{ "type": "genome", "identifier": "GCF_900186985.1", "organism": "Staphylococcus piscifermentans", "title": "Staphylococcus piscifermentans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "SC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900186985.1", "bioproject": "PRJNA224116", "biosample": "SAMEA4384060", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "70258", "species_taxid": "70258", "organism_name": "Staphylococcus piscifermentans", "infraspecific_name": "strain=NCTC13836", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/08/15", "asm_name": "50377_C01", "asm_submitter": "SC", "gbrs_paired_asm": "GCA_900186985.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/186/985/GCF_900186985.1_50377_C01", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2613271", "genome_size_ungapped": "2613271", "gc_percent": "36.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900186985.1-RS_2024_12_13", "annotation_date": "2024-12-13", "total_gene_count": "2483", "protein_coding_gene_count": "2377", "non_coding_gene_count": "84", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-08-15", "dateModified": "2017-08-15", "datePublished": "2017-08-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Staphylococcus piscifermentans" ], "sample_taxid": [ "70258" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Thailand" ], "sample_host_location_id": [], "data_size": "0.734 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)": "2613271", "Number of Sequences": "1", "Longest Sequences (bp)": "2613271", "N50 (bp)": "2613271", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "36.7", "Number of CDSs": "2433", "Average Protein Length": "306.8", "Coding Ratio (%)": "85.7", "Number of rRNAs": "18", "Number of tRNAs": "61", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Staphylococcus piscifermentans", "strain": "strain=NCTC13836", "accession": "GCA_900186985.1", "taxid": 70258, "species_taxid": 70258, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 871, "total_fragments": 871, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Staphylococcus piscifermentans", "strain": "strain=DSM 7373", "accession": "GCA_003970555.1", "taxid": 70258, "species_taxid": 70258, "relation_to_type": "type", "validated": true, "ani": 99.9145, "matched_fragments": 800, "total_fragments": 871, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Staphylococcus debuckii", "strain": "strain=SDB 2975", "accession": "GCA_003718735.1", "taxid": 2044912, "species_taxid": 2044912, "relation_to_type": "type", "validated": true, "ani": 94.6652, "matched_fragments": 802, "total_fragments": 871, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus carnosus", "strain": "strain=NCTC13825", "accession": "GCA_900458435.1", "taxid": 1281, "species_taxid": 1281, "relation_to_type": "type", "validated": true, "ani": 85.3575, "matched_fragments": 692, "total_fragments": 871, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus carnosus", "strain": "strain=FDAARGOS_883", "accession": "GCA_016028275.1", "taxid": 1281, "species_taxid": 1281, "relation_to_type": "type", "validated": true, "ani": 85.3055, "matched_fragments": 712, "total_fragments": 871, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus simulans", "strain": "strain=NCTC11046", "accession": "GCA_900474685.1", "taxid": 1286, "species_taxid": 1286, "relation_to_type": "type", "validated": true, "ani": 81.0888, "matched_fragments": 503, "total_fragments": 871, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Staphylococcus simulans", "strain": "strain=NCTC 11046", "accession": "GCA_002902285.1", "taxid": 1286, "species_taxid": 1286, "relation_to_type": "type", "validated": true, "ani": 80.8279, "matched_fragments": 477, "total_fragments": 871, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Macrococcus armenti", "strain": "strain=JEK37", "accession": "GCA_020097135.1", "taxid": 2875764, "species_taxid": 2875764, "relation_to_type": "type", "validated": true, "ani": 79.8267, "matched_fragments": 68, "total_fragments": 871, "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": 78.7213, "matched_fragments": 167, "total_fragments": 871, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_900186985.1", "gtdb_species": "s__Staphylococcus piscifermentans", "ani": 100.0, "matched_fragments": 871, "total_fragments": 871, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_003718735.1", "gtdb_species": "s__Staphylococcus debuckii", "ani": 94.6715, "matched_fragments": 803, "total_fragments": 871, "gtdb_taxonomy": "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": 85.3737, "matched_fragments": 691, "total_fragments": 871, "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_001618885.1", "gtdb_species": "s__Staphylococcus condimenti", "ani": 85.1305, "matched_fragments": 711, "total_fragments": 871, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.75", "min_intra_species_ani": "99.00", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.93", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCF_002994445.1", "gtdb_species": "s__Staphylococcus simulans_B", "ani": 81.0173, "matched_fragments": 475, "total_fragments": 871, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.89", "min_intra_species_ani": "96.89", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002902285.1", "gtdb_species": "s__Staphylococcus simulans", "ani": 80.8156, "matched_fragments": 479, "total_fragments": 871, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.92", "min_intra_species_ani": "98.61", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 77, "status": "-" }, { "accession": "GCF_003043455.1", "gtdb_species": "s__Staphylococcus simulans_A", "ani": 80.6652, "matched_fragments": 480, "total_fragments": 871, "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": "-" } ] }, "_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": 2596750.667, "gc_content": 36.625, "coding_genes": 2362.0, "rRNA16S_genes": 6.0, "tRNA_genes": 59.0, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 0.666, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.0, "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", "piscifermentans" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }