{ "type": "genome", "identifier": "GCF_008580445.1", "organism": "Clostridium diolis", "title": "Clostridium diolis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Central Region Agricultural Research Center, NARO", "publication": [ {} ], "properties": { "assembly_accession": "GCF_008580445.1", "bioproject": "PRJNA224116", "biosample": "SAMD00172919", "wgs_master": "BJLA00000000.1", "refseq_category": "na", "taxid": "223919", "species_taxid": "223919", "organism_name": "Clostridium diolis", "infraspecific_name": "strain=DSM 15410", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/09/05", "asm_name": "ASM858044v1", "asm_submitter": "Central Region Agricultural Research Center, NARO", "gbrs_paired_asm": "GCA_008580445.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/008/580/445/GCF_008580445.1_ASM858044v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5867817", "genome_size_ungapped": "5863768", "gc_percent": "29.500000", "replicon_count": "0", "scaffold_count": "85", "contig_count": "85", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_008580445.1-RS_2024_09_09", "annotation_date": "2024-09-09", "total_gene_count": "5308", "protein_coding_gene_count": "5117", "non_coding_gene_count": "127", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-09-05", "dateModified": "2019-09-05", "datePublished": "2019-09-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Clostridium diolis" ], "sample_taxid": [ "223919" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not applicable" ], "sample_host_location_id": [], "data_size": "1.606 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)": "5867817", "Number of Sequences": "85", "Longest Sequences (bp)": "676133", "N50 (bp)": "210325", "Gap Ratio (%)": "0.069004", "GCcontent (%)": "29.7", "Number of CDSs": "5208", "Average Protein Length": "302.1", "Coding Ratio (%)": "80.4", "Number of rRNAs": "16", "Number of tRNAs": "55", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Clostridium diolis", "strain": "strain=DSM 15410", "accession": "GCA_008580445.1", "taxid": 223919, "species_taxid": 223919, "relation_to_type": "suspected-type", "validated": true, "ani": 100.0, "matched_fragments": 1921, "total_fragments": 1924, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Clostridium diolis", "strain": "strain=DSM 15410", "accession": "GCA_008705175.1", "taxid": 223919, "species_taxid": 223919, "relation_to_type": "suspected-type", "validated": true, "ani": 99.9956, "matched_fragments": 1924, "total_fragments": 1924, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Clostridium beijerinckii", "strain": "strain=DSM 791", "accession": "GCA_018223745.1", "taxid": 1520, "species_taxid": 1520, "relation_to_type": "suspected-type", "validated": true, "ani": 98.2279, "matched_fragments": 1701, "total_fragments": 1924, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Clostridium beijerinckii", "strain": "strain=DSM 791", "accession": "GCA_002006445.1", "taxid": 1520, "species_taxid": 1520, "relation_to_type": "suspected-type", "validated": true, "ani": 98.2011, "matched_fragments": 1590, "total_fragments": 1924, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Clostridium beijerinckii", "strain": "strain=NCTC13035", "accession": "GCA_900447025.1", "taxid": 1520, "species_taxid": 1520, "relation_to_type": "suspected-type", "validated": true, "ani": 98.1568, "matched_fragments": 1703, "total_fragments": 1924, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Clostridium gelidum", "strain": "strain=C5S11", "accession": "GCA_019977655.1", "taxid": 704125, "species_taxid": 704125, "relation_to_type": "type", "validated": true, "ani": 81.107, "matched_fragments": 929, "total_fragments": 1924, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium butyricum", "strain": "strain=NBRC 13949", "accession": "GCA_006742065.1", "taxid": 1492, "species_taxid": 1492, "relation_to_type": "type", "validated": true, "ani": 78.7739, "matched_fragments": 494, "total_fragments": 1924, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium butyricum", "strain": "strain=DSM 10702", "accession": "GCA_014131795.1", "taxid": 1492, "species_taxid": 1492, "relation_to_type": "type", "validated": true, "ani": 78.7342, "matched_fragments": 503, "total_fragments": 1924, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium butyricum", "strain": "strain=NBRC 13949", "accession": "GCA_007992895.1", "taxid": 1492, "species_taxid": 1492, "relation_to_type": "type", "validated": true, "ani": 78.5812, "matched_fragments": 483, "total_fragments": 1924, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium butyricum", "strain": "strain=DSM 10702", "accession": "GCA_000409755.1", "taxid": 1492, "species_taxid": 1492, "relation_to_type": "type", "validated": true, "ani": 78.3523, "matched_fragments": 491, "total_fragments": 1924, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium thailandense", "strain": "strain=PL3", "accession": "GCA_019207025.1", "taxid": 2794346, "species_taxid": 2794346, "relation_to_type": "type", "validated": true, "ani": 76.7221, "matched_fragments": 273, "total_fragments": 1924, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium muellerianum", "strain": "strain=P21", "accession": "GCA_012926525.1", "taxid": 2716538, "species_taxid": 2716538, "relation_to_type": "type", "validated": true, "ani": 76.4792, "matched_fragments": 248, "total_fragments": 1924, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium simiarum", "strain": "strain=MSJ-4", "accession": "GCA_018919175.1", "taxid": 2841506, "species_taxid": 2841506, "relation_to_type": "type", "validated": true, "ani": 76.0314, "matched_fragments": 144, "total_fragments": 1924, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_018223745.1", "gtdb_species": "s__Clostridium beijerinckii", "ani": 98.2488, "matched_fragments": 1699, "total_fragments": 1924, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.01", "min_intra_species_ani": "95.18", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.79", "num_clustered_genomes": 244, "status": "conclusive" }, { "accession": "GCF_000621745.1", "gtdb_species": "s__Clostridium beijerinckii_A", "ani": 92.3252, "matched_fragments": 1530, "total_fragments": 1924, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "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_002029255.1", "gtdb_species": "s__Clostridium chromiireducens", "ani": 82.9076, "matched_fragments": 1014, "total_fragments": 1924, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.07", "min_intra_species_ani": "97.40", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000230835.1", "gtdb_species": "s__Clostridium sp000230835", "ani": 81.9864, "matched_fragments": 1028, "total_fragments": 1924, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.12", "min_intra_species_ani": "96.12", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.82", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002760435.1", "gtdb_species": "s__Clostridium sp002760435", "ani": 81.7578, "matched_fragments": 949, "total_fragments": 1924, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_003129525.1", "gtdb_species": "s__Clostridium beijerinckii_D", "ani": 81.4724, "matched_fragments": 839, "total_fragments": 1924, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "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_000340885.1", "gtdb_species": "s__Clostridium saccharoperbutylacetonicum", "ani": 80.8449, "matched_fragments": 914, "total_fragments": 1924, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.35", "min_intra_species_ani": "98.00", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.89", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_002006345.1", "gtdb_species": "s__Clostridium puniceum", "ani": 80.8253, "matched_fragments": 842, "total_fragments": 1924, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "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_000473995.1", "gtdb_species": "s__Clostridium saccharobutylicum", "ani": 80.4619, "matched_fragments": 782, "total_fragments": 1924, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.89", "min_intra_species_ani": "95.82", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.83", "num_clustered_genomes": 65, "status": "-" }, { "accession": "GCF_009928485.1", "gtdb_species": "s__Clostridium sp009928485", "ani": 80.3714, "matched_fragments": 850, "total_fragments": 1924, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "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_006742065.1", "gtdb_species": "s__Clostridium butyricum", "ani": 78.7295, "matched_fragments": 493, "total_fragments": 1924, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.58", "min_intra_species_ani": "97.46", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.80", "num_clustered_genomes": 64, "status": "-" }, { "accession": "GCF_001735765.2", "gtdb_species": "s__Clostridium taeniosporum", "ani": 78.1031, "matched_fragments": 407, "total_fragments": 1924, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "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": -0.155, "cell_length": 0.079, "doubling_h": 0.353, "growth_tmp": 35.0, "optimum_tmp": 35.173, "optimum_ph": 6.947, "genome_size": 5853885.0, "gc_content": 29.49, "coding_genes": 3796.985, "rRNA16S_genes": 9.374, "tRNA_genes": 78.312, "gram_stain": 1.0, "sporulation": 0.967, "motility": 0.92, "range_salinity": 0.0, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 0.944, "thermophilic_range_tmp": 0.055, "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": [ "Clostridium", "diolis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }