{ "type": "genome", "identifier": "GCF_014174495.1", "organism": "Amycolatopsis echigonensis", "title": "Amycolatopsis echigonensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Chulalonkorn University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014174495.1", "bioproject": "PRJNA224116", "biosample": "SAMN15742856", "wgs_master": "JACJHR000000000.1", "refseq_category": "na", "taxid": "369930", "species_taxid": "369930", "organism_name": "Amycolatopsis echigonensis", "infraspecific_name": "strain=JCM 21831", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/08/13", "asm_name": "ASM1417449v1", "asm_submitter": "Chulalonkorn University", "gbrs_paired_asm": "GCA_014174495.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/174/495/GCF_014174495.1_ASM1417449v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "9663932", "genome_size_ungapped": "9663932", "gc_percent": "69.500000", "replicon_count": "0", "scaffold_count": "302", "contig_count": "302", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014174495.1-RS_2024_09_29", "annotation_date": "2024-09-29", "total_gene_count": "9466", "protein_coding_gene_count": "9219", "non_coding_gene_count": "65", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-08-13", "dateModified": "2020-08-13", "datePublished": "2020-08-13", "_annotation": { "sample_count": 1, "sample_organism": [ "Amycolatopsis echigonensis" ], "sample_taxid": [ "369930" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan: Niigata" ], "sample_host_location_id": [], "data_size": "2.628 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.38, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "9663932", "Number of Sequences": "302", "Longest Sequences (bp)": "308460", "N50 (bp)": "92691", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "69.5", "Number of CDSs": "9297", "Average Protein Length": "303.5", "Coding Ratio (%)": "87.6", "Number of rRNAs": "0", "Number of tRNAs": "76", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Amycolatopsis nivea", "strain": "strain=CFH S0261", "accession": "GCA_004522235.1", "taxid": 1644109, "species_taxid": 1644109, "relation_to_type": "type", "validated": true, "ani": 92.3142, "matched_fragments": 2246, "total_fragments": 3084, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis dendrobii", "strain": "strain=DR6-1", "accession": "GCA_014145675.1", "taxid": 2760662, "species_taxid": 2760662, "relation_to_type": "type", "validated": true, "ani": 92.2798, "matched_fragments": 2304, "total_fragments": 3084, "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": 91.8459, "matched_fragments": 2210, "total_fragments": 3084, "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": 91.8109, "matched_fragments": 2150, "total_fragments": 3084, "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": 86.8828, "matched_fragments": 2012, "total_fragments": 3084, "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": 83.1185, "matched_fragments": 1362, "total_fragments": 3084, "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": 82.9921, "matched_fragments": 1329, "total_fragments": 3084, "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": 81.4361, "matched_fragments": 1558, "total_fragments": 3084, "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": 79.9161, "matched_fragments": 1155, "total_fragments": 3084, "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": 79.0277, "matched_fragments": 965, "total_fragments": 3084, "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": 78.076, "matched_fragments": 783, "total_fragments": 3084, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lentzea aerocolonigenes", "strain": "strain=DSM 40034", "accession": "GCA_024171805.1", "taxid": 68170, "species_taxid": 68170, "relation_to_type": "type", "validated": true, "ani": 77.7599, "matched_fragments": 866, "total_fragments": 3084, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.38, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014174495.1", "gtdb_species": "s__Amycolatopsis echigonensis", "ani": 100.0, "matched_fragments": 3074, "total_fragments": 3084, "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": "conclusive" }, { "accession": "GCF_000411975.1", "gtdb_species": "s__Amycolatopsis orientalis_D", "ani": 92.5791, "matched_fragments": 2345, "total_fragments": 3084, "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_004522235.1", "gtdb_species": "s__Amycolatopsis nivea", "ani": 92.338, "matched_fragments": 2243, "total_fragments": 3084, "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_014145675.1", "gtdb_species": "s__Amycolatopsis sp014145675", "ani": 92.2591, "matched_fragments": 2307, "total_fragments": 3084, "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_002796545.1", "gtdb_species": "s__Amycolatopsis sp002796545", "ani": 92.2588, "matched_fragments": 2231, "total_fragments": 3084, "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_900115345.1", "gtdb_species": "s__Amycolatopsis rubida", "ani": 91.8702, "matched_fragments": 2207, "total_fragments": 3084, "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_003385235.1", "gtdb_species": "s__Amycolatopsis circi", "ani": 91.817, "matched_fragments": 2148, "total_fragments": 3084, "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": 29.0, "optimum_tmp": 30.0, "optimum_ph": 9.0, "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": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "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", "echigonensis" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }