{ "type": "genome", "identifier": "GCA_018369555.1", "organism": "Thomasclavelia spiroformis", "title": "Thomasclavelia spiroformis", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "University of California, Berkeley", "publication": [ {} ], "properties": { "assembly_accession": "GCA_018369555.1", "bioproject": "PRJNA698986", "biosample": "SAMN17800701", "wgs_master": "JAGZCC000000000.1", "refseq_category": "na", "taxid": "29348", "species_taxid": "29348", "organism_name": "Thomasclavelia spiroformis", "infraspecific_name": "", "isolate": "L3_108_000G1_dasL3_108_000G1_metabat.metabat.11", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/05/16", "asm_name": "ASM1836955v1", "submitter": "University of California, Berkeley", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/018/369/555/GCA_018369555.1_ASM1836955v1", "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": "2021-05-16", "dateModified": "2021-05-16", "datePublished": "2021-05-16", "_annotation": { "sample_count": 1, "sample_organism": [ "Thomasclavelia spiroformis" ], "sample_taxid": [ "29348" ], "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": "0.638 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)": "2323706", "Number of Sequences": "132", "Longest Sequences (bp)": "72385", "N50 (bp)": "29029", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "28.5", "Number of CDSs": "2122", "Average Protein Length": "306.7", "Coding Ratio (%)": "84.0", "Number of rRNAs": "0", "Number of tRNAs": "27", "Number of CRISPRs": "5" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "[Clostridium] spiroforme", "strain": "strain=DSM 1552", "accession": "GCA_000154805.1", "taxid": 29348, "species_taxid": 29348, "relation_to_type": "type", "validated": true, "ani": 91.3701, "matched_fragments": 595, "total_fragments": 708, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Clostridium] spiroforme", "strain": "strain=DSM 1552", "accession": "GCA_025149465.1", "taxid": 29348, "species_taxid": 29348, "relation_to_type": "type", "validated": true, "ani": 91.3552, "matched_fragments": 598, "total_fragments": 708, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Clostridium] cocleatum", "strain": "strain=DSM 1551", "accession": "GCA_024622895.1", "taxid": 69824, "species_taxid": 69824, "relation_to_type": "type", "validated": true, "ani": 81.3678, "matched_fragments": 422, "total_fragments": 708, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Clostridium] cocleatum", "strain": "strain=DSM 1551", "accession": "GCA_900102365.1", "taxid": 69824, "species_taxid": 69824, "relation_to_type": "type", "validated": true, "ani": 81.3558, "matched_fragments": 425, "total_fragments": 708, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Clostridium] cocleatum", "strain": "strain=I50", "accession": "GCA_010206155.1", "taxid": 69824, "species_taxid": 69824, "relation_to_type": "type", "validated": true, "ani": 81.3381, "matched_fragments": 424, "total_fragments": 708, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Clostridium] cocleatum", "strain": "strain=ATCC 29902", "accession": "GCA_002803405.1", "taxid": 69824, "species_taxid": 69824, "relation_to_type": "type", "validated": true, "ani": 81.3016, "matched_fragments": 430, "total_fragments": 708, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Clostridium] saccharogumia", "strain": "strain=DSM 17460", "accession": "GCA_000686665.1", "taxid": 341225, "species_taxid": 341225, "relation_to_type": "type", "validated": true, "ani": 81.0829, "matched_fragments": 410, "total_fragments": 708, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Erysipelatoclostridium ramosum", "strain": "", "accession": "GCA_900660185.1", "taxid": 1547, "species_taxid": 1547, "relation_to_type": "type", "validated": true, "ani": 80.307, "matched_fragments": 343, "total_fragments": 708, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Erysipelatoclostridium ramosum", "strain": "strain=FDAARGOS_906", "accession": "GCA_016027135.1", "taxid": 1547, "species_taxid": 1547, "relation_to_type": "type", "validated": true, "ani": 80.2985, "matched_fragments": 355, "total_fragments": 708, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Erysipelatoclostridium ramosum", "strain": "strain=DSM 1402", "accession": "GCA_014131695.1", "taxid": 1547, "species_taxid": 1547, "relation_to_type": "type", "validated": true, "ani": 80.2383, "matched_fragments": 344, "total_fragments": 708, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tannockella kyphosi", "strain": "strain=BP52G", "accession": "GCA_021054785.1", "taxid": 2899121, "species_taxid": 2899121, "relation_to_type": "type", "validated": true, "ani": 77.8041, "matched_fragments": 140, "total_fragments": 708, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Longibaculum muris", "strain": "strain=DSM 29487", "accession": "GCA_024622235.1", "taxid": 1796628, "species_taxid": 1796628, "relation_to_type": "type", "validated": true, "ani": 77.6741, "matched_fragments": 176, "total_fragments": 708, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Longibaculum muris", "strain": "strain=DSM 29487", "accession": "GCA_004343035.1", "taxid": 1796628, "species_taxid": 1796628, "relation_to_type": "type", "validated": true, "ani": 77.6525, "matched_fragments": 178, "total_fragments": 708, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_018369555.1", "gtdb_species": "s__Erysipelatoclostridium spiroforme_A", "ani": 100.0, "matched_fragments": 697, "total_fragments": 708, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium", "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": "conclusive" }, { "accession": "GCF_000154805.1", "gtdb_species": "s__Erysipelatoclostridium spiroforme", "ani": 91.376, "matched_fragments": 594, "total_fragments": 708, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.13", "min_intra_species_ani": "96.38", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.79", "num_clustered_genomes": 13, "status": "-" }, { "accession": "GCF_900102365.1", "gtdb_species": "s__Erysipelatoclostridium cocleatum", "ani": 81.3658, "matched_fragments": 424, "total_fragments": 708, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.07", "min_intra_species_ani": "98.04", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.85", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000686665.1", "gtdb_species": "s__Erysipelatoclostridium saccharogumia", "ani": 81.159, "matched_fragments": 405, "total_fragments": 708, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_000508865.1", "gtdb_species": "s__Erysipelatoclostridium sp000508865", "ani": 80.8694, "matched_fragments": 412, "total_fragments": 708, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium", "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_014131695.1", "gtdb_species": "s__Erysipelatoclostridium ramosum", "ani": 80.2475, "matched_fragments": 343, "total_fragments": 708, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.66", "min_intra_species_ani": "99.35", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.87", "num_clustered_genomes": 70, "status": "-" }, { "accession": "GCF_002160495.1", "gtdb_species": "s__Erysipelatoclostridium merdavium", "ani": 80.2341, "matched_fragments": 341, "total_fragments": 708, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.70", "min_intra_species_ani": "98.24", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.83", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_017889095.1", "gtdb_species": "s__Erysipelatoclostridium sp017889095", "ani": 78.9623, "matched_fragments": 261, "total_fragments": 708, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium", "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_003480255.1", "gtdb_species": "s__Faecalibacillus sp003480255", "ani": 78.9015, "matched_fragments": 197, "total_fragments": 708, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.06", "min_intra_species_ani": "98.20", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.84", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_900544435.1", "gtdb_species": "s__Faecalibacillus sp900544435", "ani": 78.0611, "matched_fragments": 176, "total_fragments": 708, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.05", "min_intra_species_ani": "98.83", "mean_intra_species_af": "0.79", "min_intra_species_af": "0.74", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_gtdb_taxon": [ "d__Bacteria", "p__Bacillota_I", "c__Bacilli_A", "o__Erysipelotrichales", "f__Coprobacillaceae", "g__Thomasclavelia", "s__Thomasclavelia spiroformis_A" ], "_genome_taxon": [ "Thomasclavelia", "spiroformis", "d__Bacteria", "p__Bacillota_I", "c__Bacilli_A", "o__Erysipelotrichales", "f__Coprobacillaceae", "g__Thomasclavelia", "s__Thomasclavelia spiroformis_A", "Bacteria", "Bacillota", "I", "Bacilli", "A", "Erysipelotrichales", "Coprobacillaceae", "Thomasclavelia", "Thomasclavelia", "spiroformis", "A" ], "_meo": [ { "id": "MEO_0000054", "label": "feces" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }