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": 92.3756, "matched_fragments": 2208, "total_fragments": 2953, "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": 91.3789, "matched_fragments": 2312, "total_fragments": 2953, "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": 91.128, "matched_fragments": 2198, "total_fragments": 2953, "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": 90.9436, "matched_fragments": 2162, "total_fragments": 2953, "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": 90.0769, "matched_fragments": 2155, "total_fragments": 2953, "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": 89.6464, "matched_fragments": 2054, "total_fragments": 2953, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis regifaucium", "strain": "strain=GY080", "accession": "GCA_001558125.2", "taxid": 546365, "species_taxid": 546365, "relation_to_type": "type", "validated": true, "ani": 89.6216, "matched_fragments": 2049, "total_fragments": 2953, "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": 81.4706, "matched_fragments": 1570, "total_fragments": 2953, "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": 79.878, "matched_fragments": 1044, "total_fragments": 2953, "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": 79.0343, "matched_fragments": 949, "total_fragments": 2953, "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": 78.5761, "matched_fragments": 978, "total_fragments": 2953, "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": 78.0176, "matched_fragments": 769, "total_fragments": 2953, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 85.42, "contamination": 2.78, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002234405.1", "gtdb_species": "s__Amycolatopsis thailandensis", "ani": 100.0, "matched_fragments": 2944, "total_fragments": 2953, "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_001995215.1", "gtdb_species": "s__Amycolatopsis azurea", "ani": 93.5506, "matched_fragments": 2348, "total_fragments": 2953, "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": 93.3684, "matched_fragments": 2423, "total_fragments": 2953, "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": 92.4589, "matched_fragments": 2334, "total_fragments": 2953, "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_000342005.1", "gtdb_species": "s__Amycolatopsis decaplanina", "ani": 91.6088, "matched_fragments": 2118, "total_fragments": 2953, "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_014205155.1", "gtdb_species": "s__Amycolatopsis umgeniensis", "ani": 91.3361, "matched_fragments": 2318, "total_fragments": 2953, "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_000732925.1", "gtdb_species": "s__Amycolatopsis japonica", "ani": 91.1433, "matched_fragments": 2196, "total_fragments": 2953, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.30", "min_intra_species_ani": "96.67", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.88", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_002849735.1", "gtdb_species": "s__Amycolatopsis sp002849735", "ani": 91.0952, "matched_fragments": 2286, "total_fragments": 2953, "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": 91.0682, 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"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", "thailandensis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }