{ "type": "genome", "identifier": "GCF_000393975.1", "organism": "Enterococcus pallens ATCC BAA-351", "title": "Enterococcus pallens ATCC BAA-351", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Broad Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000393975.1", "bioproject": "PRJNA224116", "biosample": "SAMN00809116", "wgs_master": "AJAQ00000000.1", "refseq_category": "reference genome", "taxid": "1158607", "species_taxid": "160454", "organism_name": "Enterococcus pallens ATCC BAA-351", "infraspecific_name": "strain=ATCC BAA-351", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/05/15", "asm_name": "Ente_pall_BAA-351_V1", "asm_submitter": "Broad Institute", "gbrs_paired_asm": "GCA_000393975.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/393/975/GCF_000393975.1_Ente_pall_BAA-351_V1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5490614", "genome_size_ungapped": "5437682", "gc_percent": "40.000000", "replicon_count": "0", "scaffold_count": "14", "contig_count": "57", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000393975.1-RS_2024_05_02", "annotation_date": "2024-05-02", "total_gene_count": "5319", "protein_coding_gene_count": "5185", "non_coding_gene_count": "88", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-05-15", "dateModified": "2013-05-15", "datePublished": "2013-05-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Enterococcus pallens ATCC BAA-351" ], "sample_taxid": [ "1158607" ], "sample_host_organism": [ "unknown" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "unknown" ], "sample_host_location_id": [], "data_size": "1.538 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)": "5490614", "Number of Sequences": "14", "Longest Sequences (bp)": "1429197", "N50 (bp)": "1157468", "Gap Ratio (%)": "0.964045", "GCcontent (%)": "40.1", "Number of CDSs": "5241", "Average Protein Length": "298.7", "Coding Ratio (%)": "85.5", "Number of rRNAs": "18", "Number of tRNAs": "61", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Enterococcus pallens", "strain": "strain=ATCC BAA-351", "accession": "GCA_000393975.1", "taxid": 160454, "species_taxid": 160454, "relation_to_type": "type", "validated": true, "ani": 99.9982, "matched_fragments": 1808, "total_fragments": 1823, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Enterococcus pallens", "strain": "strain=ATCC BAA-351", "accession": "GCA_000407485.1", "taxid": 160454, "species_taxid": 160454, "relation_to_type": "type", "validated": true, "ani": 99.9813, "matched_fragments": 1792, "total_fragments": 1823, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Enterococcus pallens", "strain": "strain=DSM 15690", "accession": "GCA_001886075.1", "taxid": 160454, "species_taxid": 160454, "relation_to_type": "type", "validated": true, "ani": 99.9504, "matched_fragments": 1667, "total_fragments": 1823, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Enterococcus florum", "strain": "strain=Gos25-1", "accession": "GCA_004309355.1", "taxid": 2480627, "species_taxid": 2480627, "relation_to_type": "type", "validated": true, "ani": 79.4476, "matched_fragments": 370, "total_fragments": 1823, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus pseudoavium", "strain": "strain=NBRC 100491", "accession": "GCA_001544295.1", "taxid": 44007, "species_taxid": 44007, "relation_to_type": "type", "validated": true, "ani": 78.786, "matched_fragments": 208, "total_fragments": 1823, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus dongliensis", "strain": "strain=63-4", "accession": "GCA_005405225.1", "taxid": 2559925, "species_taxid": 2559925, "relation_to_type": "type", "validated": true, "ani": 78.5165, "matched_fragments": 171, "total_fragments": 1823, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus pingfangensis", "strain": "strain=241-2-2", "accession": "GCA_005405205.1", "taxid": 2559924, "species_taxid": 2559924, "relation_to_type": "type", "validated": true, "ani": 78.482, "matched_fragments": 167, "total_fragments": 1823, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus viikkiensis", "strain": "strain=LMG 26075", "accession": "GCA_005405345.1", "taxid": 930854, "species_taxid": 930854, "relation_to_type": "type", "validated": true, "ani": 78.4597, "matched_fragments": 211, "total_fragments": 1823, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus avium", "strain": "strain=DSM 20679", "accession": "GCA_001885775.1", "taxid": 33945, "species_taxid": 33945, "relation_to_type": "type", "validated": true, "ani": 78.3289, "matched_fragments": 287, "total_fragments": 1823, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus alishanensis", "strain": "strain=ALS3", "accession": "GCA_019218635.1", "taxid": 1303817, "species_taxid": 1303817, "relation_to_type": "type", "validated": true, "ani": 78.1257, "matched_fragments": 228, "total_fragments": 1823, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus wangshanyuanii", "strain": "strain=MN05", "accession": "GCA_002197645.1", "taxid": 2005703, "species_taxid": 2005703, "relation_to_type": "type", "validated": true, "ani": 78.0039, "matched_fragments": 112, "total_fragments": 1823, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus alcedinis", "strain": "strain=CCM 8433", "accession": "GCA_014635985.1", "taxid": 1274384, "species_taxid": 1274384, "relation_to_type": "type", "validated": true, "ani": 77.905, "matched_fragments": 71, "total_fragments": 1823, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus rotai", "strain": "strain=LMG 26678", "accession": "GCA_001465345.1", "taxid": 118060, "species_taxid": 118060, "relation_to_type": "type", "validated": true, "ani": 77.8251, "matched_fragments": 103, "total_fragments": 1823, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000407485.1", "gtdb_species": "s__Enterococcus_A pallens", "ani": 99.9815, "matched_fragments": 1792, "total_fragments": 1823, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.98", "mean_intra_species_af": "1.00", "min_intra_species_af": "0.99", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_017377655.1", "gtdb_species": "s__Enterococcus_A sp017377655", "ani": 84.4976, "matched_fragments": 1192, "total_fragments": 1823, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A", "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_017377575.1", "gtdb_species": "s__Enterococcus_A sp017377575", "ani": 80.7398, "matched_fragments": 708, "total_fragments": 1823, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A", "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_004309355.1", "gtdb_species": "s__Enterococcus_A florum", "ani": 79.4336, "matched_fragments": 371, "total_fragments": 1823, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A", "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_001544295.1", 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78.6686, "matched_fragments": 110, "total_fragments": 1823, "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_005405225.1", "gtdb_species": "s__Enterococcus_A dongliensis", "ani": 78.5165, "matched_fragments": 171, "total_fragments": 1823, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A", "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_005405205.1", "gtdb_species": "s__Enterococcus_A pingfangensis", "ani": 78.482, "matched_fragments": 167, "total_fragments": 1823, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A", "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_005405345.1", "gtdb_species": "s__Enterococcus_A viikkiensis", "ani": 78.4597, "matched_fragments": 211, "total_fragments": 1823, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A", "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_005405365.1", "gtdb_species": "s__Enterococcus_A xiangfangensis", "ani": 78.4234, "matched_fragments": 199, "total_fragments": 1823, "gtdb_taxonomy": 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"vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Enterococcus", "pallens", "ATCC", "BAA-351" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }