{ "type": "genome", "identifier": "GCF_001243045.1", "organism": "Clostridium niameyense", "title": "Clostridium niameyense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "URMITE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001243045.1", "bioproject": "PRJNA224116", "biosample": "SAMEA3381202", "wgs_master": "CVPI00000000.1", "refseq_category": "reference genome", "taxid": "1622073", "species_taxid": "1622073", "organism_name": "Clostridium niameyense", "infraspecific_name": "strain=MT5", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/07/21", "asm_name": "Clostridium niameyense", "asm_submitter": "URMITE", "gbrs_paired_asm": "GCA_001243045.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/243/045/GCF_001243045.1_Clostridium_niameyense", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2542842", "genome_size_ungapped": "2542823", "gc_percent": "27.500000", "replicon_count": "0", "scaffold_count": "6", "contig_count": "7", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001243045.1-RS_2024_04_16", "annotation_date": "2024-04-16", "total_gene_count": "2490", "protein_coding_gene_count": "2385", "non_coding_gene_count": "85", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-07-21", "dateModified": "2015-07-21", "datePublished": "2015-07-21", "_annotation": { "sample_count": 1, "sample_organism": [ "Clostridium niameyense" ], "sample_taxid": [ "1622073" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.682 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)": "2542842", "Number of Sequences": "6", "Longest Sequences (bp)": "2380284", "N50 (bp)": "2380284", "Gap Ratio (%)": "0.000747", "GCcontent (%)": "27.4", "Number of CDSs": "2424", "Average Protein Length": "305.4", "Coding Ratio (%)": "87.4", "Number of rRNAs": "7", "Number of tRNAs": "70", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Clostridium niameyense", "strain": "strain=MT5", "accession": "GCA_001243045.1", "taxid": 1622073, "species_taxid": 1622073, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 845, "total_fragments": 845, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Clostridium sporogenes", "strain": "strain=NCTC13020", "accession": "GCA_900461305.1", "taxid": 1509, "species_taxid": 1509, "relation_to_type": "type", "validated": true, "ani": 79.4991, "matched_fragments": 457, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium sporogenes", "strain": "strain=DSM 795", "accession": "GCA_001020205.1", "taxid": 1509, "species_taxid": 1509, "relation_to_type": "type", "validated": true, "ani": 79.4915, "matched_fragments": 458, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium sporogenes", "strain": "strain=NCIMB 10696", "accession": "GCA_000973705.1", "taxid": 1509, "species_taxid": 1509, "relation_to_type": "type", "validated": true, "ani": 79.4618, "matched_fragments": 455, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium sporogenes", "strain": "strain=DSM 795", "accession": "GCA_000685115.1", "taxid": 1509, "species_taxid": 1509, "relation_to_type": "type", "validated": true, "ani": 79.426, "matched_fragments": 466, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium botulinum", "strain": "strain=ATCC 25763", "accession": "GCA_001276985.1", "taxid": 1491, "species_taxid": 1491, "relation_to_type": "type", "validated": true, "ani": 79.2345, "matched_fragments": 458, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium tepidum", "strain": "strain=IEH 97212", "accession": "GCA_002008345.1", "taxid": 1962263, "species_taxid": 1962263, "relation_to_type": "type", "validated": true, "ani": 79.1931, "matched_fragments": 440, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium botulinum", "strain": "strain=ATCC 25763", "accession": "GCA_011017965.1", "taxid": 1491, "species_taxid": 1491, "relation_to_type": "type", "validated": true, "ani": 79.1841, "matched_fragments": 462, "total_fragments": 845, "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": 77.2235, "matched_fragments": 232, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium autoethanogenum", "strain": "strain=DSM 10061", "accession": "GCA_000484505.2", "taxid": 84023, "species_taxid": 84023, "relation_to_type": "suspected-type", "validated": true, "ani": 76.8122, "matched_fragments": 159, "total_fragments": 845, "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": 76.6428, "matched_fragments": 173, "total_fragments": 845, "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": 76.5952, "matched_fragments": 141, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium faecium", "strain": "strain=N37", "accession": "GCA_014836835.1", "taxid": 2762223, "species_taxid": 2762223, "relation_to_type": "type", "validated": true, "ani": 76.491, "matched_fragments": 174, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium swellfunianum", "strain": "strain=CICC 10730", "accession": "GCA_023656515.1", "taxid": 1367462, "species_taxid": 1367462, "relation_to_type": "type", "validated": true, "ani": 76.4259, "matched_fragments": 88, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium saudiense", "strain": "strain=JCC", "accession": "GCA_000577815.1", "taxid": 1414720, "species_taxid": 1414720, "relation_to_type": "type", "validated": true, "ani": 75.9282, "matched_fragments": 144, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Anaeromicrobium sediminis", "strain": "strain=DY2726D", "accession": "GCA_002270055.1", "taxid": 1478221, "species_taxid": 1478221, "relation_to_type": "type", "validated": true, "ani": 75.2409, "matched_fragments": 66, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Maledivibacter halophilus", "strain": "strain=M1", "accession": "GCA_900167445.1", "taxid": 36842, "species_taxid": 36842, "relation_to_type": "type", "validated": true, "ani": 74.7104, "matched_fragments": 88, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001243045.1", "gtdb_species": "s__Clostridium_F niameyense", "ani": 100.0, "matched_fragments": 845, "total_fragments": 845, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.56", "min_intra_species_ani": "99.11", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_001020205.1", "gtdb_species": "s__Clostridium_F sporogenes", "ani": 79.458, "matched_fragments": 461, "total_fragments": 845, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.24", "min_intra_species_ani": "98.80", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.88", "num_clustered_genomes": 81, "status": "-" }, { "accession": "GCF_001889325.1", "gtdb_species": "s__Clostridium_F botulinum_A", "ani": 79.2849, "matched_fragments": 468, "total_fragments": 845, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.92", "min_intra_species_ani": "95.51", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.85", "num_clustered_genomes": 52, "status": "-" }, { "accession": "GCF_001276985.1", "gtdb_species": "s__Clostridium_F botulinum", "ani": 79.2468, "matched_fragments": 456, "total_fragments": 845, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.69", "min_intra_species_ani": "95.97", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.83", "num_clustered_genomes": 213, "status": "-" }, { "accession": "GCF_002008345.1", "gtdb_species": "s__Clostridium_F tepidum", "ani": 79.1769, "matched_fragments": 441, "total_fragments": 845, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.70", "min_intra_species_ani": "99.54", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_001276215.1", "gtdb_species": "s__Clostridium_F sp001276215", "ani": 79.1154, "matched_fragments": 456, "total_fragments": 845, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.32", "min_intra_species_ani": "95.44", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.82", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_000968375.1", "gtdb_species": "s__Clostridium_AM scatologenes", "ani": 77.1954, "matched_fragments": 249, "total_fragments": 845, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM", "ani_circumscription_radius": 96.092, "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_002423705.1", "gtdb_species": "s__Clostridium_X sp002423705", "ani": 76.153, "matched_fragments": 123, "total_fragments": 845, "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": "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", "niameyense" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }