{ "type": "genome", "identifier": "GCF_000156515.1", "organism": "[Clostridium] hylemonae DSM 15053", "title": "[Clostridium] hylemonae DSM 15053", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Washington University Genome Sequencing Center", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000156515.1", "bioproject": "PRJNA224116", "biosample": "SAMN00008808", "wgs_master": "ABYI00000000.2", "refseq_category": "na", "taxid": "553973", "species_taxid": "89153", "organism_name": "[Clostridium] hylemonae DSM 15053", "infraspecific_name": "strain=DSM 15053", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2009/03/02", "asm_name": "ASM15651v1", "asm_submitter": "Washington University Genome Sequencing Center", "gbrs_paired_asm": "GCA_000156515.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/156/515/GCF_000156515.1_ASM15651v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3889859", "genome_size_ungapped": "3885459", "gc_percent": "49.000000", "replicon_count": "0", "scaffold_count": "123", "contig_count": "167", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-02-28", "total_gene_count": "3730", "protein_coding_gene_count": "3608", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2009-03-02", "dateModified": "2009-03-02", "datePublished": "2009-03-02", "_annotation": { "sample_count": 1, "sample_organism": [ "[Clostridium] hylemonae DSM 15053" ], "sample_taxid": [ "553973" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not determined" ], "sample_host_location_id": [], "data_size": "1.100 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)": "3889859", "Number of Sequences": "123", "Longest Sequences (bp)": "2898417", "N50 (bp)": "2898417", "Gap Ratio (%)": "0.113115", "GCcontent (%)": "48.9", "Number of CDSs": "3545", "Average Protein Length": "326.7", "Coding Ratio (%)": "89.3", "Number of rRNAs": "0", "Number of tRNAs": "51", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "[Clostridium] hylemonae", "strain": "strain=DSM 15053", "accession": "GCA_000156515.1", "taxid": 89153, "species_taxid": 89153, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1270, "total_fragments": 1270, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "[Clostridium] hylemonae", "strain": "strain=DSM 15053", "accession": "GCA_008281175.1", "taxid": 89153, "species_taxid": 89153, "relation_to_type": "type", "validated": true, "ani": 99.9503, "matched_fragments": 1263, "total_fragments": 1270, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "[Clostridium] scindens", "strain": "strain=ATCC 35704", "accession": "GCA_004295125.1", "taxid": 29347, "species_taxid": 29347, "relation_to_type": "suspected-type", "validated": true, "ani": 78.3099, "matched_fragments": 270, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Clostridium] scindens", "strain": "strain=ATCC 35704", "accession": "GCA_000154505.1", "taxid": 29347, "species_taxid": 29347, "relation_to_type": "suspected-type", "validated": true, "ani": 78.2822, "matched_fragments": 268, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dorea formicigenerans", "strain": "strain=ATCC 27755", "accession": "GCA_025150245.1", "taxid": 39486, "species_taxid": 39486, "relation_to_type": "suspected-type", "validated": true, "ani": 77.9653, "matched_fragments": 106, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dorea phocaeensis", "strain": "strain=Marseille-P4003", "accession": "GCA_900240315.1", "taxid": 2040291, "species_taxid": 2040291, "relation_to_type": "type", "validated": true, "ani": 77.897, "matched_fragments": 150, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dorea longicatena", "strain": "strain=DSM 13814", "accession": "GCA_000154065.1", "taxid": 88431, "species_taxid": 88431, "relation_to_type": "type", "validated": true, "ani": 77.8796, "matched_fragments": 143, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dorea longicatena", "strain": "strain=DSM 13814", "accession": "GCA_025150085.1", "taxid": 88431, "species_taxid": 88431, "relation_to_type": "type", "validated": true, "ani": 77.7118, "matched_fragments": 142, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Coprococcus comes", "strain": "strain=ATCC 27758", "accession": "GCA_025149785.1", "taxid": 410072, "species_taxid": 410072, "relation_to_type": "type", "validated": true, "ani": 77.5684, "matched_fragments": 91, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Coprococcus phoceensis", "strain": "strain=Marseille-P3062", "accession": "GCA_900104635.1", "taxid": 1870993, "species_taxid": 1870993, "relation_to_type": "type", "validated": true, "ani": 77.4573, "matched_fragments": 82, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Blautia coccoides", "strain": "strain=NCTC11035", "accession": "GCA_900461125.1", "taxid": 1532, "species_taxid": 1532, "relation_to_type": "type", "validated": true, "ani": 77.4051, "matched_fragments": 78, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Muricomes intestini", "strain": "strain=DSM 29489", "accession": "GCA_004346165.1", "taxid": 1796634, "species_taxid": 1796634, "relation_to_type": "type", "validated": true, "ani": 77.2309, "matched_fragments": 76, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Blautia