{ "type": "genome", "identifier": "GCF_029023945.1", "organism": "Staphylococcus haemolyticus", "title": "Staphylococcus haemolyticus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Agroscope", "publication": [ {} ], "properties": { "assembly_accession": "GCF_029023945.1", "bioproject": "PRJNA224116", "biosample": "SAMN33336507", "wgs_master": "na", "refseq_category": "na", "taxid": "1283", "species_taxid": "1283", "organism_name": "Staphylococcus haemolyticus", "infraspecific_name": "strain=DSM 20263", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2023/03/08", "asm_name": "ASM2902394v1", "asm_submitter": "Agroscope", "gbrs_paired_asm": "GCA_029023945.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/029/023/945/GCF_029023945.1_ASM2902394v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2571027", "genome_size_ungapped": "2571027", "gc_percent": "33.000000", "replicon_count": "3", "scaffold_count": "3", "contig_count": "3", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_029023945.1-RS_2024_03_29", "annotation_date": "2024-03-29", "total_gene_count": "2511", "protein_coding_gene_count": "2360", "non_coding_gene_count": "85", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2023-03-08", "dateModified": "2023-03-08", "datePublished": "2023-03-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Staphylococcus haemolyticus" ], "sample_taxid": [ "1283" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Unknown" ], "sample_host_location_id": [], "data_size": "0.709 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)": "2571027", "Number of Sequences": "3", "Longest Sequences (bp)": "2516900", "N50 (bp)": "2516900", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "32.9", "Number of CDSs": "2451", "Average Protein Length": "298.6", "Coding Ratio (%)": "85.4", "Number of rRNAs": "19", "Number of tRNAs": "63", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Staphylococcus haemolyticus", "strain": "strain=ATCC 29970", "accession": "GCA_006094395.1", "taxid": 1283, "species_taxid": 1283, "relation_to_type": "type", "validated": true, "ani": 99.9938, "matched_fragments": 851, "total_fragments": 855, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Staphylococcus haemolyticus", "strain": "strain=NCTC11042", "accession": "GCA_900458595.1", "taxid": 1283, "species_taxid": 1283, "relation_to_type": "type", "validated": true, "ani": 99.9924, "matched_fragments": 851, "total_fragments": 855, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Staphylococcus haemolyticus", "strain": "strain=NCTC 11042", "accession": "GCA_002901805.1", "taxid": 1283, "species_taxid": 1283, "relation_to_type": "type", "validated": true, "ani": 99.9315, "matched_fragments": 788, "total_fragments": 855, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Staphylococcus borealis", "strain": "strain=51-48", "accession": "GCA_013345165.1", "taxid": 2742203, "species_taxid": 2742203, "relation_to_type": "type", "validated": true, "ani": 88.2739, "matched_fragments": 755, "total_fragments": 855, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus borealis", "strain": "strain=51-48", "accession": "GCA_001224225.1", "taxid": 2742203, "species_taxid": 2742203, "relation_to_type": "type", "validated": true, "ani": 88.0637, "matched_fragments": 731, "total_fragments": 855, "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": 83.8533, "matched_fragments": 644, "total_fragments": 855, "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": 79.7382, "matched_fragments": 305, "total_fragments": 855, "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": 79.1821, "matched_fragments": 299, "total_fragments": 855, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_006094395.1", "gtdb_species": "s__Staphylococcus haemolyticus", "ani": 99.9938, "matched_fragments": 851, "total_fragments": 855, "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": "conclusive" }, { "accession": "GCF_001224225.1", "gtdb_species": "s__Staphylococcus borealis", "ani": 88.0734, "matched_fragments": 730, "total_fragments": 855, "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_004785665.1", "gtdb_species": "s__Staphylococcus pragensis", "ani": 82.4092, "matched_fragments": 574, "total_fragments": 855, "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": 82.217, "matched_fragments": 531, "total_fragments": 855, "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": 82.0679, "matched_fragments": 522, "total_fragments": 855, "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_003035445.1", "gtdb_species": "s__Staphylococcus devriesei_A", "ani": 81.8762, "matched_fragments": 538, "total_fragments": 855, "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_002902625.1", "gtdb_species": "s__Staphylococcus devriesei", "ani": 81.5456, "matched_fragments": 518, "total_fragments": 855, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.59", "min_intra_species_ani": "98.61", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.91", "num_clustered_genomes": 9, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.041, "cell_length": -0.052, "doubling_h": -0.365, "growth_tmp": 34.0, "optimum_tmp": 34.312, "optimum_ph": 6.75, "genome_size": 2539716.402, "gc_content": 32.116, "coding_genes": 2448.667, "rRNA16S_genes": 5.333, "tRNA_genes": 60.0, "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": 0.0, "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", "haemolyticus" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }