{ "type": "genome", "identifier": "GCF_001620365.2", "organism": "Amycolatopsis keratiniphila subsp. keratiniphila", "title": "Amycolatopsis keratiniphila subsp. keratiniphila", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Institute of Microbial Technology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001620365.2", "bioproject": "PRJNA224116", "biosample": "SAMN04384022", "wgs_master": "LQMT00000000.2", "refseq_category": "na", "taxid": "227715", "species_taxid": "129921", "organism_name": "Amycolatopsis keratiniphila subsp. keratiniphila", "infraspecific_name": "strain=DSM 44409", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/02/01", "asm_name": "ASM162036v2", "asm_submitter": "Institute of Microbial Technology", "gbrs_paired_asm": "GCA_001620365.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/620/365/GCF_001620365.2_ASM162036v2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "9091838", "genome_size_ungapped": "9081535", "gc_percent": "69.000000", "replicon_count": "0", "scaffold_count": "72", "contig_count": "72", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001620365.2-RS_2024_10_22", "annotation_date": "2024-10-22", "total_gene_count": "8561", "protein_coding_gene_count": "8401", "non_coding_gene_count": "55", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-02-01", "dateModified": "2017-02-01", "datePublished": "2017-02-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Amycolatopsis keratiniphila subsp. keratiniphila" ], "sample_taxid": [ "227715" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Kuwait: Omariya Agricultural Station" ], "sample_host_location_id": [], "data_size": "2.463 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 3.82, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "9091838", "Number of Sequences": "72", "Longest Sequences (bp)": "592765", "N50 (bp)": "313356", "Gap Ratio (%)": "0.115334", "GCcontent (%)": "69.0", "Number of CDSs": "8522", "Average Protein Length": "323.3", "Coding Ratio (%)": "90.9", "Number of rRNAs": "2", "Number of tRNAs": "63", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Amycolatopsis keratiniphila subsp. keratiniphila", "strain": "strain=DSM 44409", 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"matched_fragments": 1652, "total_fragments": 2996, "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": 79.9573, "matched_fragments": 1123, "total_fragments": 2996, "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": 79.1257, "matched_fragments": 1027, "total_fragments": 2996, "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": 78.7036, "matched_fragments": 1039, "total_fragments": 2996, "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": 78.1022, "matched_fragments": 811, "total_fragments": 2996, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 3.82, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001620365.2", "gtdb_species": "s__Amycolatopsis keratiniphila", "ani": 100.0, "matched_fragments": 2992, "total_fragments": 2996, "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": "conclusive" }, { "accession": "GCF_000732925.1", "gtdb_species": "s__Amycolatopsis japonica", "ani": 94.9667, "matched_fragments": 2558, "total_fragments": 2996, "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_014873915.1", "gtdb_species": "s__Amycolatopsis roodepoortensis", "ani": 92.5039, "matched_fragments": 2463, "total_fragments": 2996, "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": "-" }, 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"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", "keratiniphila", "subsp.", "keratiniphila" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }