{ "type": "genome", "identifier": "GCF_016027375.1", "organism": "Clostridium perfringens", "title": "Clostridium perfringens", "description": "na", "data type": "Genome sequencing and assembly", "organization": "US Food and Drug Administration", "publication": [ {} ], "properties": { "assembly_accession": "GCF_016027375.1", "bioproject": "PRJNA224116", "biosample": "SAMN13450433", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "1502", "species_taxid": "1502", "organism_name": "Clostridium perfringens", "infraspecific_name": "strain=FDAARGOS_903", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/12/14", "asm_name": "ASM1602737v1", "asm_submitter": "US Food and Drug Administration", "gbrs_paired_asm": "GCA_016027375.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/016/027/375/GCF_016027375.1_ASM1602737v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3355233", "genome_size_ungapped": "3355233", "gc_percent": "28.500000", "replicon_count": "2", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_016027375.1-RS_2024_10_16", "annotation_date": "2024-10-16", "total_gene_count": "3062", "protein_coding_gene_count": "2908", "non_coding_gene_count": "128", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-12-14", "dateModified": "2020-12-14", "datePublished": "2020-12-14", "_annotation": { "sample_count": 1, "sample_organism": [ "Clostridium perfringens" ], "sample_taxid": [ "1502" ], "sample_host_organism": [ "missing" ], "sample_host_organism_id": [], "sample_host_disease": [ "Unknown", "Unknown" ], "sample_host_disease_id": [], "sample_host_location": [ "Not applicable" ], "sample_host_location_id": [], "data_size": "0.899 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)": "3355233", "Number of Sequences": "2", "Longest Sequences (bp)": "3300922", "N50 (bp)": "3300922", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "28.3", "Number of CDSs": "2969", "Average Protein Length": "314.6", "Coding Ratio (%)": "83.5", "Number of rRNAs": "30", "Number of tRNAs": "94", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Clostridium perfringens", "strain": "strain=FDAARGOS_903", "accession": "GCA_016027375.1", "taxid": 1502, "species_taxid": 1502, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1118, "total_fragments": 1118, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Clostridium perfringens", "strain": "strain=ATCC 13124", "accession": "GCA_000013285.1", "taxid": 1502, "species_taxid": 1502, "relation_to_type": "type", "validated": true, "ani": 98.9286, "matched_fragments": 1024, "total_fragments": 1118, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Clostridium massiliamazoniense", "strain": "strain=ND2", "accession": "GCA_001403635.1", "taxid": 1347366, "species_taxid": 1347366, "relation_to_type": "type", "validated": true, "ani": 78.5847, "matched_fragments": 308, "total_fragments": 1118, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium mediterraneense", "strain": "strain=Marseille-P2434", "accession": "GCA_900091705.1", "taxid": 1805472, "species_taxid": 1805472, "relation_to_type": "type", "validated": true, "ani": 78.5546, "matched_fragments": 269, "total_fragments": 1118, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium tarantellae", "strain": "strain=DSM 3997", "accession": "GCA_009295725.1", "taxid": 39493, "species_taxid": 39493, "relation_to_type": "type", "validated": true, "ani": 78.5261, "matched_fragments": 360, "total_fragments": 1118, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium fallax", "strain": "strain=NCTC8380", "accession": "GCA_900461065.1", "taxid": 1533, "species_taxid": 1533, "relation_to_type": "type", "validated": true, "ani": 78.4298, "matched_fragments": 283, "total_fragments": 1118, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sarcina ventriculi", "strain": "strain=NCTC12966", "accession": "GCA_900456775.1", "taxid": 1267, "species_taxid": 1267, "relation_to_type": "type", "validated": true, "ani": 78.3163, "matched_fragments": 245, "total_fragments": 1118, "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": 78.0891, "matched_fragments": 270, "total_fragments": 1118, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium fallax", "strain": "strain=DSM 2631", "accession": "GCA_900129365.1", "taxid": 1533, "species_taxid": 1533, "relation_to_type": "type", "validated": true, "ani": 77.7847, "matched_fragments": 271, "total_fragments": 1118, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium celatum", "strain": "strain=DSM 1785", "accession": "GCA_000320405.1", "taxid": 36834, "species_taxid": 36834, "relation_to_type": "type", "validated": true, "ani": 77.5628, "matched_fragments": 226, "total_fragments": 1118, "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": 77.4318, "matched_fragments": 221, "total_fragments": 1118, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium cagae", "strain": "strain=Marseille-P4344", "accession": "GCA_900290265.1", "taxid": 2080751, "species_taxid": 2080751, "relation_to_type": "type", "validated": true, "ani": 77.3049, "matched_fragments": 232, "total_fragments": 1118, "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": 77.1638, "matched_fragments": 243, "total_fragments": 1118, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium felsineum", "strain": "strain=DSM 794", "accession": "GCA_002006355.2", "taxid": 36839, "species_taxid": 36839, "relation_to_type": "type", "validated": true, "ani": 76.914, "matched_fragments": 162, "total_fragments": 1118, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium felsineum", "strain": "strain=DSM 7320", "accession": "GCA_002006215.2", "taxid": 36839, "species_taxid": 36839, "relation_to_type": "type", "validated": true, "ani": 76.8752, "matched_fragments": 163, "total_fragments": 1118, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium felsineum", "strain": "strain=DSM 793", "accession": "GCA_002006235.2", "taxid": 36839, "species_taxid": 36839, "relation_to_type": "type", "validated": true, "ani": 76.726, "matched_fragments": 173, "total_fragments": 1118, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Abyssisolibacter fermentans", "strain": "strain=MCWD3", "accession": "GCA_001559865.1", "taxid": 1766203, "species_taxid": 1766203, "relation_to_type": "type", "validated": true, "ani": 74.9283, "matched_fragments": 85, "total_fragments": 1118, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000013285.1", "gtdb_species": "s__Clostridium_P perfringens", "ani": 98.9283, "matched_fragments": 1024, "total_fragments": 1118, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.05", "min_intra_species_ani": "95.74", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.81", "num_clustered_genomes": 315, "status": "conclusive" }, { "accession": "GCF_900091705.1", "gtdb_species": "s__Clostridium_P mediterraneense", "ani": 78.5725, "matched_fragments": 268, "total_fragments": 1118, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P", "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": "GCF_009295725.1", "gtdb_species": "s__Clostridium_P tarantellae", "ani": 78.5112, "matched_fragments": 362, "total_fragments": 1118, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P", "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_001403635.1", "gtdb_species": "s__Clostridium_P massiliamazoniense", "ani": 78.459, "matched_fragments": 309, "total_fragments": 1118, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900456775.1", "gtdb_species": "s__Clostridium_P ventriculi", "ani": 78.2809, "matched_fragments": 245, "total_fragments": 1118, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.93", "min_intra_species_ani": "98.34", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.94", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_002327185.1", "gtdb_species": "s__Clostridium chauvoei", "ani": 78.0856, "matched_fragments": 276, "total_fragments": 1118, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.96", "min_intra_species_ani": "99.88", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_900129365.1", "gtdb_species": "s__Clostridium_AH fallax", "ani": 77.7486, "matched_fragments": 272, "total_fragments": 1118, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AH", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000498355.1", "gtdb_species": "s__Clostridium sp000498355", "ani": 77.6949, "matched_fragments": 310, "total_fragments": 1118, "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_015555905.1", "gtdb_species": "s__Clostridium sp015555905", "ani": 77.6658, "matched_fragments": 219, "total_fragments": 1118, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.95", "min_intra_species_ani": "98.95", "mean_intra_species_af": "0.73", "min_intra_species_af": "0.73", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001735765.2", "gtdb_species": "s__Clostridium taeniosporum", "ani": 77.6021, "matched_fragments": 262, "total_fragments": 1118, "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": "GCA_900547475.1", "gtdb_species": "s__Clostridium sp900547475", "ani": 77.52, "matched_fragments": 271, "total_fragments": 1118, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.47", "min_intra_species_ani": "95.30", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.84", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_015667795.1", "gtdb_species": "s__Clostridium sp015667795", "ani": 77.3768, "matched_fragments": 278, "total_fragments": 1118, "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": "GCA_017435645.1", "gtdb_species": "s__Clostridium sp017435645", "ani": 77.232, "matched_fragments": 116, "total_fragments": 1118, "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": "GCA_900543325.1", "gtdb_species": "s__Clostridium sp900543325", "ani": 77.2233, "matched_fragments": 218, "total_fragments": 1118, "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": "GCA_000435835.1", "gtdb_species": "s__Clostridium sp000435835", "ani": 77.1979, "matched_fragments": 177, "total_fragments": 1118, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.44", "min_intra_species_ani": "99.22", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.88", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_017873245.1", "gtdb_species": "s__Clostridium tertium", "ani": 77.1631, "matched_fragments": 244, "total_fragments": 1118, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.32", "min_intra_species_ani": "97.37", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 19, "status": "-" }, { "accession": "GCF_000424205.1", "gtdb_species": "s__Clostridium_X cadaveris", "ani": 77.1276, "matched_fragments": 150, "total_fragments": 1118, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_X", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.52", "min_intra_species_ani": "99.40", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.82", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCA_015058405.1", "gtdb_species": "s__Clostridium sp015058405", "ani": 76.8756, "matched_fragments": 206, "total_fragments": 1118, "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": "GCA_015058375.1", "gtdb_species": "s__Clostridium sp015058375", "ani": 76.8674, "matched_fragments": 120, "total_fragments": 1118, "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": -0.222, "cell_length": 0.113, "doubling_h": -0.568, "growth_tmp": 40.333, "optimum_tmp": 37.0, "optimum_ph": 6.947, "genome_size": 3407398.591, "gc_content": 27.58, "coding_genes": 2869.882, "rRNA16S_genes": 9.333, "tRNA_genes": 94.357, "gram_stain": 1.0, "sporulation": 1.0, "motility": 1.0, "range_salinity": 0.0, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "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", "perfringens" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }