{ "type": "genome", "identifier": "GCF_900457095.1", "organism": "Shigella boydii", "title": "Shigella boydii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "SC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900457095.1", "bioproject": "PRJNA224116", "biosample": "SAMEA104281632", "wgs_master": "UAUO00000000.1", "refseq_category": "na", "taxid": "621", "species_taxid": "621", "organism_name": "Shigella boydii", "infraspecific_name": "strain=NCTC12985", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/06/29", "asm_name": "57940_F01", "asm_submitter": "SC", "gbrs_paired_asm": "GCA_900457095.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/457/095/GCF_900457095.1_57940_F01", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5019753", "genome_size_ungapped": "5019753", "gc_percent": "51.000000", "replicon_count": "0", "scaffold_count": "66", "contig_count": "66", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900457095.1-RS_2024_09_03", "annotation_date": "2024-09-03", "total_gene_count": "5254", "protein_coding_gene_count": "4125", "non_coding_gene_count": "141", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-06-29", "dateModified": "2018-06-29", "datePublished": "2018-06-29", "_annotation": { "sample_count": 1, "sample_organism": [ "Shigella boydii" ], "sample_taxid": [ "621" ], "sample_host_organism": [ "not available" ], "sample_host_organism_id": [], "sample_host_disease": [ "not available: to be reported later" ], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.411 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5019753", "Number of Sequences": "66", "Longest Sequences (bp)": "768129", "N50 (bp)": "370424", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "51.0", "Number of CDSs": "5393", "Average Protein Length": "261.9", "Coding Ratio (%)": "84.4", "Number of rRNAs": "33", "Number of tRNAs": "101", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Shigella boydii", "strain": "strain=NCTC12985", "accession": "GCA_900457095.1", "taxid": 621, "species_taxid": 621, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1631, "total_fragments": 1643, "ani_threshold": 95, "status": "indistinguishable" }, { "organism_name": "Shigella boydii", "strain": "strain=FDAARGOS_1139", "accession": "GCA_016726285.1", "taxid": 621, "species_taxid": 621, "relation_to_type": "type", "validated": true, "ani": 99.9941, "matched_fragments": 1496, "total_fragments": 1643, "ani_threshold": 95, "status": "indistinguishable" }, { "organism_name": "Shigella boydii", "strain": "strain=DMB SH130", "accession": "GCA_003572535.1", "taxid": 621, "species_taxid": 621, "relation_to_type": "type", "validated": true, "ani": 99.7086, "matched_fragments": 1091, "total_fragments": 1643, "ani_threshold": 95, "status": "indistinguishable" }, { "organism_name": "Shigella sonnei", "strain": "strain=ATCC 29930", "accession": "GCA_002950395.1", "taxid": 624, "species_taxid": 624, "relation_to_type": "type", "validated": true, "ani": 98.2095, "matched_fragments": 1304, "total_fragments": 1643, "ani_threshold": 95, "status": "indistinguishable" }, { "organism_name": "Shigella sonnei", "strain": "strain=NCTC12984", "accession": "GCA_900457155.1", "taxid": 624, "species_taxid": 624, "relation_to_type": "type", "validated": true, "ani": 98.1584, "matched_fragments": 1303, "total_fragments": 1643, "ani_threshold": 95, "status": "indistinguishable" }, { "organism_name": "Shigella flexneri 2a", "strain": "strain=ATCC 29903", "accession": "GCA_002950215.1", "taxid": 42897, "species_taxid": 623, "relation_to_type": "type", "validated": true, "ani": 97.8283, "matched_fragments": 1278, "total_fragments": 1643, "ani_threshold": 95, "status": "indistinguishable" }, { "organism_name": "Escherichia coli", "strain": "strain=ATCC 11775", "accession": "GCA_003697165.2", "taxid": 562, "species_taxid": 562, "relation_to_type": "neotype", "validated": true, "ani": 96.5679, "matched_fragments": 1197, "total_fragments": 1643, "ani_threshold": 95, "status": "indistinguishable" }, { "organism_name": "Escherichia coli", "strain": "strain=ATCC 11775", "accession": "GCA_000734955.1", "taxid": 562, "species_taxid": 562, "relation_to_type": "neotype", "validated": true, "ani": 96.4582, "matched_fragments": 1175, "total_fragments": 1643, "ani_threshold": 95, "status": "indistinguishable" }, { "organism_name": "Escherichia coli", "strain": "strain=DSM 30083", "accession": "GCA_024519395.1", "taxid": 562, "species_taxid": 562, "relation_to_type": "neotype", "validated": true, "ani": 96.4379, "matched_fragments": 1194, "total_fragments": 1643, "ani_threshold": 95, "status": "indistinguishable" }, { "organism_name": "Escherichia albertii", "strain": "strain=DSM 17582", "accession": "GCA_022833075.1", "taxid": 208962, "species_taxid": 208962, "relation_to_type": "type", "validated": true, "ani": 90.2514, "matched_fragments": 1110, "total_fragments": 1643, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Escherichia albertii", "strain": "strain=NBRC 107761", "accession": "GCA_000759775.1", "taxid": 208962, "species_taxid": 208962, "relation_to_type": "type", "validated": true, "ani": 89.843, "matched_fragments": 1044, 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"s__Escherichia albertii", "ani": 89.9567, "matched_fragments": 1036, "total_fragments": 1643, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.47", "min_intra_species_ani": "97.95", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.82", "num_clustered_genomes": 107, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": 1.0, "doubling_h": -0.417, "growth_tmp": 35.0, "optimum_tmp": 37.0, "optimum_ph": 7.2, "genome_size": 4839369.591, "gc_content": 49.741, "coding_genes": 4433.4, "rRNA16S_genes": 7.0, "tRNA_genes": 94.333, "gram_stain": 0.0, "sporulation": 0.0, "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": [ "Shigella", "boydii" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }