{ "type": "genome", "identifier": "GCA_018371155.1", "organism": "Clostridioides difficile", "title": "Clostridioides difficile", "description": "unverified source organism; derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "University of California, Berkeley", "publication": [ {} ], "properties": { "assembly_accession": "GCA_018371155.1", "bioproject": "PRJNA698986", "biosample": "SAMN17801621", "wgs_master": "JAHALM000000000.1", "refseq_category": "na", "taxid": "1496", "species_taxid": "1496", "organism_name": "Clostridioides difficile", "infraspecific_name": "", "isolate": "L2_041_000G1_dasL2_041_000G1_concoct_33", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/05/16", "asm_name": "ASM1837115v1", "submitter": "University of California, Berkeley", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/018/371/155/GCA_018371155.1_ASM1837115v1", "excluded_from_refseq": "unverified source organism; derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-05-16", "dateModified": "2021-05-16", "datePublished": "2021-05-16", "_annotation": { "sample_count": 1, "sample_organism": [ "Clostridioides difficile" ], "sample_taxid": [ "1496" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Pittsburgh, Magee-Womens Hospital of UPMC" ], "sample_host_location_id": [], "data_size": "0.786 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)": "2838866", "Number of Sequences": "29", "Longest Sequences (bp)": "353436", "N50 (bp)": "186168", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "30.4", "Number of CDSs": "2697", "Average Protein Length": "296.0", "Coding Ratio (%)": "84.4", "Number of rRNAs": "1", "Number of tRNAs": "24", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Clostridioides mangenotii", "strain": "strain=DSM 1289", "accession": "GCA_017873185.1", "taxid": 1540, "species_taxid": 1540, "relation_to_type": "suspected-type", "validated": true, "ani": 83.9288, "matched_fragments": 701, "total_fragments": 930, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Clostridium] dakarense", "strain": "strain=FF1", "accession": "GCA_000499525.1", "taxid": 1301100, "species_taxid": 1301100, "relation_to_type": "type", "validated": true, "ani": 77.7917, 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"ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Romboutsia ilealis", "strain": "strain=CRIB", "accession": "GCA_900015215.1", "taxid": 1115758, "species_taxid": 1115758, "relation_to_type": "type", "validated": true, "ani": 77.5327, "matched_fragments": 148, "total_fragments": 930, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paeniclostridium sordellii", "strain": "strain=ATCC9714", "accession": "GCA_000953675.1", "taxid": 1505, "species_taxid": 1505, "relation_to_type": "type", "validated": true, "ani": 77.3207, "matched_fragments": 189, "total_fragments": 930, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Intestinibacter bartlettii", "strain": "strain=DSM 16795", "accession": "GCA_900167285.1", "taxid": 261299, "species_taxid": 261299, "relation_to_type": "type", "validated": true, "ani": 77.2926, "matched_fragments": 124, "total_fragments": 930, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Romboutsia hominis", "strain": "strain=FRIFI", "accession": "GCA_900002575.1", "taxid": 1507512, "species_taxid": 1507512, "relation_to_type": "type", "validated": true, "ani": 77.2725, "matched_fragments": 181, "total_fragments": 930, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Terrisporobacter glycolicus", "strain": "strain=DSM 1288", "accession": "GCA_000439105.1", "taxid": 36841, "species_taxid": 36841, "relation_to_type": "suspected-type", "validated": true, "ani": 77.2279, "matched_fragments": 154, "total_fragments": 930, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Romboutsia timonensis", "strain": "strain=Marseille-P326", "accession": "GCA_900106845.1", "taxid": 1776391, "species_taxid": 1776391, "relation_to_type": "type", "validated": true, "ani": 77.2246, "matched_fragments": 170, "total_fragments": 930, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Terrisporobacter glycolicus", "strain": "strain=ATCC 14880", "accession": "GCA_000373865.1", "taxid": 36841, "species_taxid": 36841, "relation_to_type": "suspected-type", "validated": true, "ani": 77.2152, "matched_fragments": 154, "total_fragments": 930, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Terrisporobacter petrolearius", "strain": "strain=LAM0A37", "accession": "GCA_020748185.1", "taxid": 1460447, "species_taxid": 1460447, "relation_to_type": "type", "validated": true, "ani": 77.1328, "matched_fragments": 151, "total_fragments": 930, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Peptacetobacter hiranonis", "strain": "strain=DSM 13275", "accession": "GCA_008151785.1", "taxid": 89152, "species_taxid": 89152, "relation_to_type": "type", "validated": true, "ani": 76.9179, "matched_fragments": 111, "total_fragments": 930, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tepidibacter thalassicus", "strain": "strain=DSM 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"GCF_018917235.1", "gtdb_species": "s__Clostridioides_A sp002390935", "ani": 96.4064, "matched_fragments": 849, "total_fragments": 930, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Clostridioides_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.42", "min_intra_species_ani": "96.30", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_017873185.1", "gtdb_species": "s__Clostridioides_A mangenotii", "ani": 83.9342, "matched_fragments": 701, "total_fragments": 930, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Clostridioides_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.86", "min_intra_species_ani": "96.86", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { 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