coccoides", "strain": "strain=DSM 935", "accession": "GCA_004340925.1", "taxid": 1532, "species_taxid": 1532, "relation_to_type": "type", "validated": true, "ani": 77.1986, "matched_fragments": 74, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sellimonas caecigallum", "strain": "strain=SW451", "accession": "GCA_019754295.1", "taxid": 2592333, "species_taxid": 2592333, "relation_to_type": "type", "validated": true, "ani": 77.0267, "matched_fragments": 101, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Blautia producta", "strain": "strain=ATCC 27340", "accession": "GCA_000373885.1", "taxid": 33035, "species_taxid": 33035, "relation_to_type": "suspected-type", "validated": true, "ani": 76.6763, "matched_fragments": 73, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Diplocloster agilis", "strain": "strain=ASD5720", "accession": "GCA_019042275.1", "taxid": 2850323, "species_taxid": 2850323, "relation_to_type": "type", "validated": true, "ani": 76.4268, "matched_fragments": 56, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_008281175.1", "gtdb_species": "s__Extibacter hylemonae", "ani": 99.9503, "matched_fragments": 1263, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Extibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.20", "min_intra_species_ani": "98.44", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.93", "num_clustered_genomes": 5, "status": "conclusive" }, { "accession": "GCF_004345005.1", "gtdb_species": "s__Extibacter muris", "ani": 82.6929, "matched_fragments": 738, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Extibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.70", "min_intra_species_ani": "95.67", "mean_intra_species_af": "0.77", "min_intra_species_af": "0.77", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_017566055.1", "gtdb_species": "s__Extibacter sp017566055", "ani": 82.4657, "matched_fragments": 802, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Extibacter", "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_001185345.1", "gtdb_species": "s__Extibacter sp001185345", "ani": 82.2345, "matched_fragments": 832, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Extibacter", "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": "GCA_000509125.1", "gtdb_species": "s__Clostridium_AP sp000509125", "ani": 78.3297, "matched_fragments": 292, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_AP", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.12", "min_intra_species_ani": "98.62", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_004295125.1", "gtdb_species": "s__Clostridium_AP scindens", "ani": 78.3079, "matched_fragments": 269, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_AP", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.44", "min_intra_species_ani": "99.12", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.78", "num_clustered_genomes": 13, "status": "-" }, { "accession": "GCA_900543415.1", "gtdb_species": "s__CAG-317 sp900543415", "ani": 77.908, "matched_fragments": 152, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.35", "min_intra_species_ani": "95.87", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.78", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_000433535.1", "gtdb_species": "s__CAG-317 sp000433535", "ani": 77.9049, "matched_fragments": 162, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.49", "min_intra_species_ani": "98.19", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.83", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_011960625.1", "gtdb_species": "s__Sporofaciens sp011960625", "ani": 77.6421, "matched_fragments": 57, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens", "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_900461125.1", "gtdb_species": "s__Blautia coccoides", "ani": 77.4051, "matched_fragments": 78, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.33", "min_intra_species_ani": "97.47", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.79", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCF_016901695.1", "gtdb_species": "s__Lachnoclostridium_B massiliensis_A", "ani": 77.3968, "matched_fragments": 132, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B", "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_004560705.1", "gtdb_species": "s__Bariatricus sp004560705", "ani": 77.3554, "matched_fragments": 79, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.19", "min_intra_species_ani": "99.19", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.81", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900553355.1", "gtdb_species": "s__Merdimonas sp900553355", "ani": 77.111, "matched_fragments": 160, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdimonas", "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": -0.699, "cell_length": 0.0, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 37.0, "optimum_ph": 7.6, "genome_size": 3802096.0, "gc_content": 48.9, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 1.0, "sporulation": 1.0, "motility": null, "range_salinity": null, "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]", "hylemonae", "DSM", "15053" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }