{ "type": "genome", "identifier": "GCF_900458605.1", "organism": "Staphylococcus epidermidis", "title": "Staphylococcus epidermidis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "SC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900458605.1", "bioproject": "PRJNA224116", "biosample": "SAMEA3233545", "wgs_master": "UHDF00000000.1", "refseq_category": "na", "taxid": "1282", "species_taxid": "1282", "organism_name": "Staphylococcus epidermidis", "infraspecific_name": "strain=NCTC11047", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/08/01", "asm_name": "35910_G02", "asm_submitter": "SC", "gbrs_paired_asm": "GCA_900458605.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/458/605/GCF_900458605.1_35910_G02", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2538008", "genome_size_ungapped": "2538008", "gc_percent": "32.000000", "replicon_count": "0", "scaffold_count": "5", "contig_count": "5", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900458605.1-RS_2024_08_15", "annotation_date": "2024-08-15", "total_gene_count": "2423", "protein_coding_gene_count": "2202", "non_coding_gene_count": "84", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-08-01", "dateModified": "2018-08-01", "datePublished": "2018-08-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Staphylococcus epidermidis" ], "sample_taxid": [ "1282" ], "sample_host_organism": [ "not available" ], "sample_host_organism_id": [], "sample_host_disease": [ "not available: to be reported later" ], "sample_host_disease_id": [], "sample_host_location": [ "Czechoslovakia" ], "sample_host_location_id": [], "data_size": "0.702 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)": "2538008", "Number of Sequences": "5", "Longest Sequences (bp)": "2477430", "N50 (bp)": "2477430", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "32.2", "Number of CDSs": "2417", "Average Protein Length": "289.8", "Coding Ratio (%)": "82.8", "Number of rRNAs": "19", "Number of tRNAs": "60", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Staphylococcus epidermidis", "strain": "strain=NCTC11047", "accession": "GCA_900458605.1", "taxid": 1282, "species_taxid": 1282, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 841, "total_fragments": 843, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Staphylococcus epidermidis", "strain": "strain=NBRC 100911", "accession": "GCA_006742205.1", "taxid": 1282, "species_taxid": 1282, "relation_to_type": "type", "validated": true, "ani": 99.9963, "matched_fragments": 805, "total_fragments": 843, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Staphylococcus epidermidis", "strain": "strain=ATCC 14990", "accession": "GCA_006094375.1", "taxid": 1282, "species_taxid": 1282, "relation_to_type": "type", "validated": true, "ani": 99.9943, "matched_fragments": 824, "total_fragments": 843, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Staphylococcus epidermidis", "strain": "strain=ATCC 14990", "accession": "GCA_002087975.1", "taxid": 1282, "species_taxid": 1282, "relation_to_type": "type", "validated": true, "ani": 99.9664, "matched_fragments": 798, "total_fragments": 843, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Staphylococcus 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"accession": "GCA_002902205.1", "taxid": 1280, "species_taxid": 1280, "relation_to_type": "type", "validated": true, "ani": 78.8418, "matched_fragments": 313, "total_fragments": 843, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_006742205.1", "gtdb_species": "s__Staphylococcus epidermidis", "ani": 99.9964, "matched_fragments": 805, "total_fragments": 843, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.01", "min_intra_species_ani": "96.59", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.83", "num_clustered_genomes": 1079, "status": "conclusive" }, { "accession": "GCF_900458815.1", "gtdb_species": "s__Staphylococcus saccharolyticus", "ani": 81.6471, "matched_fragments": 533, "total_fragments": 843, 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