{ "type": "genome", "identifier": "GCF_900478415.1", "organism": "Staphylococcus auricularis", "title": "Staphylococcus auricularis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "SC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900478415.1", "bioproject": "PRJNA224116", "biosample": "SAMEA3233547", "wgs_master": "na", "refseq_category": "na", "taxid": "29379", "species_taxid": "29379", "organism_name": "Staphylococcus auricularis", "infraspecific_name": "strain=NCTC12101", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/06/18", "asm_name": "35910_E02", "asm_submitter": "SC", "gbrs_paired_asm": "GCA_900478415.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/478/415/GCF_900478415.1_35910_E02", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2216666", "genome_size_ungapped": "2216666", "gc_percent": "37.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900478415.1-RS_2024_04_05", "annotation_date": "2024-04-05", "total_gene_count": "2141", "protein_coding_gene_count": "1971", "non_coding_gene_count": "79", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-06-18", "dateModified": "2018-06-18", "datePublished": "2018-06-18", "_annotation": { "sample_count": 1, "sample_organism": [ "Staphylococcus auricularis" ], "sample_taxid": [ "29379" ], "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": [], "sample_host_location_id": [], "data_size": "0.625 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)": "2216666", "Number of Sequences": "1", "Longest Sequences (bp)": "2216666", "N50 (bp)": "2216666", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "37.4", "Number of CDSs": "2146", "Average Protein Length": "290.6", "Coding Ratio (%)": "84.4", "Number of rRNAs": "16", "Number of tRNAs": "60", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Staphylococcus auricularis", "strain": "strain=NCTC12101", "accession": "GCA_900478415.1", "taxid": 29379, "species_taxid": 29379, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 737, "total_fragments": 738, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Staphylococcus auricularis", "strain": "strain=FDAARGOS_882", "accession": "GCA_016028295.1", "taxid": 29379, "species_taxid": 29379, "relation_to_type": "type", "validated": true, "ani": 99.9955, "matched_fragments": 737, "total_fragments": 738, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Staphylococcus auricularis", "strain": "strain=DSM 20609", "accession": "GCA_001500315.1", "taxid": 29379, "species_taxid": 29379, "relation_to_type": "type", "validated": true, "ani": 99.9569, "matched_fragments": 719, "total_fragments": 738, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Staphylococcus auricularis", "strain": "strain=NCTC 12101", "accession": "GCA_002902455.1", "taxid": 29379, "species_taxid": 29379, "relation_to_type": "type", "validated": true, "ani": 99.9151, "matched_fragments": 684, "total_fragments": 738, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Staphylococcus capitis subsp. capitis", "strain": "strain=DSM 20326", "accession": "GCA_025272975.1", "taxid": 72758, "species_taxid": 29388, "relation_to_type": "type", "validated": true, "ani": 79.0791, "matched_fragments": 200, "total_fragments": 738, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus saprophyticus", "strain": "strain=NCTC7292", "accession": "GCA_900458885.1", "taxid": 29385, "species_taxid": 29385, "relation_to_type": "type", "validated": true, "ani": 78.9827, "matched_fragments": 238, "total_fragments": 738, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus aureus", "strain": "strain=PartF-Saureus-RM8376", "accession": "GCA_022869625.1", "taxid": 1280, "species_taxid": 1280, "relation_to_type": "type", "validated": true, "ani": 78.93, "matched_fragments": 193, "total_fragments": 738, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus taiwanensis", "strain": "strain=NTUH-S172", "accession": "GCA_020544305.1", "taxid": 2750012, "species_taxid": 2750012, "relation_to_type": "type", "validated": true, "ani": 78.8063, "matched_fragments": 196, "total_fragments": 738, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus pasteuri", "strain": "strain=DSM 10656", "accession": "GCA_003970495.1", "taxid": 45972, "species_taxid": 45972, "relation_to_type": "type", "validated": true, "ani": 78.7856, "matched_fragments": 188, "total_fragments": 738, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus warneri", "strain": "strain=NCTC 11044", "accession": "GCA_002901765.1", "taxid": 1292, "species_taxid": 1292, "relation_to_type": "type", "validated": true, "ani": 78.4928, "matched_fragments": 198, "total_fragments": 738, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus schleiferi", "strain": "strain=NCTC12218", "accession": "GCA_900458895.2", "taxid": 1295, "species_taxid": 1295, "relation_to_type": "type", "validated": true, "ani": 78.4464, "matched_fragments": 138, "total_fragments": 738, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus croceilyticus", "strain": "strain=CCUG 62728", "accession": "GCA_002902575.1", "taxid": 319942, "species_taxid": 319942, "relation_to_type": "type", "validated": true, "ani": 78.4087, "matched_fragments": 220, "total_fragments": 738, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus haemolyticus", "strain": "strain=NCTC 11042", "accession": "GCA_002901805.1", "taxid": 1283, "species_taxid": 1283, "relation_to_type": "type", "validated": true, "ani": 78.25, "matched_fragments": 198, "total_fragments": 738, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus aureus", "strain": "strain=NCTC 08532", "accession": "GCA_002902205.1", "taxid": 1280, "species_taxid": 1280, "relation_to_type": "type", "validated": true, "ani": 78.1361, "matched_fragments": 188, "total_fragments": 738, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001500315.1", "gtdb_species": "s__Staphylococcus auricularis", "ani": 99.9569, "matched_fragments": 719, "total_fragments": 738, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.97", "min_intra_species_ani": "95.76", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.93", "num_clustered_genomes": 10, "status": "conclusive" }, { "accession": "GCF_001027105.1", "gtdb_species": "s__Staphylococcus aureus", "ani": 79.1252, "matched_fragments": 190, "total_fragments": 738, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.78", "min_intra_species_ani": "97.08", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.88", "num_clustered_genomes": 13059, "status": "-" }, { "accession": "GCF_900636385.1", "gtdb_species": "s__Staphylococcus warneri", "ani": 79.0925, "matched_fragments": 203, "total_fragments": 738, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.98", "min_intra_species_ani": "95.90", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.90", "num_clustered_genomes": 73, "status": "-" }, { "accession": "GCF_006094395.1", "gtdb_species": "s__Staphylococcus haemolyticus", "ani": 79.0064, "matched_fragments": 211, "total_fragments": 738, "gtdb_taxonomy": 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"d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus", "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_900458435.1", "gtdb_species": "s__Staphylococcus carnosus", "ani": 78.6913, "matched_fragments": 194, "total_fragments": 738, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.71", "min_intra_species_ani": "99.56", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.93", "num_clustered_genomes": 12, "status": "-" }, { "accession": "GCF_001224225.1", "gtdb_species": "s__Staphylococcus borealis", "ani": 78.6522, "matched_fragments": 200, "total_fragments": 738, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.37", "min_intra_species_ani": "97.44", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 22, "status": "-" }, { "accession": "GCF_003035445.1", "gtdb_species": "s__Staphylococcus devriesei_A", "ani": 78.5347, "matched_fragments": 213, "total_fragments": 738, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.92", "min_intra_species_ani": "97.92", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002902565.1", "gtdb_species": "s__Staphylococcus petrasii", "ani": 78.4716, "matched_fragments": 223, "total_fragments": 738, "gtdb_taxonomy": 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37.4, "coding_genes": 1951.0, "rRNA16S_genes": 5.698, "tRNA_genes": 58.0, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 0.666, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.029, "coccus_cell_shape": 0.97, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Staphylococcus", "auricularis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }