{ "type": "genome", "identifier": "GCF_014145675.1", "organism": "Amycolatopsis dendrobii", "title": "Amycolatopsis dendrobii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Chulalonkorn University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014145675.1", "bioproject": "PRJNA224116", "biosample": "SAMN15719521", "wgs_master": "JACGZW000000000.1", "refseq_category": "reference genome", "taxid": "2760662", "species_taxid": "2760662", "organism_name": "Amycolatopsis dendrobii", "infraspecific_name": "strain=DR6-1", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/08/10", "asm_name": "ASM1414567v1", "asm_submitter": "Chulalonkorn University", "gbrs_paired_asm": "GCA_014145675.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/145/675/GCF_014145675.1_ASM1414567v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "9690793", "genome_size_ungapped": "9690793", "gc_percent": "69.500000", "replicon_count": "0", "scaffold_count": "59", "contig_count": "59", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014145675.1-RS_2024_09_29", "annotation_date": "2024-09-29", "total_gene_count": "9069", "protein_coding_gene_count": "8943", "non_coding_gene_count": "65", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-08-10", "dateModified": "2020-08-10", "datePublished": "2020-08-10", "_annotation": { "sample_count": 1, "sample_organism": [ "Amycolatopsis dendrobii" ], "sample_taxid": [ "2760662" ], "sample_host_organism": [ "Dendrobium heterocarpum" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Thailand: Ubon Ratchathani" ], "sample_host_location_id": [], "data_size": "2.618 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 8.33, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "9690793", "Number of Sequences": "59", "Longest Sequences (bp)": "882917", "N50 (bp)": "530751", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "69.6", "Number of CDSs": "9116", "Average Protein Length": "318.6", "Coding Ratio (%)": "89.9", "Number of rRNAs": "2", "Number of tRNAs": "94", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Amycolatopsis dendrobii", "strain": "strain=DR6-1", "accession": "GCA_014145675.1", "taxid": 2760662, "species_taxid": 2760662, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 3201, "total_fragments": 3203, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Amycolatopsis nivea", "strain": "strain=CFH S0261", "accession": "GCA_004522235.1", "taxid": 1644109, "species_taxid": 1644109, "relation_to_type": "type", "validated": true, "ani": 93.8385, "matched_fragments": 2668, "total_fragments": 3203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis rubida", "strain": "strain=DSM 44637", "accession": "GCA_900115345.1", "taxid": 112413, "species_taxid": 112413, "relation_to_type": "type", "validated": true, "ani": 93.6888, "matched_fragments": 2511, "total_fragments": 3203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis circi", "strain": "strain=DSM 45561", "accession": "GCA_003385235.1", "taxid": 871959, "species_taxid": 871959, "relation_to_type": "type", "validated": true, "ani": 92.1772, "matched_fragments": 2488, "total_fragments": 3203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis benzoatilytica", "strain": "strain=AK 16/65", "accession": "GCA_000383915.1", "taxid": 346045, "species_taxid": 346045, "relation_to_type": "type", "validated": true, "ani": 86.6742, "matched_fragments": 2034, "total_fragments": 3203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis sulphurea", "strain": "strain=DSM 46092", "accession": "GCA_002564045.1", "taxid": 76022, "species_taxid": 76022, "relation_to_type": "type", "validated": true, "ani": 83.0678, "matched_fragments": 1403, "total_fragments": 3203, "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": 83.0037, "matched_fragments": 1383, "total_fragments": 3203, "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": 81.4738, "matched_fragments": 1665, "total_fragments": 3203, "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": 79.8014, "matched_fragments": 1165, "total_fragments": 3203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis acidiphila", "strain": "strain=KCTC 39523", "accession": "GCA_021391495.1", "taxid": 715473, "species_taxid": 715473, "relation_to_type": "type", "validated": true, "ani": 79.4293, "matched_fragments": 1162, "total_fragments": 3203, "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": 78.9305, "matched_fragments": 983, "total_fragments": 3203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinokineospora diospyrosa", "strain": "strain=DSM 44255", "accession": "GCA_024171925.1", "taxid": 103728, "species_taxid": 103728, "relation_to_type": "type", "validated": true, "ani": 77.8236, "matched_fragments": 822, "total_fragments": 3203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kibdelosporangium philippinense", "strain": "strain=ATCC 49844", "accession": "GCA_021390435.3", "taxid": 211113, "species_taxid": 211113, "relation_to_type": "type", "validated": true, "ani": 77.4411, "matched_fragments": 776, "total_fragments": 3203, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 8.33, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014145675.1", "gtdb_species": "s__Amycolatopsis sp014145675", "ani": 100.0, "matched_fragments": 3201, "total_fragments": 3203, "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_004522235.1", "gtdb_species": "s__Amycolatopsis nivea", "ani": 93.8378, "matched_fragments": 2667, "total_fragments": 3203, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.97", "min_intra_species_ani": "97.28", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_900115345.1", "gtdb_species": "s__Amycolatopsis rubida", "ani": 93.6796, "matched_fragments": 2512, "total_fragments": 3203, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.28", "min_intra_species_ani": "99.27", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.87", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_002796545.1", "gtdb_species": "s__Amycolatopsis sp002796545", "ani": 92.7284, "matched_fragments": 2494, "total_fragments": 3203, "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_014174495.1", "gtdb_species": "s__Amycolatopsis echigonensis", "ani": 92.2377, "matched_fragments": 2318, "total_fragments": 3203, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.67", "min_intra_species_ani": "98.67", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003385235.1", "gtdb_species": "s__Amycolatopsis circi", "ani": 92.1775, "matched_fragments": 2486, "total_fragments": 3203, "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_000411975.1", "gtdb_species": "s__Amycolatopsis orientalis_D", "ani": 92.1661, "matched_fragments": 2350, "total_fragments": 3203, "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_000383915.1", "gtdb_species": "s__Amycolatopsis benzoatilytica", "ani": 86.6433, "matched_fragments": 2039, "total_fragments": 3203, "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": 85.2537, "matched_fragments": 1874, "total_fragments": 3203, "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_002564045.1", "gtdb_species": "s__Amycolatopsis sulphurea", "ani": 83.0906, "matched_fragments": 1399, "total_fragments": 3203, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.19", "min_intra_species_ani": "95.19", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.83", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_016889705.1", "gtdb_species": "s__Amycolatopsis sp016889705", "ani": 82.4097, "matched_fragments": 1608, "total_fragments": 3203, "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_014647915.1", "gtdb_species": "s__Pilimelia terevasa", "ani": 76.01, "matched_fragments": 456, "total_fragments": 3203, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Pilimelia", "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", "dendrobii" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }