{ "type": "genome", "identifier": "GCA_947178385.1", "organism": "Escherichia coli", "title": "Escherichia coli", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "EMG", "publication": [ {} ], "properties": { "assembly_accession": "GCA_947178385.1", "bioproject": "PRJEB56464", "biosample": "SAMEA111500875", "wgs_master": "CAMWYG000000000.1", "refseq_category": "na", "taxid": "562", "species_taxid": "562", "organism_name": "Escherichia coli", "infraspecific_name": "", "isolate": "SRR14411341_bin.3_metawrap_v1.3_MAG", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/10/28", "asm_name": "SRR14411341_bin.3_metawrap_v1.3_MAG", "submitter": "EMG", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/947/178/385/GCA_947178385.1_SRR14411341_bin.3_metawrap_v1.3_MAG", "excluded_from_refseq": "derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-10-28", "dateModified": "2022-10-28", "datePublished": "2022-10-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Escherichia coli" ], "sample_taxid": [ "562" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "United Kingdom" ], "sample_host_location_id": [], "data_size": "1.330 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": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "4635675", "Number of Sequences": "78", "Longest Sequences (bp)": "338504", "N50 (bp)": "97894", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "50.7", "Number of CDSs": "4317", "Average Protein Length": "313.6", "Coding Ratio (%)": "87.6", "Number of rRNAs": "0", "Number of tRNAs": "55", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Shigella boydii", "strain": "strain=DMB SH130", "accession": "GCA_003572535.1", "taxid": 621, "species_taxid": 621, "relation_to_type": "type", "validated": true, "ani": 98.3658, "matched_fragments": 1034, "total_fragments": 1509, "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": 98.2483, "matched_fragments": 1334, "total_fragments": 1509, "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": 98.2006, "matched_fragments": 1333, "total_fragments": 1509, "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": 98.0908, "matched_fragments": 1241, "total_fragments": 1509, "ani_threshold": 95, "status": "indistinguishable" }, { "organism_name": "Shigella boydii", "strain": "strain=NCTC12985", "accession": "GCA_900457095.1", "taxid": 621, "species_taxid": 621, "relation_to_type": "type", "validated": true, "ani": 98.076, "matched_fragments": 1248, "total_fragments": 1509, "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": 97.9108, "matched_fragments": 1286, "total_fragments": 1509, "ani_threshold": 95, "status": "indistinguishable" }, { "organism_name": "Shigella dysenteriae", "strain": "strain=ATCC 13313", "accession": "GCA_002949675.1", "taxid": 622, "species_taxid": 622, "relation_to_type": "suspected-type", "validated": true, "ani": 97.0525, "matched_fragments": 1186, "total_fragments": 1509, "ani_threshold": 95, "status": "indistinguishable" }, { "organism_name": "Shigella dysenteriae", "strain": "strain=NCTC4837", "accession": "GCA_900457215.1", "taxid": 622, "species_taxid": 622, "relation_to_type": "suspected-type", "validated": true, "ani": 97.0069, "matched_fragments": 1182, "total_fragments": 1509, "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": 96.8463, "matched_fragments": 1283, "total_fragments": 1509, "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": 96.8463, "matched_fragments": 1306, "total_fragments": 1509, "ani_threshold": 95, "status": "indistinguishable" }, { "organism_name": "Escherichia coli", "strain": "strain=DSM 30083", "accession": "GCA_000690815.1", "taxid": 562, "species_taxid": 562, "relation_to_type": "neotype", "validated": true, "ani": 96.8279, "matched_fragments": 1315, "total_fragments": 1509, "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": 96.7602, "matched_fragments": 1322, "total_fragments": 1509, "ani_threshold": 95, "status": "indistinguishable" }, { "organism_name": "Escherichia albertii", "strain": "strain=NBRC 107761", "accession": "GCA_000759775.1", "taxid": 208962, "species_taxid": 208962, "relation_to_type": "type", "validated": true, "ani": 90.0906, "matched_fragments": 1082, "total_fragments": 1509, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Escherichia albertii", "strain": "strain=DSM 17582", "accession": "GCA_022833075.1", "taxid": 208962, "species_taxid": 208962, "relation_to_type": "type", "validated": true, "ani": 90.0013, "matched_fragments": 1163, "total_fragments": 1509, "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": 82.0304, "matched_fragments": 851, "total_fragments": 1509, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003697165.2", "gtdb_species": "s__Escherichia coli", "ani": 96.8474, "matched_fragments": 1306, "total_fragments": 1509, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.07", "min_intra_species_ani": "95.57", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.72", "num_clustered_genomes": 26859, "status": "conclusive" }, { "accession": "GCF_002965065.1", "gtdb_species": "s__Escherichia sp002965065", "ani": 94.4533, "matched_fragments": 1106, "total_fragments": 1509, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia", "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_004211955.1", "gtdb_species": "s__Escherichia sp004211955", "ani": 93.0517, "matched_fragments": 1239, "total_fragments": 1509, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_005843885.1", "gtdb_species": "s__Escherichia sp005843885", "ani": 92.8322, "matched_fragments": 1262, "total_fragments": 1509, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.83", "min_intra_species_ani": "95.39", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.80", "num_clustered_genomes": 37, "status": "-" }, { "accession": "GCF_902498915.1", "gtdb_species": "s__Escherichia ruysiae", "ani": 92.8147, "matched_fragments": 1261, "total_fragments": 1509, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.82", "min_intra_species_ani": "96.45", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.86", "num_clustered_genomes": 36, "status": "-" }, { "accession": "GCF_011881725.1", "gtdb_species": "s__Escherichia coli_E", "ani": 92.2838, "matched_fragments": 1178, "total_fragments": 1509, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia", "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_001660175.1", "gtdb_species": "s__Escherichia sp001660175", "ani": 91.8542, "matched_fragments": 1260, "total_fragments": 1509, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.53", "min_intra_species_ani": "99.22", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002900365.1", "gtdb_species": "s__Escherichia marmotae", "ani": 91.0739, "matched_fragments": 1243, "total_fragments": 1509, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.02", "min_intra_species_ani": "98.77", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.85", "num_clustered_genomes": 82, "status": "-" }, { "accession": "GCF_000026225.1", "gtdb_species": "s__Escherichia fergusonii", "ani": 90.8977, "matched_fragments": 1090, "total_fragments": 1509, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.80", "min_intra_species_ani": "98.39", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 77, "status": "-" }, { "accession": "GCF_000759775.1", "gtdb_species": "s__Escherichia albertii", "ani": 90.1048, "matched_fragments": 1081, "total_fragments": 1509, "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": -0.288, "cell_length": 0.301, "doubling_h": -0.472, "growth_tmp": 37.875, "optimum_tmp": 36.971, "optimum_ph": 6.75, "genome_size": 5146432.283, "gc_content": 50.433, "coding_genes": 4934.661, "rRNA16S_genes": 7.101, "tRNA_genes": 90.772, "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 }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Enterobacterales", "f__Enterobacteriaceae", "g__Escherichia", "s__Escherichia coli" ], "_genome_taxon": [ "Escherichia", "coli", "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Enterobacterales", "f__Enterobacteriaceae", "g__Escherichia", "s__Escherichia coli", "Bacteria", "Pseudomonadota", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia", "Escherichia", "coli" ], "_meo": [ { "id": "MEO_0000054", "label": "feces" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }