{ "type": "genome", "identifier": "GCF_024341905.1", "organism": "Clostridium folliculivorans", "title": "Clostridium folliculivorans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Research Center of Genetic Resources, NARO", "publication": [ {} ], "properties": { "assembly_accession": "GCF_024341905.1", "bioproject": "PRJNA224116", "biosample": "SAMD00451122", "wgs_master": "BQXY00000000.1", "refseq_category": "reference genome", "taxid": "2886038", "species_taxid": "2886038", "organism_name": "Clostridium folliculivorans", "infraspecific_name": "strain=D1-1", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/06/20", "asm_name": "ASM2434190v1", "asm_submitter": "Research Center of Genetic Resources, NARO", "gbrs_paired_asm": "GCA_024341905.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/024/341/905/GCF_024341905.1_ASM2434190v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5358041", "genome_size_ungapped": "5357482", "gc_percent": "31.000000", "replicon_count": "0", "scaffold_count": "61", "contig_count": "61", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_024341905.1-RS_2024_05_13", "annotation_date": "2024-05-13", "total_gene_count": "4778", "protein_coding_gene_count": "4620", "non_coding_gene_count": "115", "pubmed_id": "37103467" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-06-20", "dateModified": "2022-06-20", "datePublished": "2022-06-20", "_annotation": { "sample_count": 1, "sample_organism": [ "Clostridium folliculivorans" ], "sample_taxid": [ "2886038" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan:Ibaraki, Tsukubamirai" ], "sample_host_location_id": [], "data_size": "1.475 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5358041", "Number of Sequences": "61", "Longest Sequences (bp)": "1431126", "N50 (bp)": "625199", "Gap Ratio (%)": "0.010433", "GCcontent (%)": "31.0", "Number of CDSs": "4721", "Average Protein Length": "306.5", "Coding Ratio (%)": "81.0", "Number of rRNAs": "2", "Number of tRNAs": "69", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Clostridium fungisolvens", "strain": "strain=TW1", "accession": "GCA_014193895.1", "taxid": 1604897, "species_taxid": 1604897, "relation_to_type": "type", "validated": true, "ani": 91.2402, "matched_fragments": 1515, "total_fragments": 1768, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium zeae", "strain": "strain=CSC2", "accession": "GCA_017312485.1", "taxid": 2759022, "species_taxid": 2759022, "relation_to_type": "type", "validated": true, "ani": 90.118, "matched_fragments": 1482, "total_fragments": 1768, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium manihotivorum", "strain": "strain=CT4", "accession": "GCA_004015185.1", "taxid": 2320868, "species_taxid": 2320868, "relation_to_type": "type", "validated": true, "ani": 81.0212, "matched_fragments": 856, "total_fragments": 1768, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium polyendosporum", "strain": "strain=JCM 30710", "accession": "GCA_018332455.1", "taxid": 69208, "species_taxid": 69208, "relation_to_type": "type", "validated": true, "ani": 77.3929, "matched_fragments": 243, "total_fragments": 1768, "ani_threshold": 95, "status": "below_threshold" }, { "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": 77.1314, "matched_fragments": 222, "total_fragments": 1768, "ani_threshold": 95, "status": "below_threshold" }, { "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": 77.1116, "matched_fragments": 223, "total_fragments": 1768, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium nigeriense", "strain": "strain=Marseille-P2414", "accession": "GCA_900086595.1", "taxid": 1805470, "species_taxid": 1805470, "relation_to_type": "type", "validated": true, "ani": 77.0383, "matched_fragments": 176, "total_fragments": 1768, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium tertium", "strain": "strain=DSM 2485", "accession": "GCA_017873245.1", "taxid": 1559, "species_taxid": 1559, "relation_to_type": "type", "validated": true, "ani": 76.9512, "matched_fragments": 191, "total_fragments": 1768, "ani_threshold": 95, "status": "below_threshold" }, { "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": 76.923, "matched_fragments": 211, "total_fragments": 1768, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium gelidum", "strain": "strain=C5S11", "accession": "GCA_019977655.1", "taxid": 704125, "species_taxid": 704125, "relation_to_type": "type", "validated": true, "ani": 76.9191, "matched_fragments": 225, "total_fragments": 1768, "ani_threshold": 95, "status": "below_threshold" }, { "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": 76.907, "matched_fragments": 226, "total_fragments": 1768, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium chauvoei", "strain": "strain=DSM 7528", "accession": "GCA_002327185.1", "taxid": 46867, "species_taxid": 46867, "relation_to_type": "type", "validated": true, "ani": 76.8965, "matched_fragments": 174, "total_fragments": 1768, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium neonatale", "strain": "strain=LCDC 99A005", "accession": "GCA_002553615.1", "taxid": 137838, "species_taxid": 137838, "relation_to_type": "type", "validated": true, "ani": 76.686, "matched_fragments": 172, "total_fragments": 1768, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium neonatale", "strain": "strain=LCDC no.99-A-005", "accession": "GCA_001458595.1", "taxid": 137838, "species_taxid": 137838, "relation_to_type": "type", "validated": true, "ani": 76.6783, "matched_fragments": 174, "total_fragments": 1768, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium gallinarum", "strain": "strain=Sa3CUN1", "accession": "GCA_014836325.1", "taxid": 2762246, "species_taxid": 2762246, "relation_to_type": "type", "validated": true, "ani": 76.6703, "matched_fragments": 188, "total_fragments": 1768, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium chrysemydis", "strain": "strain=PT", "accession": "GCA_015234215.1", "taxid": 2665504, "species_taxid": 2665504, "relation_to_type": "type", "validated": true, "ani": 76.6582, "matched_fragments": 140, "total_fragments": 1768, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium weizhouense", "strain": "strain=YB-6", "accession": "GCA_019431045.1", "taxid": 2859781, "species_taxid": 2859781, "relation_to_type": "type", "validated": true, "ani": 76.631, "matched_fragments": 201, "total_fragments": 1768, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium cibarium", "strain": "strain=Sa3CVN1", "accession": "GCA_014836335.1", "taxid": 2762247, "species_taxid": 2762247, "relation_to_type": "type", "validated": true, "ani": 76.5967, "matched_fragments": 173, "total_fragments": 1768, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium massiliamazoniense", "strain": "strain=ND2", "accession": "GCA_001403635.1", "taxid": 1347366, "species_taxid": 1347366, "relation_to_type": "type", "validated": true, "ani": 76.5227, "matched_fragments": 181, "total_fragments": 1768, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium hydrogenum", "strain": "strain=CUEA01", "accession": "GCA_021432385.1", "taxid": 2855764, "species_taxid": 2855764, "relation_to_type": "type", "validated": true, "ani": 76.5099, "matched_fragments": 149, "total_fragments": 1768, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium mobile", "strain": "strain=MSJ-11", "accession": "GCA_018918285.1", "taxid": 2841512, "species_taxid": 2841512, "relation_to_type": "type", "validated": true, "ani": 75.8665, "matched_fragments": 120, "total_fragments": 1768, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014193895.1", "gtdb_species": "s__Clostridium_AR fungisolvens", "ani": 91.2386, "matched_fragments": 1515, "total_fragments": 1768, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR", "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_017312485.1", "gtdb_species": "s__Clostridium_AR sp017312485", "ani": 90.1104, "matched_fragments": 1483, "total_fragments": 1768, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR", "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_016595795.1", "gtdb_species": "s__Clostridium_AR sp016595795", "ani": 89.5066, "matched_fragments": 1361, "total_fragments": 1768, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR", "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_004015185.1", "gtdb_species": "s__Clostridium_AR sp004015185", "ani": 80.9862, "matched_fragments": 862, "total_fragments": 1768, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR", "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_009928445.1", "gtdb_species": "s__Clostridium_AR sp009928445", "ani": 80.9692, "matched_fragments": 843, "total_fragments": 1768, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR", "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_003606265.1", "gtdb_species": "s__Clostridium septicum", "ani": 77.1997, "matched_fragments": 161, "total_fragments": 1768, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.65", "min_intra_species_ani": "99.48", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_001458595.1", "gtdb_species": "s__Clostridium neonatale", "ani": 76.6937, "matched_fragments": 173, "total_fragments": 1768, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.07", "min_intra_species_ani": "98.42", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.80", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCA_018372555.1", "gtdb_species": "s__Clostridium sp018372555", "ani": 76.3727, "matched_fragments": 143, "total_fragments": 1768, "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": -0.16, "cell_length": 0.434, "doubling_h": 0.353, "growth_tmp": 33.457, "optimum_tmp": 35.173, "optimum_ph": 6.947, "genome_size": 4165901.003, "gc_content": 29.49, "coding_genes": 3796.985, "rRNA16S_genes": 9.374, "tRNA_genes": 78.312, "gram_stain": 0.945, "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", "folliculivorans" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }