{ "type": "genome", "identifier": "GCF_000407245.1", "organism": "Enterococcus avium ATCC 14025", "title": "Enterococcus avium ATCC 14025", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Broad Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000407245.1", "bioproject": "PRJNA224116", "biosample": "SAMN02596897", "wgs_master": "ASWL00000000.1", "refseq_category": "na", "taxid": "1140002", "species_taxid": "33945", "organism_name": "Enterococcus avium ATCC 14025", "infraspecific_name": "strain=ATCC 14025", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/06/04", "asm_name": "Ente_aviu_ATCC14025_V2", "asm_submitter": "Broad Institute", "gbrs_paired_asm": "GCA_000407245.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/407/245/GCF_000407245.1_Ente_aviu_ATCC14025_V2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4614282", "genome_size_ungapped": "4613601", "gc_percent": "39.000000", "replicon_count": "0", "scaffold_count": "12", "contig_count": "13", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-01-16", "total_gene_count": "4574", "protein_coding_gene_count": "4460", "non_coding_gene_count": "62", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-06-04", "dateModified": "2013-06-04", "datePublished": "2013-06-04", "_annotation": { "sample_count": 1, "sample_organism": [ "Enterococcus avium ATCC 14025" ], "sample_taxid": [ "1140002" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.304 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)": "4614282", "Number of Sequences": "12", "Longest Sequences (bp)": "1309494", "N50 (bp)": "652010", "Gap Ratio (%)": "0.014759", "GCcontent (%)": "39.0", "Number of CDSs": "4553", "Average Protein Length": "292.5", "Coding Ratio (%)": "86.6", "Number of rRNAs": "4", "Number of tRNAs": "48", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Enterococcus avium", "strain": "strain=ATCC 14025", "accession": "GCA_000407245.1", "taxid": 33945, "species_taxid": 33945, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1531, "total_fragments": 1533, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Enterococcus avium", "strain": "strain=NCTC9938", "accession": "GCA_900447655.1", "taxid": 33945, "species_taxid": 33945, "relation_to_type": "type", "validated": true, "ani": 99.9949, "matched_fragments": 1532, "total_fragments": 1533, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Enterococcus avium", "strain": "strain=ATCC 14025", "accession": "GCA_000406965.1", "taxid": 33945, "species_taxid": 33945, "relation_to_type": "type", "validated": true, "ani": 99.9591, "matched_fragments": 1525, "total_fragments": 1533, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Enterococcus avium", "strain": "strain=DSM 20679", "accession": "GCA_001885775.1", "taxid": 33945, "species_taxid": 33945, "relation_to_type": "type", "validated": true, "ani": 99.9046, "matched_fragments": 1401, "total_fragments": 1533, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Enterococcus malodoratus", "strain": "strain=DSM 20681", "accession": "GCA_001886025.1", "taxid": 71451, "species_taxid": 71451, "relation_to_type": "type", "validated": true, "ani": 81.892, "matched_fragments": 810, "total_fragments": 1533, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus hulanensis", "strain": "strain=190-7", "accession": "GCA_005405485.1", "taxid": 2559929, "species_taxid": 2559929, "relation_to_type": "type", "validated": true, "ani": 81.6276, "matched_fragments": 824, "total_fragments": 1533, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus gilvus", "strain": "strain=ATCC BAA-350", "accession": "GCA_000394615.1", "taxid": 160453, "species_taxid": 160453, "relation_to_type": "type", "validated": true, "ani": 81.1936, "matched_fragments": 637, "total_fragments": 1533, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000406965.1", "gtdb_species": "s__Enterococcus_A avium", "ani": 99.9599, "matched_fragments": 1525, "total_fragments": 1533, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.01", "min_intra_species_ani": "97.91", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.78", "num_clustered_genomes": 43, "status": "conclusive" }, { "accession": "GCF_018917525.1", "gtdb_species": "s__Enterococcus_A raffinosus_A", "ani": 91.594, "matched_fragments": 1139, "total_fragments": 1533, "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_000407185.1", "gtdb_species": "s__Enterococcus_A malodoratus", "ani": 82.1046, "matched_fragments": 815, "total_fragments": 1533, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.33", "min_intra_species_ani": "98.27", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.84", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_001886185.1", "gtdb_species": "s__Enterococcus_A raffinosus", "ani": 82.025, "matched_fragments": 741, "total_fragments": 1533, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.27", "min_intra_species_ani": "97.96", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.87", "num_clustered_genomes": 12, "status": "-" }, { "accession": "GCF_005405485.1", "gtdb_species": "s__Enterococcus_A hulanensis", "ani": 81.6362, "matched_fragments": 823, "total_fragments": 1533, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.15", "min_intra_species_ani": "97.02", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.81", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_017315985.1", "gtdb_species": "s__Enterococcus_A sp017315985", "ani": 81.3538, "matched_fragments": 796, "total_fragments": 1533, "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": 81.3323, "matched_fragments": 396, "total_fragments": 1533, "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_000407545.1", "gtdb_species": "s__Enterococcus_A gilvus", "ani": 81.1632, "matched_fragments": 643, "total_fragments": 1533, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.79", "min_intra_species_ani": "97.90", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.83", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_005405225.1", "gtdb_species": "s__Enterococcus_A dongliensis", "ani": 81.0422, "matched_fragments": 361, "total_fragments": 1533, "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": 80.962, "matched_fragments": 467, "total_fragments": 1533, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.65", "min_intra_species_ani": "99.31", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001544295.1", "gtdb_species": "s__Enterococcus_A pseudoavium", "ani": 80.936, "matched_fragments": 524, "total_fragments": 1533, "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": 80.41, "matched_fragments": 443, "total_fragments": 1533, "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_001885905.1", "gtdb_species": "s__Enterococcus_A devriesei", "ani": 80.2056, "matched_fragments": 544, "total_fragments": 1533, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.13", "min_intra_species_ani": "98.05", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.04, "cell_length": -0.019, "doubling_h": -0.346, "growth_tmp": 34.5, "optimum_tmp": 34.173, "optimum_ph": 9.6, "genome_size": 4450250.0, "gc_content": 38.565, "coding_genes": 2937.768, "rRNA16S_genes": 5.5, "tRNA_genes": 60.871, "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", "avium", "ATCC", "14025" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }