{ "type": "genome", "identifier": "GCF_000381885.1", "organism": "Actinomadura atramentaria DSM 43919", "title": "Actinomadura atramentaria DSM 43919", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000381885.1", "bioproject": "PRJNA224116", "biosample": "SAMN02441315", "wgs_master": "ARMS00000000.1", "refseq_category": "reference genome", "taxid": "1120936", "species_taxid": "1990", "organism_name": "Actinomadura atramentaria DSM 43919", "infraspecific_name": "strain=SF2197", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/04/24", "asm_name": "ASM38188v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000381885.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/381/885/GCF_000381885.1_ASM38188v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6710579", "genome_size_ungapped": "6709047", "gc_percent": "73.500000", "replicon_count": "0", "scaffold_count": "37", "contig_count": "44", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000381885.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "6345", "protein_coding_gene_count": "6233", "non_coding_gene_count": "75", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-04-24", "dateModified": "2013-04-24", "datePublished": "2013-04-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Actinomadura atramentaria DSM 43919" ], "sample_taxid": [ "1120936" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan" ], "sample_host_location_id": [], "data_size": "1.758 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "6710579", "Number of Sequences": "37", "Longest Sequences (bp)": "759081", "N50 (bp)": "422996", "Gap Ratio (%)": "0.022830", "GCcontent (%)": "73.7", "Number of CDSs": "6369", "Average Protein Length": "313.8", "Coding Ratio (%)": "89.3", "Number of rRNAs": "6", "Number of tRNAs": "94", "Number of CRISPRs": "15" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Actinomadura atramentaria", "strain": "strain=SF2197", "accession": "GCA_000381885.1", "taxid": 1990, "species_taxid": 1990, 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"total_fragments": 2217, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura violacea", "strain": "strain=LCR2-06", "accession": "GCA_017573465.1", "taxid": 2819934, "species_taxid": 2819934, "relation_to_type": "type", "validated": true, "ani": 81.5942, "matched_fragments": 1461, "total_fragments": 2217, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura mexicana", "strain": "strain=DSM 44485", "accession": "GCA_900188105.1", "taxid": 134959, "species_taxid": 134959, "relation_to_type": "type", "validated": true, "ani": 81.2335, "matched_fragments": 1286, "total_fragments": 2217, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura cremea", "strain": "strain=JCM 3308", "accession": "GCA_014648495.1", "taxid": 1991, "species_taxid": 1991, "relation_to_type": "type", "validated": true, "ani": 80.9835, "matched_fragments": 1338, "total_fragments": 2217, "ani_threshold": 95, "status": 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