{ "type": "genome", "identifier": "GCF_900447935.1", "organism": "Enterococcus gallinarum", "title": "Enterococcus gallinarum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "SC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900447935.1", "bioproject": "PRJNA224116", "biosample": "SAMEA3679189", "wgs_master": "UFYU00000000.1", "refseq_category": "na", "taxid": "1353", "species_taxid": "1353", "organism_name": "Enterococcus gallinarum", "infraspecific_name": "strain=NCTC12359", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/08/01", "asm_name": "43071_G02", "asm_submitter": "SC", "gbrs_paired_asm": "GCA_900447935.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/447/935/GCF_900447935.1_43071_G02", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3931773", "genome_size_ungapped": "3931773", "gc_percent": "39.500000", "replicon_count": "0", "scaffold_count": "9", "contig_count": "9", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900447935.1-RS_2024_12_23", "annotation_date": "2024-12-23", "total_gene_count": "3850", "protein_coding_gene_count": "3691", "non_coding_gene_count": "85", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-08-01", "dateModified": "2018-08-01", "datePublished": "2018-08-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Enterococcus gallinarum" ], "sample_taxid": [ "1353" ], "sample_host_organism": [ "Chicken" ], "sample_host_organism_id": [], "sample_host_disease": [ "not available: to be reported later" ], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.109 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)": "3931773", "Number of Sequences": "9", "Longest Sequences (bp)": "1941722", "N50 (bp)": "1400470", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "39.7", "Number of CDSs": "3808", "Average Protein Length": "293.9", "Coding Ratio (%)": "85.4", "Number of rRNAs": "16", "Number of tRNAs": "64", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Enterococcus gallinarum", "strain": "strain=NCTC12359", "accession": "GCA_900447935.1", "taxid": 1353, "species_taxid": 1353, "relation_to_type": "suspected-type", "validated": true, "ani": 100.0, "matched_fragments": 1303, "total_fragments": 1306, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Enterococcus gallinarum", "strain": "strain=NBRC 100675", "accession": "GCA_001544275.1", "taxid": 1353, "species_taxid": 1353, "relation_to_type": "suspected-type", "validated": true, "ani": 99.938, "matched_fragments": 1215, "total_fragments": 1306, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Enterococcus gallinarum", "strain": "strain=DSM 24841", "accession": "GCA_001886155.1", "taxid": 1353, "species_taxid": 1353, "relation_to_type": "suspected-type", "validated": true, "ani": 99.9199, "matched_fragments": 1177, "total_fragments": 1306, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Enterococcus casseliflavus", "strain": "strain=NBRC 100478", "accession": "GCA_001544095.1", "taxid": 37734, "species_taxid": 37734, "relation_to_type": "type", "validated": true, "ani": 80.7479, "matched_fragments": 406, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus casseliflavus", "strain": "strain=DSM 20680", "accession": "GCA_001885845.1", "taxid": 37734, "species_taxid": 37734, "relation_to_type": "type", "validated": true, "ani": 80.6297, "matched_fragments": 408, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus mediterraneensis", "strain": "strain=Marseille-P4358", "accession": "GCA_900604485.1", "taxid": 2364791, "species_taxid": 2364791, "relation_to_type": "type", "validated": true, "ani": 79.6855, "matched_fragments": 187, "total_fragments": 1306, "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": 78.5983, "matched_fragments": 122, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001544275.1", "gtdb_species": "s__Enterococcus_D gallinarum", "ani": 99.938, "matched_fragments": 1215, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.60", "min_intra_species_ani": "97.23", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.80", "num_clustered_genomes": 74, "status": "conclusive" }, { "accession": "GCF_001544095.1", "gtdb_species": "s__Enterococcus_D casseliflavus", "ani": 80.7328, "matched_fragments": 407, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.00", "min_intra_species_ani": "95.35", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.83", "num_clustered_genomes": 83, "status": "-" }, { "accession": "GCF_002850555.1", "gtdb_species": "s__Enterococcus_D sp002850555", "ani": 80.3098, "matched_fragments": 426, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.34", "min_intra_species_ani": "95.31", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.74", "num_clustered_genomes": 46, "status": "-" }, { "accession": "GCF_900604485.1", "gtdb_species": "s__Enterococcus_C mediterraneensis", "ani": 79.6833, "matched_fragments": 187, "total_fragments": 1306, "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_002140915.1", "gtdb_species": "s__Enterococcus_D sp002140915", "ani": 79.6238, "matched_fragments": 337, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D", "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_001297065.1", "gtdb_species": "s__Enterococcus_D sp001297065", "ani": 79.4922, "matched_fragments": 349, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.01", "min_intra_species_ani": "96.72", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.84", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_003795145.1", "gtdb_species": "s__Tetragenococcus koreensis", "ani": 78.8643, "matched_fragments": 87, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Tetragenococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.21", "min_intra_species_ani": "98.98", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.90", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_000407285.1", "gtdb_species": "s__Enterococcus_F saccharolyticus", "ani": 78.72, "matched_fragments": 141, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_F", "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_002197645.1", "gtdb_species": "s__Enterococcus wangshanyuanii", "ani": 78.5983, "matched_fragments": 122, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus", "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": "GCF_017315945.1", "gtdb_species": "s__Enterococcus_B sp017315945", "ani": 78.4344, "matched_fragments": 150, "total_fragments": 1306, "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_001544255.1", "gtdb_species": "s__Enterococcus_B faecium", "ani": 78.2953, "matched_fragments": 148, "total_fragments": 1306, "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_005405485.1", "gtdb_species": "s__Enterococcus_A hulanensis", "ani": 78.1127, "matched_fragments": 117, "total_fragments": 1306, "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_014635985.1", "gtdb_species": "s__Enterococcus_I alcedinis", "ani": 77.8732, "matched_fragments": 83, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_I", "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": "GCF_001730285.1", "gtdb_species": "s__Enterococcus ureasiticus", "ani": 77.7408, "matched_fragments": 116, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.19", "min_intra_species_ani": "96.18", "mean_intra_species_af": "0.80", "min_intra_species_af": "0.79", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.04, "cell_length": -0.019, "doubling_h": -0.346, "growth_tmp": 37.0, "optimum_tmp": 34.173, "optimum_ph": 8.805, "genome_size": 3578473.375, "gc_content": 40.891, "coding_genes": 3417.5, "rRNA16S_genes": 5.0, "tRNA_genes": 61.0, "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", "gallinarum" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }