{ "type": "genome", "identifier": "GCF_016029065.1", "organism": "Salmonella enterica subsp. salamae", "title": "Salmonella enterica subsp. salamae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Center for Biotechnology Information", "publication": [ {} ], "properties": { "assembly_accession": "GCF_016029065.1", "bioproject": "PRJNA224116", "biosample": "SAMEA7114072", "wgs_master": "DACWUI000000000.1", "refseq_category": "na", "taxid": "59202", "species_taxid": "28901", "organism_name": "Salmonella enterica subsp. salamae", "infraspecific_name": "strain=CCUG30039", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/12/14", "asm_name": "PDT000910284.1", "asm_submitter": "National Center for Biotechnology Information", "gbrs_paired_asm": "GCA_016029065.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/016/029/065/GCF_016029065.1_PDT000910284.1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4822376", "genome_size_ungapped": "4822376", "gc_percent": "52.000000", "replicon_count": "0", "scaffold_count": "40", "contig_count": "40", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_016029065.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "4649", "protein_coding_gene_count": "4410", "non_coding_gene_count": "93", "pubmed_id": "30286803" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-12-14", "dateModified": "2020-12-14", "datePublished": "2020-12-14", "_annotation": { "sample_count": 1, "sample_organism": [ "Salmonella enterica" ], "sample_taxid": [ "28901" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.372 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)": "4822376", "Number of Sequences": "40", "Longest Sequences (bp)": "789660", "N50 (bp)": "390309", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "52.0", "Number of CDSs": "4424", "Average Protein Length": "316.3", "Coding Ratio (%)": "87.1", "Number of rRNAs": "3", "Number of tRNAs": "78", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Salmonella enterica subsp. salamae", "strain": "strain=CCUG30039", "accession": "GCA_016029065.1", "taxid": 59202, "species_taxid": 28901, 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96.0462, "matched_fragments": 1341, "total_fragments": 1590, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Salmonella enterica subsp. enterica", "strain": "strain=PartC-Senterica-RM8376", "accession": "GCA_022869965.1", "taxid": 59201, "species_taxid": 28901, "relation_to_type": "suspected-type", "validated": true, "ani": 96.0195, "matched_fragments": 1361, "total_fragments": 1590, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Salmonella enterica subsp. indica", "strain": "strain=CCUG30038", "accession": "GCA_018033035.1", "taxid": 59207, "species_taxid": 28901, "relation_to_type": "type", "validated": true, "ani": 95.8333, "matched_fragments": 1346, "total_fragments": 1590, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Salmonella enterica subsp. diarizonae", "strain": "strain=CCUG30040", "accession": "GCA_016030095.1", "taxid": 59204, "species_taxid": 28901, "relation_to_type": "type", "validated": true, "ani": 95.7543, 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"total_fragments": 1590, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter farmeri", "strain": "strain=FDAARGOS 1423", "accession": "GCA_019048065.1", "taxid": 67824, "species_taxid": 67824, "relation_to_type": "type", "validated": true, "ani": 82.7266, "matched_fragments": 952, "total_fragments": 1590, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter roggenkampii", "strain": "strain=DSM 16690", "accession": "GCA_024390995.1", "taxid": 1812935, "species_taxid": 1812935, "relation_to_type": "type", "validated": true, "ani": 81.1903, "matched_fragments": 762, "total_fragments": 1590, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudocitrobacter corydidari", "strain": "", "accession": "GCA_021172065.1", "taxid": 2891570, "species_taxid": 2891570, "relation_to_type": "type", "validated": true, "ani": 81.0236, "matched_fragments": 805, "total_fragments": 1590, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter sichuanensis", "strain": "strain=WCHECL1597", "accession": "GCA_025002605.1", "taxid": 2071710, "species_taxid": 2071710, "relation_to_type": "type", "validated": true, "ani": 80.893, "matched_fragments": 753, "total_fragments": 1590, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rahnella inusitata", "strain": "strain=DSM 30078", "accession": "GCA_003263515.1", "taxid": 58169, "species_taxid": 58169, "relation_to_type": "type", "validated": true, "ani": 77.9045, "matched_fragments": 302, "total_fragments": 1590, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leminorella richardii", "strain": "strain=NCTC12151", "accession": "GCA_900478135.1", "taxid": 158841, "species_taxid": 158841, "relation_to_type": "type", "validated": true, "ani": 77.2844, "matched_fragments": 191, "total_fragments": 1590, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000006945.2", "gtdb_species": "s__Salmonella enterica", "ani": 96.0503, "matched_fragments": 1360, "total_fragments": 1590, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella", "ani_circumscription_radius": 95.0604, "mean_intra_species_ani": "98.80", "min_intra_species_ani": "95.43", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.81", "num_clustered_genomes": 12285, "status": "inconclusive" }, { "accession": "GCF_008692785.1", "gtdb_species": "s__Salmonella diarizonae", "ani": 95.7505, "matched_fragments": 1310, "total_fragments": 1590, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella", "ani_circumscription_radius": 95.0604, "mean_intra_species_ani": "98.90", "min_intra_species_ani": "95.36", "mean_intra_species_af": "0.91", 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"N/A", "num_clustered_genomes": 1, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": -0.36, "growth_tmp": 36.956, "optimum_tmp": 36.989, "optimum_ph": null, "genome_size": 4811759.817, "gc_content": 51.852, "coding_genes": 4628.245, "rRNA16S_genes": 6.931, "tRNA_genes": 83.616, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "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": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Salmonella", "enterica", "subsp.", "salamae" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }