{ "type": "genome", "identifier": "GCF_002902305.1", "organism": "Staphylococcus argensis", "title": "Staphylococcus argensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Modernising Medical Microbiology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002902305.1", "bioproject": "PRJNA224116", "biosample": "SAMN06177167", "wgs_master": "PPPX00000000.1", "refseq_category": "reference genome", "taxid": "1607738", "species_taxid": "1607738", "organism_name": "Staphylococcus argensis", "infraspecific_name": "strain=DSM 29875", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/01/27", "asm_name": "ASM290230v1", "asm_submitter": "Modernising Medical Microbiology", "gbrs_paired_asm": "GCA_002902305.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/902/305/GCF_002902305.1_ASM290230v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2452468", "genome_size_ungapped": "2451913", "gc_percent": "39.000000", "replicon_count": "0", "scaffold_count": "19", "contig_count": "19", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002902305.1-RS_2024_03_29", "annotation_date": "2024-03-29", "total_gene_count": "2365", "protein_coding_gene_count": "2244", "non_coding_gene_count": "59", "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 argensis" ], "sample_taxid": [ "1607738" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Germany: Braunschweig" ], "sample_host_location_id": [], "data_size": "0.696 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)": "2452468", "Number of Sequences": "19", "Longest Sequences (bp)": "1290125", "N50 (bp)": "1290125", "Gap Ratio (%)": "0.022630", "GCcontent (%)": "38.9", "Number of CDSs": "2353", "Average Protein Length": "287.9", "Coding Ratio (%)": "82.9", "Number of rRNAs": "2", "Number of tRNAs": "51", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Staphylococcus argensis", "strain": "strain=DSM 29875", "accession": "GCA_002902305.1", "taxid": 1607738, "species_taxid": 1607738, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 809, "total_fragments": 809, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Staphylococcus pettenkoferi", "strain": "strain=CCUG 51270", "accession": "GCA_002902685.1", "taxid": 170573, "species_taxid": 170573, "relation_to_type": "type", "validated": true, "ani": 92.296, "matched_fragments": 721, "total_fragments": 809, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus pettenkoferi", "strain": "strain=FDAARGOS_1071", "accession": "GCA_016127935.1", "taxid": 170573, "species_taxid": 170573, "relation_to_type": "type", "validated": true, "ani": 92.2758, "matched_fragments": 749, "total_fragments": 809, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus pragensis", "strain": "strain=CCM 8529", "accession": "GCA_004785665.1", "taxid": 1611836, "species_taxid": 1611836, "relation_to_type": "type", "validated": true, "ani": 78.5796, "matched_fragments": 193, "total_fragments": 809, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus arlettae", "strain": "strain=NCTC12413", "accession": "GCA_900457375.1", "taxid": 29378, "species_taxid": 29378, "relation_to_type": "type", "validated": true, "ani": 78.554, "matched_fragments": 161, "total_fragments": 809, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus pragensis", "strain": "strain=CCM 8529", "accession": "GCA_014635505.1", "taxid": 1611836, "species_taxid": 1611836, "relation_to_type": "type", "validated": true, "ani": 78.5229, "matched_fragments": 190, "total_fragments": 809, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus petrasii", "strain": "strain=NCTC13835", "accession": "GCA_900458665.1", "taxid": 1276936, "species_taxid": 1276936, "relation_to_type": "type", "validated": true, "ani": 78.472, "matched_fragments": 208, "total_fragments": 809, "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": 78.4429, "matched_fragments": 191, "total_fragments": 809, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus arlettae", "strain": "strain=NCTC 12413", "accession": "GCA_002902345.1", "taxid": 29378, "species_taxid": 29378, "relation_to_type": "type", "validated": true, "ani": 78.4349, "matched_fragments": 162, "total_fragments": 809, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus petrasii", "strain": "strain=CCUG 62727", "accession": "GCA_002902565.1", "taxid": 1276936, "species_taxid": 1276936, "relation_to_type": "type", "validated": true, "ani": 78.4048, "matched_fragments": 200, "total_fragments": 809, "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": 78.3959, "matched_fragments": 135, "total_fragments": 809, "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": 78.3018, "matched_fragments": 137, "total_fragments": 809, "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": 78.2768, "matched_fragments": 200, "total_fragments": 809, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Macrococcus goetzii", "strain": "strain=CCM 4927", "accession": "GCA_002742385.2", "taxid": 1891097, "species_taxid": 1891097, "relation_to_type": "type", "validated": true, "ani": 78.1416, "matched_fragments": 61, "total_fragments": 809, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus durrellii", "strain": "strain=27_4_6_LY", "accession": "GCA_015594545.1", "taxid": 2781773, "species_taxid": 2781773, "relation_to_type": "type", "validated": true, "ani": 78.0978, "matched_fragments": 157, "total_fragments": 809, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus xylosus", "strain": "strain=NCTC11043", "accession": "GCA_900458755.1", "taxid": 1288, "species_taxid": 1288, "relation_to_type": "type", "validated": true, "ani": 78.0388, "matched_fragments": 178, "total_fragments": 809, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002902305.1", "gtdb_species": "s__Staphylococcus argensis", "ani": 100.0, "matched_fragments": 809, "total_fragments": 809, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.94", "min_intra_species_ani": "99.94", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 8, "status": "conclusive" }, { "accession": "GCF_002902685.1", "gtdb_species": "s__Staphylococcus pettenkoferi", "ani": 92.3035, "matched_fragments": 720, "total_fragments": 809, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.48", "min_intra_species_ani": "96.01", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.89", "num_clustered_genomes": 21, "status": "-" }, { "accession": "GCF_006742205.1", "gtdb_species": "s__Staphylococcus epidermidis", 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153, "total_fragments": 809, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.25", "min_intra_species_ani": "98.25", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_002902575.1", "gtdb_species": "s__Staphylococcus croceilyticus", "ani": 78.462, "matched_fragments": 190, "total_fragments": 809, "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_002902345.1", "gtdb_species": "s__Staphylococcus arlettae", "ani": 78.4349, "matched_fragments": 162, "total_fragments": 809, 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"vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Staphylococcus", "argensis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }