{ "type": "genome", "identifier": "GCF_000982825.1", "organism": "Cronobacter sakazakii", "title": "Cronobacter sakazakii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Food-borne Pathogen Omics Research Center", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000982825.1", "bioproject": "PRJNA224116", "biosample": "SAMN03371468", "wgs_master": "na", "refseq_category": "na", "taxid": "28141", "species_taxid": "28141", "organism_name": "Cronobacter sakazakii", "infraspecific_name": "strain=ATCC 29544", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/04/30", "asm_name": "ASM98282v1", "asm_submitter": "Food-borne Pathogen Omics Research Center", "gbrs_paired_asm": "GCA_000982825.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/982/825/GCF_000982825.1_ASM98282v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4663565", "genome_size_ungapped": "4663565", "gc_percent": "56.500000", "replicon_count": "4", "scaffold_count": "4", "contig_count": "4", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000982825.1-RS_2024_09_04", "annotation_date": "2024-09-04", "total_gene_count": "4542", "protein_coding_gene_count": "4311", "non_coding_gene_count": "122", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-04-30", "dateModified": "2015-04-30", "datePublished": "2015-04-30", "_annotation": { "sample_count": 1, "sample_organism": [ "Cronobacter sakazakii" ], "sample_taxid": [ "28141" ], "sample_host_organism": [ "infants" ], "sample_host_organism_id": [], "sample_host_disease": [ "neonatal necrotizing enterocolitis" ], "sample_host_disease_id": [], "sample_host_location": [ "USA:Tennessee" ], "sample_host_location_id": [], "data_size": "1.310 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 97.92, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4663565", "Number of Sequences": "4", "Longest Sequences (bp)": "4511265", "N50 (bp)": "4511265", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "56.6", "Number of CDSs": "4476", "Average Protein Length": "303.3", "Coding Ratio (%)": "87.3", "Number of rRNAs": "22", "Number of tRNAs": "84", "Number of CRISPRs": "4" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Cronobacter sakazakii", "strain": "strain=ATCC 29544", "accession": "GCA_000982825.1", "taxid": 28141, "species_taxid": 28141, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1547, "total_fragments": 1552, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Cronobacter sakazakii", "strain": "strain=FDAARGOS_927", "accession": "GCA_016103025.1", "taxid": 28141, "species_taxid": 28141, "relation_to_type": "type", "validated": true, "ani": 99.9943, "matched_fragments": 1537, "total_fragments": 1552, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Cronobacter sakazakii", "strain": "strain=NBRC 102416", "accession": "GCA_000684935.1", "taxid": 28141, "species_taxid": 28141, "relation_to_type": "type", "validated": true, "ani": 99.9715, "matched_fragments": 1453, "total_fragments": 1552, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Cronobacter sakazakii", "strain": "strain=ATCC 29544", "accession": "GCA_001971035.1", "taxid": 28141, "species_taxid": 28141, "relation_to_type": "type", "validated": true, "ani": 99.8073, "matched_fragments": 1314, "total_fragments": 1552, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Cronobacter malonaticus", "strain": "strain=LMG 23826", "accession": "GCA_001277215.2", "taxid": 413503, "species_taxid": 413503, "relation_to_type": "type", "validated": true, "ani": 94.963, "matched_fragments": 1355, "total_fragments": 1552, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cronobacter malonaticus", "strain": "strain=LMG 23826", "accession": "GCA_000409305.1", "taxid": 413503, "species_taxid": 413503, "relation_to_type": "type", "validated": true, "ani": 94.8951, "matched_fragments": 1301, "total_fragments": 1552, "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": 81.5635, "matched_fragments": 829, "total_fragments": 1552, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter hormaechei", "strain": "strain=FDAARGOS 1433", "accession": "GCA_019048245.1", "taxid": 158836, "species_taxid": 158836, "relation_to_type": "suspected-type", "validated": true, "ani": 81.4004, "matched_fragments": 857, "total_fragments": 1552, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter wuhouensis", "strain": "strain=WCHEW120002", "accession": "GCA_004331265.1", "taxid": 2529381, "species_taxid": 2529381, "relation_to_type": "type", "validated": true, "ani": 81.0312, "matched_fragments": 833, "total_fragments": 1552, "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": 80.8004, "matched_fragments": 825, "total_fragments": 1552, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { 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"min_intra_species_af": "0.89", "num_clustered_genomes": 18, "status": "-" }, { "accession": "GCF_001277235.1", "gtdb_species": "s__Cronobacter dublinensis", "ani": 89.6018, "matched_fragments": 1278, "total_fragments": 1552, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.74", "min_intra_species_ani": "96.92", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 42, "status": "-" }, { "accession": "GCF_001277195.1", "gtdb_species": "s__Cronobacter muytjensii", "ani": 89.5387, "matched_fragments": 1257, "total_fragments": 1552, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.13", "min_intra_species_ani": "98.83", "mean_intra_species_af": "0.94", 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"N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_001590905.1", "gtdb_species": "s__Serratia grimesii", "ani": 78.3071, "matched_fragments": 384, "total_fragments": 1552, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.09", "min_intra_species_ani": "98.89", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.93", "num_clustered_genomes": 7, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": 0.0, "cell_length": 0.477, "doubling_h": -0.639, "growth_tmp": 34.333, "optimum_tmp": 36.0, "optimum_ph": null, "genome_size": 4607581.231, "gc_content": 56.018, "coding_genes": 4506.154, "rRNA16S_genes": 7.0, "tRNA_genes": 91.875, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.0, "facultative_respiration": 0.75, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.25, 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