{ "type": "genome", "identifier": "GCF_014287825.1", "organism": "Clostridium hominis", "title": "Clostridium hominis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "WFCC-MRCEN World Data Centre for Microoganisms(WDCM)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014287825.1", "bioproject": "PRJNA224116", "biosample": "SAMN15806947", "wgs_master": "JACOOO000000000.1", "refseq_category": "reference genome", "taxid": "2763036", "species_taxid": "2763036", "organism_name": "Clostridium hominis", "infraspecific_name": "strain=NSJ-6", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/08/24", "asm_name": "ASM1428782v1", "asm_submitter": "WFCC-MRCEN World Data Centre for Microoganisms(WDCM)", "gbrs_paired_asm": "GCA_014287825.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/287/825/GCF_014287825.1_ASM1428782v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4155764", "genome_size_ungapped": "4155764", "gc_percent": "29.000000", "replicon_count": "0", "scaffold_count": "52", "contig_count": "52", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014287825.1-RS_2024_07_15", "annotation_date": "2024-07-15", "total_gene_count": "4085", "protein_coding_gene_count": "3930", "non_coding_gene_count": "122", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-08-24", "dateModified": "2020-08-24", "datePublished": "2020-08-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Clostridium hominis" ], "sample_taxid": [ "2763036" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China:Beijing" ], "sample_host_location_id": [], "data_size": "1.131 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)": "4155764", "Number of Sequences": "52", "Longest Sequences (bp)": "649317", "N50 (bp)": "164721", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "29.1", "Number of CDSs": "3948", "Average Protein Length": "304.2", "Coding Ratio (%)": "86.7", "Number of rRNAs": "7", "Number of tRNAs": "89", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Clostridium celatum", "strain": "strain=DSM 1785", "accession": "GCA_000320405.1", "taxid": 36834, "species_taxid": 36834, "relation_to_type": "type", "validated": true, "ani": 79.7437, "matched_fragments": 439, "total_fragments": 1361, "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": 79.7148, "matched_fragments": 439, "total_fragments": 1361, "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": 78.237, "matched_fragments": 311, "total_fragments": 1361, "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": 78.2232, "matched_fragments": 308, "total_fragments": 1361, "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": 78.1881, "matched_fragments": 316, "total_fragments": 1361, "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": 78.186, "matched_fragments": 315, "total_fragments": 1361, "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": 78.1827, "matched_fragments": 316, "total_fragments": 1361, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium moniliforme", "strain": "strain=DSM 3984", "accession": "GCA_017873235.1", "taxid": 39489, "species_taxid": 39489, "relation_to_type": "type", "validated": true, "ani": 77.4484, "matched_fragments": 236, "total_fragments": 1361, "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": 77.3569, "matched_fragments": 203, "total_fragments": 1361, "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": 77.2376, "matched_fragments": 203, "total_fragments": 1361, "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": 77.1134, "matched_fragments": 240, "total_fragments": 1361, "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": 77.0732, "matched_fragments": 232, "total_fragments": 1361, "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": 76.6385, "matched_fragments": 215, "total_fragments": 1361, "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": 76.6106, "matched_fragments": 117, "total_fragments": 1361, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium putrefaciens", "strain": "strain=NCTC9836", "accession": "GCA_900461105.1", "taxid": 99675, "species_taxid": 99675, "relation_to_type": "type", "validated": true, "ani": 76.2468, "matched_fragments": 90, "total_fragments": 1361, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium liquoris", "strain": "strain=DSM 100320", "accession": "GCA_002995785.1", "taxid": 1289519, "species_taxid": 1289519, "relation_to_type": "type", "validated": true, "ani": 76.1191, "matched_fragments": 74, "total_fragments": 1361, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium tetanomorphum", "strain": "strain=DSM 4474", "accession": "GCA_017873215.1", "taxid": 1553, "species_taxid": 1553, "relation_to_type": "type", "validated": true, "ani": 76.0158, "matched_fragments": 151, "total_fragments": 1361, "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": 75.9446, "matched_fragments": 144, "total_fragments": 1361, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium lundense", "strain": "strain=DSM 17049", "accession": "GCA_000619945.1", "taxid": 319475, "species_taxid": 319475, "relation_to_type": "type", "validated": true, "ani": 75.9372, "matched_fragments": 143, "total_fragments": 1361, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium arbusti", "strain": "strain=SL206", "accession": "GCA_000246895.2", "taxid": 1137848, "species_taxid": 1137848, "relation_to_type": "type", "validated": true, "ani": 75.6889, "matched_fragments": 101, "total_fragments": 1361, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium pasteurianum", "strain": "strain=ATCC 6013", "accession": "GCA_001856645.1", "taxid": 1501, "species_taxid": 1501, "relation_to_type": "type", "validated": true, "ani": 75.4201, "matched_fragments": 121, "total_fragments": 1361, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium pasteurianum", "strain": "strain=ATCC 6013", "accession": "GCA_000724205.3", "taxid": 1501, "species_taxid": 1501, "relation_to_type": "type", "validated": true, "ani": 75.4156, "matched_fragments": 120, "total_fragments": 1361, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium pasteurianum", "strain": "strain=DSM 525", "accession": "GCA_000807255.1", "taxid": 1501, "species_taxid": 1501, "relation_to_type": "type", "validated": true, "ani": 75.4102, "matched_fragments": 120, "total_fragments": 1361, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium pasteurianum", "strain": "strain=DSM 525", "accession": "GCA_000330945.1", "taxid": 1501, "species_taxid": 1501, "relation_to_type": "type", "validated": true, "ani": 75.357, "matched_fragments": 121, "total_fragments": 1361, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_000753455.2", "gtdb_species": "s__Clostridium sp000753455", "ani": 99.1277, "matched_fragments": 1231, "total_fragments": 1361, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.13", "min_intra_species_ani": "99.13", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_001405015.1", "gtdb_species": "s__Clostridium disporicum", "ani": 87.152, "matched_fragments": 891, "total_fragments": 1361, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.24", "min_intra_species_ani": "98.87", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.88", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000320405.1", "gtdb_species": "s__Clostridium celatum", "ani": 79.7761, "matched_fragments": 435, "total_fragments": 1361, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.74", "min_intra_species_ani": "99.48", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000577815.1", "gtdb_species": "s__Clostridium saudiense", "ani": 79.7406, "matched_fragments": 436, "total_fragments": 1361, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.39", "min_intra_species_ani": "99.24", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.87", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_004353185.1", "gtdb_species": "s__Clostridium cuniculi", "ani": 79.7257, "matched_fragments": 484, "total_fragments": 1361, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.75", "min_intra_species_ani": "97.60", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.82", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_015670405.1", "gtdb_species": "s__Clostridium sp015670405", "ani": 79.5549, "matched_fragments": 407, "total_fragments": 1361, "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": 79.5111, "matched_fragments": 424, "total_fragments": 1361, "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": "GCA_900766315.1", "gtdb_species": "s__Clostridium sp900766315", "ani": 79.4711, "matched_fragments": 472, "total_fragments": 1361, "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": 79.456, "matched_fragments": 410, "total_fragments": 1361, "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_015667795.1", "gtdb_species": "s__Clostridium sp015667795", "ani": 79.2295, "matched_fragments": 492, "total_fragments": 1361, "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": 79.1768, "matched_fragments": 396, "total_fragments": 1361, "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_900540255.1", "gtdb_species": "s__Clostridium sp900540255", "ani": 79.1558, "matched_fragments": 386, "total_fragments": 1361, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.08", "min_intra_species_ani": "99.08", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.89", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_002327185.1", "gtdb_species": "s__Clostridium chauvoei", "ani": 78.1977, "matched_fragments": 309, "total_fragments": 1361, "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": "GCA_018372875.1", "gtdb_species": "s__Clostridium sp018372875", "ani": 77.8215, "matched_fragments": 246, "total_fragments": 1361, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.91", "min_intra_species_ani": "98.91", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_012520205.1", "gtdb_species": "s__Clostridium sp012520205", "ani": 77.65, "matched_fragments": 160, "total_fragments": 1361, "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_000619945.1", "gtdb_species": "s__Clostridium_AO lundense", "ani": 75.9364, "matched_fragments": 141, "total_fragments": 1361, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AO", "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_000246895.1", "gtdb_species": "s__Clostridium_I arbusti", "ani": 75.6779, "matched_fragments": 102, "total_fragments": 1361, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_I", "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", "hominis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }