{ "type": "genome", "identifier": "GCF_002902725.1", "organism": "Staphylococcus caprae", "title": "Staphylococcus caprae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Modernising Medical Microbiology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002902725.1", "bioproject": "PRJNA224116", "biosample": "SAMN05977978", "wgs_master": "PPRT00000000.1", "refseq_category": "na", "taxid": "29380", "species_taxid": "29380", "organism_name": "Staphylococcus caprae", "infraspecific_name": "strain=NCTC 12196", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/01/27", "asm_name": "ASM290272v1", "asm_submitter": "Modernising Medical Microbiology", "gbrs_paired_asm": "GCA_002902725.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/902/725/GCF_002902725.1_ASM290272v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2606761", "genome_size_ungapped": "2606700", "gc_percent": "33.500000", "replicon_count": "0", "scaffold_count": "101", "contig_count": "101", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002902725.1-RS_2024_09_03", "annotation_date": "2024-09-03", "total_gene_count": "2564", "protein_coding_gene_count": "2430", "non_coding_gene_count": "72", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-01-27", "dateModified": "2018-01-27", "datePublished": "2018-01-27", "_annotation": { "sample_count": 1, "sample_organism": [ "Staphylococcus caprae" ], "sample_taxid": [ "29380" ], "sample_host_organism": [ "Goat" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "United Kingdom: London" ], "sample_host_location_id": [], "data_size": "0.736 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)": "2606761", "Number of Sequences": "101", "Longest Sequences (bp)": "196830", "N50 (bp)": "70101", "Gap Ratio (%)": "0.002340", "GCcontent (%)": "33.5", "Number of CDSs": "2498", "Average Protein Length": "295.5", "Coding Ratio (%)": "85.0", "Number of rRNAs": "3", "Number of tRNAs": "58", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Staphylococcus caprae", "strain": "strain=NCTC 12196", "accession": "GCA_002902725.1", "taxid": 29380, "species_taxid": 29380, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 827, "total_fragments": 827, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Staphylococcus caprae", "strain": "strain=NCTC12196", "accession": "GCA_900458385.1", "taxid": 29380, "species_taxid": 29380, "relation_to_type": "type", "validated": true, "ani": 99.9914, "matched_fragments": 827, "total_fragments": 827, "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": 84.1993, "matched_fragments": 657, "total_fragments": 827, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus capitis subsp. capitis", "strain": "strain=NCTC 11045", "accession": "GCA_002902325.1", "taxid": 72758, "species_taxid": 29388, "relation_to_type": "type", "validated": true, "ani": 84.1948, "matched_fragments": 644, "total_fragments": 827, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus capitis", "strain": "strain=NCTC11045", "accession": "GCA_901482635.1", "taxid": 29388, "species_taxid": 29388, "relation_to_type": "type", "validated": true, "ani": 84.185, "matched_fragments": 657, "total_fragments": 827, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus capitis subsp. urealyticus", "strain": "strain=DSM 6717", "accession": "GCA_002901925.1", "taxid": 74703, "species_taxid": 29388, "relation_to_type": "type", "validated": true, "ani": 84.0787, "matched_fragments": 639, "total_fragments": 827, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus croceilyticus", "strain": "strain=CCM 8421", "accession": "GCA_004684875.1", "taxid": 319942, "species_taxid": 319942, "relation_to_type": "type", "validated": true, "ani": 80.0018, "matched_fragments": 389, "total_fragments": 827, "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": 79.9765, "matched_fragments": 376, "total_fragments": 827, "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": 79.5813, "matched_fragments": 389, "total_fragments": 827, "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": 79.2123, "matched_fragments": 351, "total_fragments": 827, "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": 79.0705, "matched_fragments": 357, "total_fragments": 827, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus shinii", "strain": "strain=K22-5M", "accession": "GCA_017583065.1", "taxid": 2912228, "species_taxid": 2912228, "relation_to_type": "type", "validated": true, "ani": 78.5072, "matched_fragments": 252, "total_fragments": 827, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002902725.1", "gtdb_species": "s__Staphylococcus caprae", "ani": 100.0, "matched_fragments": 827, "total_fragments": 827, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.57", "min_intra_species_ani": "98.10", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.91", "num_clustered_genomes": 18, "status": "conclusive" }, { "accession": "GCF_002902325.1", "gtdb_species": "s__Staphylococcus capitis", "ani": 84.2127, "matched_fragments": 643, "total_fragments": 827, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.07", "min_intra_species_ani": "96.40", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.88", "num_clustered_genomes": 151, "status": "-" }, { "accession": "GCF_900458815.1", "gtdb_species": "s__Staphylococcus saccharolyticus", "ani": 81.3384, "matched_fragments": 532, "total_fragments": 827, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.11", "min_intra_species_ani": "97.94", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.95", "num_clustered_genomes": 15, "status": "-" }, { "accession": "GCF_006742205.1", "gtdb_species": "s__Staphylococcus epidermidis", "ani": 80.871, "matched_fragments": 464, "total_fragments": 827, "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": "-" }, { "accession": "GCF_900636385.1", "gtdb_species": "s__Staphylococcus warneri", "ani": 80.146, "matched_fragments": 454, "total_fragments": 827, "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_003970495.1", "gtdb_species": "s__Staphylococcus pasteuri", "ani": 80.121, "matched_fragments": 434, "total_fragments": 827, "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": "98.67", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.89", "num_clustered_genomes": 34, "status": "-" }, { "accession": "GCF_004785665.1", "gtdb_species": "s__Staphylococcus pragensis", "ani": 80.1167, "matched_fragments": 374, "total_fragments": 827, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.69", "min_intra_species_ani": "99.09", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.94", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_002902565.1", "gtdb_species": "s__Staphylococcus petrasii", "ani": 80.007, "matched_fragments": 383, "total_fragments": 827, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.66", "min_intra_species_ani": "97.62", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.85", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCA_002902575.1", "gtdb_species": "s__Staphylococcus croceilyticus", "ani": 79.9764, "matched_fragments": 376, "total_fragments": 827, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.95", "min_intra_species_ani": "99.95", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_006094395.1", "gtdb_species": "s__Staphylococcus haemolyticus", "ani": 79.8904, "matched_fragments": 350, "total_fragments": 827, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.59", "min_intra_species_ani": "96.62", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.87", "num_clustered_genomes": 385, "status": "-" }, { "accession": "GCF_001224225.1", "gtdb_species": "s__Staphylococcus borealis", "ani": 79.6242, "matched_fragments": 364, "total_fragments": 827, "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_002901845.1", "gtdb_species": "s__Staphylococcus hominis", "ani": 79.3947, "matched_fragments": 346, "total_fragments": 827, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.87", "min_intra_species_ani": "96.99", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.86", "num_clustered_genomes": 183, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.041, "cell_length": -0.052, "doubling_h": -0.365, "growth_tmp": 37.0, "optimum_tmp": 34.151, "optimum_ph": 6.75, "genome_size": 2637565.0, "gc_content": 33.598, "coding_genes": 2370.685, "rRNA16S_genes": 5.698, "tRNA_genes": 58.094, "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": 0.0, "coccus_cell_shape": 1.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Staphylococcus", "caprae" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }