{ "type": "genome", "identifier": "GCF_000384315.1", "organism": "Amycolatopsis nigrescens CSC17Ta-90", "title": "Amycolatopsis nigrescens CSC17Ta-90", "description": "na", "data type": "Genome sequencing and assembly", "organization": "JGI", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000384315.1", "bioproject": "PRJNA224116", "biosample": "SAMN02261308", "wgs_master": "ARVW00000000.1", "refseq_category": "reference genome", "taxid": "1068980", "species_taxid": "381445", "organism_name": "Amycolatopsis nigrescens CSC17Ta-90", "infraspecific_name": "strain=CSC17Ta-90", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/04/26", "asm_name": "ASM38431v1", "asm_submitter": "JGI", "gbrs_paired_asm": "GCA_000384315.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/384/315/GCF_000384315.1_ASM38431v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "9111009", "genome_size_ungapped": "9111009", "gc_percent": "70.000000", "replicon_count": "0", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000384315.1-RS_2024_05_02", "annotation_date": "2024-05-02", "total_gene_count": "8635", "protein_coding_gene_count": "8521", "non_coding_gene_count": "60", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-04-26", "dateModified": "2013-04-26", "datePublished": "2013-04-26", "_annotation": { "sample_count": 1, "sample_organism": [ "Amycolatopsis nigrescens CSC17Ta-90" ], "sample_taxid": [ "1068980" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [ "None" ], "sample_host_disease_id": [], "sample_host_location": [ "Italy" ], "sample_host_location_id": [], "data_size": "2.448 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "9111009", "Number of Sequences": "1", "Longest Sequences (bp)": "9111009", "N50 (bp)": "9111009", "Gap Ratio (%)": "0.000022", "GCcontent (%)": "70.0", "Number of CDSs": "8728", "Average Protein Length": "318.9", "Coding Ratio (%)": "91.7", "Number of rRNAs": "9", "Number of tRNAs": "64", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Amycolatopsis nigrescens", "strain": "strain=CSC17Ta-90", "accession": "GCA_000384315.1", "taxid": 381445, "species_taxid": 381445, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 3037, "total_fragments": 3037, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Amycolatopsis anabasis", "strain": "strain=EGI 650086", "accession": "GCA_009765355.1", "taxid": 1840409, "species_taxid": 1840409, "relation_to_type": "type", "validated": true, "ani": 82.028, "matched_fragments": 1744, "total_fragments": 3037, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis albispora", "strain": "strain=WP1", "accession": "GCA_003312875.1", "taxid": 1804986, "species_taxid": 1804986, "relation_to_type": "type", "validated": true, "ani": 81.2063, "matched_fragments": 1538, "total_fragments": 3037, "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": 80.7371, "matched_fragments": 1349, "total_fragments": 3037, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis arida", "strain": "strain=DSM 45648", "accession": "GCA_004365925.1", "taxid": 587909, "species_taxid": 587909, "relation_to_type": "type", "validated": true, "ani": 80.7297, "matched_fragments": 1196, "total_fragments": 3037, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis arida", "strain": "strain=CGMCC 4.5579", "accession": "GCA_900115565.1", "taxid": 587909, "species_taxid": 587909, "relation_to_type": "type", "validated": true, "ani": 80.7257, "matched_fragments": 1194, "total_fragments": 3037, "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": 80.5007, "matched_fragments": 1257, "total_fragments": 3037, "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": 80.3196, "matched_fragments": 1228, "total_fragments": 3037, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis viridis", "strain": "strain=DSM 45668", "accession": "GCA_011758765.1", "taxid": 185678, "species_taxid": 185678, "relation_to_type": "type", "validated": true, "ani": 80.2906, "matched_fragments": 1084, "total_fragments": 3037, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis methanolica", "strain": "strain=239", "accession": "GCA_000739085.1", "taxid": 1814, "species_taxid": 1814, "relation_to_type": "type", "validated": true, "ani": 80.2629, "matched_fragments": 1216, "total_fragments": 3037, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis rhizosphaerae", "strain": "strain=TBRC 6029", "accession": "GCA_007713715.1", "taxid": 2053003, "species_taxid": 2053003, "relation_to_type": "type", "validated": true, "ani": 80.2157, "matched_fragments": 944, "total_fragments": 3037, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis thermoflava", "strain": "strain=N1165", "accession": "GCA_000473265.1", "taxid": 84480, "species_taxid": 84480, "relation_to_type": "type", "validated": true, "ani": 80.1472, "matched_fragments": 1304, "total_fragments": 3037, "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": 80.089, "matched_fragments": 1363, "total_fragments": 3037, "ani_threshold": 95, "status": "below_threshold" }, { "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": 80.0329, "matched_fragments": 1378, "total_fragments": 3037, "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": 79.9979, "matched_fragments": 1371, "total_fragments": 3037, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis acidicola", "strain": "strain=K81G1", "accession": "GCA_007713735.2", "taxid": 2596893, "species_taxid": 2596893, "relation_to_type": "type", "validated": true, "ani": 79.9817, "matched_fragments": 1202, "total_fragments": 3037, "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": 79.9603, "matched_fragments": 1366, "total_fragments": 3037, "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": 79.8028, "matched_fragments": 1300, "total_fragments": 3037, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis australiensis", "strain": "strain=DSM 44671", "accession": "GCA_900119165.1", "taxid": 546364, "species_taxid": 546364, "relation_to_type": "type", "validated": true, "ani": 79.7777, "matched_fragments": 1408, "total_fragments": 3037, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis vastitatis", "strain": "strain=H5", "accession": "GCA_002234595.1", "taxid": 1905142, "species_taxid": 1905142, "relation_to_type": "type", "validated": 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