{ "type": "genome", "identifier": "GCF_017873245.1", "organism": "Clostridium tertium", "title": "Clostridium tertium", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_017873245.1", "bioproject": "PRJNA224116", "biosample": "SAMN18250258", "wgs_master": "JAGGJY000000000.1", "refseq_category": "na", "taxid": "1559", "species_taxid": "1559", "organism_name": "Clostridium tertium", "infraspecific_name": "strain=DSM 2485", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/04/08", "asm_name": "ASM1787324v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_017873245.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/017/873/245/GCF_017873245.1_ASM1787324v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3877854", "genome_size_ungapped": "3877854", "gc_percent": "28.000000", "replicon_count": "0", "scaffold_count": "39", "contig_count": "39", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_017873245.1-RS_2024_04_29", "annotation_date": "2024-04-29", "total_gene_count": "3721", "protein_coding_gene_count": "3589", "non_coding_gene_count": "93", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-04-08", "dateModified": "2021-04-08", "datePublished": "2021-04-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Clostridium tertium" ], "sample_taxid": [ "1559" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.048 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)": "3877854", "Number of Sequences": "39", "Longest Sequences (bp)": "650361", "N50 (bp)": "184539", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "27.8", "Number of CDSs": "3635", "Average Protein Length": "304.4", "Coding Ratio (%)": "85.6", "Number of rRNAs": "5", "Number of tRNAs": "77", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Clostridium tertium", "strain": "strain=DSM 2485", "accession": "GCA_017873245.1", "taxid": 1559, "species_taxid": 1559, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1271, "total_fragments": 1273, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Clostridium nigeriense", "strain": "strain=Marseille-P2414", "accession": "GCA_900086595.1", "taxid": 1805470, "species_taxid": 1805470, "relation_to_type": "type", "validated": true, "ani": 81.6105, "matched_fragments": 730, "total_fragments": 1273, "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": 81.2015, "matched_fragments": 650, "total_fragments": 1273, "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": 79.4061, "matched_fragments": 433, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium septicum", "strain": "strain=FDAARGOS_1551", "accession": "GCA_020736665.1", "taxid": 1504, "species_taxid": 1504, "relation_to_type": "type", "validated": true, "ani": 79.1999, "matched_fragments": 458, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium septicum", "strain": "strain=DSM 7534", "accession": "GCA_003606265.1", "taxid": 1504, "species_taxid": 1504, "relation_to_type": "type", "validated": true, "ani": 79.1301, "matched_fragments": 464, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium isatidis", "strain": "strain=DSM 15098", "accession": "GCA_002285495.1", "taxid": 182773, "species_taxid": 182773, "relation_to_type": "type", "validated": true, "ani": 78.9165, "matched_fragments": 390, "total_fragments": 1273, "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": 77.3097, "matched_fragments": 312, "total_fragments": 1273, "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": 77.0733, "matched_fragments": 240, "total_fragments": 1273, "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": 76.9928, "matched_fragments": 257, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium puniceum", "strain": "strain=DSM 2619", "accession": "GCA_002006345.1", "taxid": 29367, "species_taxid": 29367, "relation_to_type": "type", "validated": true, "ani": 76.8628, "matched_fragments": 297, "total_fragments": 1273, "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": 76.6956, "matched_fragments": 278, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium punense", "strain": "strain=DSM 28650", "accession": "GCA_017874425.1", "taxid": 1054297, "species_taxid": 1054297, "relation_to_type": "type", "validated": true, "ani": 76.4285, "matched_fragments": 119, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium carboxidivorans", "strain": "strain=P7", "accession": "GCA_000175595.1", "taxid": 217159, "species_taxid": 217159, "relation_to_type": "type", "validated": true, "ani": 76.3458, "matched_fragments": 157, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium carboxidivorans", "strain": "strain=P7", "accession": "GCA_001038625.1", "taxid": 217159, "species_taxid": 217159, "relation_to_type": "type", "validated": true, "ani": 76.3092, "matched_fragments": 167, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium drakei", "strain": "strain=SL1", "accession": "GCA_003096175.1", "taxid": 332101, "species_taxid": 332101, "relation_to_type": "type", "validated": true, "ani": 76.2519, "matched_fragments": 167, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium ihumii", "strain": "strain=AP5", "accession": "GCA_000612845.1", "taxid": 1470356, "species_taxid": 1470356, "relation_to_type": "type", "validated": true, "ani": 76.2001, "matched_fragments": 222, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium cellulovorans", "strain": "strain=743B", "accession": "GCA_000145275.1", "taxid": 1493, "species_taxid": 1493, "relation_to_type": "type", "validated": true, "ani": 76.1201, "matched_fragments": 155, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_017873245.1", "gtdb_species": "s__Clostridium tertium", "ani": 100.0, "matched_fragments": 1271, "total_fragments": 1273, "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": "conclusive" }, { "accession": "GCA_017888565.1", "gtdb_species": "s__Clostridium sp017888565", "ani": 92.8854, "matched_fragments": 1072, "total_fragments": 1273, "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_015550425.1", "gtdb_species": "s__Clostridium sp015550425", "ani": 90.9809, "matched_fragments": 1020, "total_fragments": 1273, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.01", "min_intra_species_ani": "99.01", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000401215.1", "gtdb_species": "s__Clostridium sartagoforme_A", "ani": 84.4716, "matched_fragments": 794, "total_fragments": 1273, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.25", "min_intra_species_ani": "98.25", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900086595.1", "gtdb_species": "s__Clostridium nigeriense", "ani": 81.5947, "matched_fragments": 732, "total_fragments": 1273, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.98", "min_intra_species_ani": "98.98", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014836325.1", "gtdb_species": "s__Clostridium sp014836325", "ani": 81.2085, "matched_fragments": 649, "total_fragments": 1273, "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_900759995.1", "gtdb_species": "s__Clostridium sp900759995", "ani": 80.9064, "matched_fragments": 560, "total_fragments": 1273, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.46", "min_intra_species_ani": "98.18", "mean_intra_species_af": "0.80", "min_intra_species_af": "0.79", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_004794105.1", "gtdb_species": "s__Clostridium sartagoforme_B", "ani": 80.6, "matched_fragments": 680, "total_fragments": 1273, "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": "98.58", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_018372555.1", "gtdb_species": "s__Clostridium sp018372555", "ani": 80.2823, "matched_fragments": 500, "total_fragments": 1273, "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_002327185.1", "gtdb_species": "s__Clostridium chauvoei", "ani": 79.4055, "matched_fragments": 433, "total_fragments": 1273, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.302, "cell_length": 0.176, "doubling_h": 0.353, "growth_tmp": 37.0, "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": 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": 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", "tertium" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }