{ "type": "genome", "identifier": "GCF_000409365.1", "organism": "Cronobacter dublinensis subsp. lausannensis LMG 23824", "title": "Cronobacter dublinensis subsp. lausannensis LMG 23824", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Cronobacter Genus Genome Sequencing Consortium", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000409365.1", "bioproject": "PRJNA224116", "biosample": "SAMN02952932", "wgs_master": "AJKY00000000.1", "refseq_category": "na", "taxid": "1159560", "species_taxid": "413497", "organism_name": "Cronobacter dublinensis subsp. lausannensis LMG 23824", "infraspecific_name": "strain=LMG 23824", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/06/07", "asm_name": "cdlau515 final contigs", "asm_submitter": "Cronobacter Genus Genome Sequencing Consortium", "gbrs_paired_asm": "GCA_000409365.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/409/365/GCF_000409365.1_cdlau515_final_contigs", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4613339", "genome_size_ungapped": "4613339", "gc_percent": "58.000000", "replicon_count": "0", "scaffold_count": "105", "contig_count": "105", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000409365.1-RS_2024_12_13", "annotation_date": "2024-12-13", "total_gene_count": "4462", "protein_coding_gene_count": "4200", "non_coding_gene_count": "148", "pubmed_id": "23724777" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-06-07", "dateModified": "2013-06-07", "datePublished": "2013-06-07", "_annotation": { "sample_count": 1, "sample_organism": [ "Cronobacter dublinensis subsp. lausannensis LMG 23824" ], "sample_taxid": [ "1159560" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Switzerland: Lausanne" ], "sample_host_location_id": [], "data_size": "1.296 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)": "4613339", "Number of Sequences": "105", "Longest Sequences (bp)": "446397", "N50 (bp)": "243660", "Gap Ratio (%)": "0.000087", "GCcontent (%)": "57.9", "Number of CDSs": "4212", "Average Protein Length": "309.8", "Coding Ratio (%)": "84.8", "Number of rRNAs": "38", "Number of tRNAs": "92", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Cronobacter dublinensis subsp. lausannensis", "strain": "strain=LMG 23824", "accession": "GCA_000409365.1", "taxid": 413500, "species_taxid": 413497, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1486, "total_fragments": 1489, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Cronobacter dublinensis subsp. lactaridi", "strain": "strain=LMG 23825", "accession": "GCA_000409345.1", "taxid": 413499, "species_taxid": 413497, "relation_to_type": "type", "validated": true, "ani": 98.3058, "matched_fragments": 1342, "total_fragments": 1489, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Cronobacter dublinensis subsp. dublinensis", "strain": "strain=LMG 23823", "accession": "GCA_001277235.1", "taxid": 413498, "species_taxid": 413497, "relation_to_type": "type", "validated": true, "ani": 97.4035, "matched_fragments": 1339, "total_fragments": 1489, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Cronobacter dublinensis subsp. dublinensis", "strain": "strain=LMG 23823", "accession": "GCA_000409225.1", "taxid": 413498, "species_taxid": 413497, "relation_to_type": "type", "validated": true, "ani": 97.3737, "matched_fragments": 1320, "total_fragments": 1489, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Cronobacter muytjensii", "strain": "strain=ATCC 51329", "accession": "GCA_000409285.1", "taxid": 413501, "species_taxid": 413501, "relation_to_type": "type", "validated": true, "ani": 92.5714, "matched_fragments": 1265, "total_fragments": 1489, "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": 89.782, "matched_fragments": 1226, "total_fragments": 1489, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cronobacter sakazakii", "strain": "strain=ATCC 29544", "accession": "GCA_001971035.1", "taxid": 28141, "species_taxid": 28141, "relation_to_type": "type", "validated": true, "ani": 89.6671, "matched_fragments": 1145, "total_fragments": 1489, "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": 81.3199, "matched_fragments": 820, "total_fragments": 1489, "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": 81.3087, "matched_fragments": 835, "total_fragments": 1489, "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": 80.9624, "matched_fragments": 782, "total_fragments": 1489, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter cloacae", "strain": "strain=DSM 30054", "accession": "GCA_021469225.1", "taxid": 550, "species_taxid": 550, "relation_to_type": "type", "validated": true, "ani": 80.8018, "matched_fragments": 818, "total_fragments": 1489, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 97.92, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001277235.1", "gtdb_species": "s__Cronobacter dublinensis", "ani": 97.4158, "matched_fragments": 1338, "total_fragments": 1489, "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", 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"min_intra_species_af": "0.98", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_000027065.2", "gtdb_species": "s__Cronobacter turicensis", "ani": 89.9801, "matched_fragments": 1304, "total_fragments": 1489, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.17", "min_intra_species_ani": "96.06", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 18, "status": "-" }, { "accession": "GCF_001277215.2", "gtdb_species": "s__Cronobacter malonaticus", "ani": 89.8857, "matched_fragments": 1268, "total_fragments": 1489, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.86", "min_intra_species_ani": "98.11", "mean_intra_species_af": "0.94", 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"min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": 0.0, "cell_length": 0.477, "doubling_h": -0.639, "growth_tmp": 37.0, "optimum_tmp": 30.0, "optimum_ph": null, "genome_size": 4631441.222, "gc_content": 57.536, "coding_genes": 4169.0, "rRNA16S_genes": 7.0, "tRNA_genes": 82.0, "gram_stain": 0.0, "sporulation": 1.0, "motility": 1.0, "range_salinity": 0.0, "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": [ "Cronobacter", "dublinensis", "subsp.", "lausannensis", "LMG", "23824" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }