{ "type": "genome", "identifier": "GCF_014131695.1", "organism": "Thomasclavelia ramosa DSM 1402", "title": "Thomasclavelia ramosa DSM 1402", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Helmholtz Centre for Environmental Research - UFZ", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014131695.1", "bioproject": "PRJNA224116", "biosample": "SAMN10972983", "wgs_master": "na", "refseq_category": "na", "taxid": "445974", "species_taxid": "1547", "organism_name": "Thomasclavelia ramosa DSM 1402", "infraspecific_name": "strain=DSM 1402", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/08/10", "asm_name": "ASM1413169v1", "asm_submitter": "Helmholtz Centre for Environmental Research - UFZ", "gbrs_paired_asm": "GCA_014131695.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/131/695/GCF_014131695.1_ASM1413169v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3247604", "genome_size_ungapped": "3247604", "gc_percent": "31.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-03-08", "total_gene_count": "3132", "protein_coding_gene_count": "3029", "non_coding_gene_count": "83", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-08-10", "dateModified": "2020-08-10", "datePublished": "2020-08-10", "_annotation": { "sample_count": 1, "sample_organism": [ "Thomasclavelia ramosa DSM 1402" ], "sample_taxid": [ "445974" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not determined" ], "sample_host_location_id": [], "data_size": "0.892 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": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3247604", "Number of Sequences": "1", "Longest Sequences (bp)": "3247604", "N50 (bp)": "3247604", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "31.5", "Number of CDSs": "3093", "Average Protein Length": "308.4", "Coding Ratio (%)": "88.1", "Number of rRNAs": "18", "Number of tRNAs": "62", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Erysipelatoclostridium ramosum", "strain": "strain=DSM 1402", "accession": "GCA_014131695.1", "taxid": 1547, "species_taxid": 1547, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1079, "total_fragments": 1082, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Erysipelatoclostridium ramosum", "strain": "strain=FDAARGOS_906", "accession": "GCA_016027135.1", "taxid": 1547, "species_taxid": 1547, "relation_to_type": "type", "validated": true, "ani": 99.998, "matched_fragments": 1076, "total_fragments": 1082, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Erysipelatoclostridium ramosum", "strain": "strain=DSM 1402", "accession": "GCA_000154485.1", "taxid": 1547, "species_taxid": 1547, "relation_to_type": "type", "validated": true, "ani": 99.993, "matched_fragments": 1068, "total_fragments": 1082, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Erysipelatoclostridium ramosum", "strain": "", "accession": "GCA_900660185.1", "taxid": 1547, "species_taxid": 1547, "relation_to_type": "type", "validated": true, "ani": 99.7388, "matched_fragments": 1018, "total_fragments": 1082, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "[Clostridium] cocleatum", "strain": "strain=I50", "accession": "GCA_010206155.1", "taxid": 69824, "species_taxid": 69824, "relation_to_type": "type", "validated": true, "ani": 81.165, "matched_fragments": 455, "total_fragments": 1082, "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": 80.327, "matched_fragments": 393, "total_fragments": 1082, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Clostridium] spiroforme", "strain": "strain=DSM 1552", "accession": "GCA_000154805.1", "taxid": 29348, "species_taxid": 29348, "relation_to_type": "type", "validated": true, "ani": 80.2495, "matched_fragments": 391, "total_fragments": 1082, "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": 78.8974, "matched_fragments": 153, "total_fragments": 1082, "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": 78.1792, "matched_fragments": 215, "total_fragments": 1082, "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": 78.0732, "matched_fragments": 217, "total_fragments": 1082, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014131695.1", "gtdb_species": "s__Erysipelatoclostridium ramosum", "ani": 100.0, "matched_fragments": 1078, "total_fragments": 1082, "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": "conclusive" }, { "accession": "GCF_900102365.1", "gtdb_species": "s__Erysipelatoclostridium cocleatum", "ani": 81.0601, "matched_fragments": 449, "total_fragments": 1082, "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": 80.4254, "matched_fragments": 443, "total_fragments": 1082, "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": 80.2813, "matched_fragments": 428, "total_fragments": 1082, "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_000154805.1", "gtdb_species": "s__Erysipelatoclostridium spiroforme", "ani": 80.2646, "matched_fragments": 390, "total_fragments": 1082, "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": "GCA_018369555.1", "gtdb_species": "s__Erysipelatoclostridium spiroforme_A", "ani": 80.1546, "matched_fragments": 362, "total_fragments": 1082, "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_002160495.1", "gtdb_species": "s__Erysipelatoclostridium merdavium", "ani": 79.9765, "matched_fragments": 449, "total_fragments": 1082, "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": "GCF_003480255.1", "gtdb_species": "s__Faecalibacillus sp003480255", "ani": 78.5748, "matched_fragments": 237, "total_fragments": 1082, "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_900538465.1", "gtdb_species": "s__Longibaculum sp900538465", "ani": 78.0552, "matched_fragments": 184, "total_fragments": 1082, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Longibaculum", "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": "-" } ] }, "_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 }, "_genome_taxon": [ "Thomasclavelia", "ramosa", "DSM", "1402" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }