{ "type": "genome", "identifier": "GCF_000379745.1", "organism": "Enterococcus cecorum DSM 20682 = ATCC 43198", "title": "Enterococcus cecorum DSM 20682 = ATCC 43198", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000379745.1", "bioproject": "PRJNA224116", "biosample": "SAMN02256445", "wgs_master": "ARBO00000000.1", "refseq_category": "na", "taxid": "1121864", "species_taxid": "44008", "organism_name": "Enterococcus cecorum DSM 20682 = ATCC 43198", "infraspecific_name": "strain=DSM 20682", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/04/23", "asm_name": "ASM37974v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000379745.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/379/745/GCF_000379745.1_ASM37974v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2340853", "genome_size_ungapped": "2336810", "gc_percent": "36.500000", "replicon_count": "0", "scaffold_count": "47", "contig_count": "50", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000379745.1-RS_2024_12_23", "annotation_date": "2024-12-23", "total_gene_count": "2433", "protein_coding_gene_count": "2312", "non_coding_gene_count": "63", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-04-23", "dateModified": "2013-04-23", "datePublished": "2013-04-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Enterococcus cecorum DSM 20682 = ATCC 43198" ], "sample_taxid": [ "1121864" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Belgium" ], "sample_host_location_id": [], "data_size": "0.661 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)": "2340853", "Number of Sequences": "47", "Longest Sequences (bp)": "282143", "N50 (bp)": "109686", "Gap Ratio (%)": "0.175705", "GCcontent (%)": "36.4", "Number of CDSs": "2349", "Average Protein Length": "288.1", "Coding Ratio (%)": "86.7", "Number of rRNAs": "4", "Number of tRNAs": "47", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Enterococcus cecorum", "strain": "strain=DSM 20682", "accession": "GCA_000379745.1", "taxid": 44008, "species_taxid": 44008, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 754, "total_fragments": 758, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Enterococcus cecorum", "strain": "strain=ATCC 43198", "accession": "GCA_000492155.1", "taxid": 44008, "species_taxid": 44008, "relation_to_type": "type", "validated": true, "ani": 99.9877, "matched_fragments": 757, "total_fragments": 758, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Enterococcus cecorum", "strain": "strain=ATCC 43198", "accession": "GCA_000407565.1", "taxid": 44008, "species_taxid": 44008, "relation_to_type": "type", "validated": true, "ani": 99.9819, "matched_fragments": 754, "total_fragments": 758, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Enterococcus cecorum", "strain": "strain=NCTC12421", "accession": "GCA_900474605.1", "taxid": 44008, "species_taxid": 44008, "relation_to_type": "type", "validated": true, "ani": 99.9818, "matched_fragments": 757, "total_fragments": 758, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Enterococcus cecorum", "strain": "strain=DSM 20682", "accession": "GCA_001885885.1", "taxid": 44008, "species_taxid": 44008, "relation_to_type": "type", "validated": true, "ani": 99.9641, "matched_fragments": 724, "total_fragments": 758, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Enterococcus hirae", "strain": "strain=ATCC 9790", "accession": "GCA_000271405.2", "taxid": 1354, "species_taxid": 1354, "relation_to_type": "type", "validated": true, "ani": 78.0958, "matched_fragments": 83, "total_fragments": 758, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000407565.1", "gtdb_species": "s__Enterococcus_E cecorum", "ani": 99.9819, "matched_fragments": 754, "total_fragments": 758, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.77", "min_intra_species_ani": "96.06", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.77", "num_clustered_genomes": 49, "status": "conclusive" }, { "accession": "GCA_019120335.1", "gtdb_species": "s__Enterococcus_E stercoripullorum", "ani": 94.8497, "matched_fragments": 578, "total_fragments": 758, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_E", "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_000406925.1", "gtdb_species": "s__Enterococcus_E columbae", "ani": 80.3664, "matched_fragments": 326, "total_fragments": 758, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.97", "mean_intra_species_af": "1.00", "min_intra_species_af": "0.99", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_002140715.1", "gtdb_species": "s__Enterococcus sp002140715", "ani": 78.2809, "matched_fragments": 82, "total_fragments": 758, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus", "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_016908885.1", "gtdb_species": "s__Enterococcus_C diestrammenae", "ani": 78.1693, "matched_fragments": 64, "total_fragments": 758, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_C", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.93", "min_intra_species_ani": "97.75", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001886265.1", "gtdb_species": "s__Enterococcus_B thailandicus", "ani": 78.1495, "matched_fragments": 95, "total_fragments": 758, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.46", "min_intra_species_ani": "99.20", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_001544255.1", "gtdb_species": "s__Enterococcus_B faecium", "ani": 78.0775, "matched_fragments": 78, "total_fragments": 758, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.30", "min_intra_species_ani": "98.03", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.72", "num_clustered_genomes": 2177, "status": "-" }, { "accession": "GCF_000407505.1", "gtdb_species": "s__Enterococcus_B phoeniculicola", "ani": 77.8497, "matched_fragments": 87, "total_fragments": 758, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003950315.1", "gtdb_species": "s__Vagococcus bubulae", "ani": 77.7433, "matched_fragments": 68, "total_fragments": 758, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus", "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_009933335.1", "gtdb_species": "s__Enterococcus_F sp009933335", "ani": 77.733, "matched_fragments": 126, "total_fragments": 758, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_F", "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_001730365.1", "gtdb_species": "s__Enterococcus quebecensis", "ani": 77.7257, "matched_fragments": 89, "total_fragments": 758, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000407445.1", "gtdb_species": "s__Enterococcus moraviensis", "ani": 77.6855, "matched_fragments": 78, "total_fragments": 758, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_017426705.1", "gtdb_species": "s__Enterococcus_F sp017426705", "ani": 77.6355, "matched_fragments": 162, "total_fragments": 758, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_F", "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_017316025.1", "gtdb_species": "s__Enterococcus_C sp017316025", "ani": 77.4925, "matched_fragments": 101, "total_fragments": 758, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_C", "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_001886195.1", "gtdb_species": "s__Enterococcus_B ratti", "ani": 77.3933, "matched_fragments": 80, "total_fragments": 758, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_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": "GCF_003987495.1", "gtdb_species": "s__Vagococcus_D salmoninarum", "ani": 77.2266, "matched_fragments": 62, "total_fragments": 758, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.18", "min_intra_species_ani": "98.18", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000423785.1", "gtdb_species": "s__Tetragenococcus muriaticus", "ani": 76.593, "matched_fragments": 53, "total_fragments": 758, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Tetragenococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.93", "min_intra_species_ani": "98.87", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": 0.0, "cell_length": 0.0, "doubling_h": -0.346, "growth_tmp": 35.0, "optimum_tmp": 34.173, "optimum_ph": 8.805, "genome_size": 2339601.588, "gc_content": 36.463, "coding_genes": 2297.0, "rRNA16S_genes": 5.5, "tRNA_genes": 68.0, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 1.0, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 1.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Enterococcus", "cecorum", "DSM", "20682", "=", "ATCC", "43198" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }