{ "type": "genome", "identifier": "GCF_005405345.1", "organism": "Enterococcus viikkiensis", "title": "Enterococcus viikkiensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Northeast Agricultural University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_005405345.1", "bioproject": "PRJNA224116", "biosample": "SAMD00164313", "wgs_master": "BJDW00000000.1", "refseq_category": "reference genome", "taxid": "930854", "species_taxid": "930854", "organism_name": "Enterococcus viikkiensis", "infraspecific_name": "strain=LMG 26075", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/29", "asm_name": "ASM540534v1", "asm_submitter": "Northeast Agricultural University", "gbrs_paired_asm": "GCA_005405345.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/005/405/345/GCF_005405345.1_ASM540534v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2545311", "genome_size_ungapped": "2545311", "gc_percent": "40.500000", "replicon_count": "0", "scaffold_count": "45", "contig_count": "45", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_005405345.1-RS_2024_08_26", "annotation_date": "2024-08-26", "total_gene_count": "2470", "protein_coding_gene_count": "2387", "non_coding_gene_count": "47", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-29", "dateModified": "2019-03-29", "datePublished": "2019-03-29", "_annotation": { "sample_count": 1, "sample_organism": [ "Enterococcus viikkiensis" ], "sample_taxid": [ "930854" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Finland" ], "sample_host_location_id": [], "data_size": "0.726 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "2545311", "Number of Sequences": "45", "Longest Sequences (bp)": "299606", "N50 (bp)": "118649", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "40.3", "Number of CDSs": "2423", "Average Protein Length": "302.3", "Coding Ratio (%)": "86.3", "Number of rRNAs": "2", "Number of tRNAs": "39", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Enterococcus viikkiensis", "strain": "strain=LMG 26075", "accession": "GCA_005405345.1", "taxid": 930854, "species_taxid": 930854, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 819, "total_fragments": 825, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Enterococcus devriesei", "strain": "strain=DSM 22802", "accession": "GCA_001885905.1", "taxid": 319970, "species_taxid": 319970, "relation_to_type": "type", "validated": true, "ani": 91.7632, "matched_fragments": 731, "total_fragments": 825, "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": 81.0624, "matched_fragments": 411, "total_fragments": 825, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus malodoratus", "strain": "strain=NCTC12365", "accession": "GCA_900447955.1", "taxid": 71451, "species_taxid": 71451, "relation_to_type": "type", "validated": true, "ani": 80.818, "matched_fragments": 480, "total_fragments": 825, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus malodoratus", "strain": "strain=ATCC 43197", "accession": "GCA_000407185.1", "taxid": 71451, "species_taxid": 71451, "relation_to_type": "type", "validated": true, "ani": 80.7226, "matched_fragments": 484, "total_fragments": 825, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus malodoratus", "strain": "strain=DSM 20681", "accession": "GCA_001886025.1", "taxid": 71451, "species_taxid": 71451, "relation_to_type": "type", "validated": true, "ani": 80.6761, "matched_fragments": 475, "total_fragments": 825, "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": 80.5629, "matched_fragments": 488, "total_fragments": 825, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus raffinosus", "strain": "strain=DSM 5633", "accession": "GCA_001886185.1", "taxid": 71452, "species_taxid": 71452, "relation_to_type": "type", "validated": true, "ani": 80.5305, "matched_fragments": 433, "total_fragments": 825, "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": 80.4986, "matched_fragments": 286, "total_fragments": 825, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus avium", "strain": "strain=NCTC9938", "accession": "GCA_900447655.1", "taxid": 33945, "species_taxid": 33945, "relation_to_type": "type", "validated": true, "ani": 80.4917, "matched_fragments": 446, "total_fragments": 825, "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": 80.4876, "matched_fragments": 436, "total_fragments": 825, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus xiangfangensis", "strain": "strain=11097", "accession": "GCA_005405365.1", "taxid": 1296537, "species_taxid": 1296537, "relation_to_type": "type", "validated": true, "ani": 80.4689, "matched_fragments": 396, "total_fragments": 825, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus raffinosus", "strain": "strain=NBRC 100492", "accession": "GCA_001544115.1", "taxid": 71452, "species_taxid": 71452, "relation_to_type": "type", "validated": true, "ani": 80.4627, "matched_fragments": 433, "total_fragments": 825, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus avium", "strain": "strain=ATCC 14025", "accession": "GCA_000407245.1", "taxid": 33945, "species_taxid": 33945, "relation_to_type": "type", "validated": true, "ani": 80.4026, "matched_fragments": 446, "total_fragments": 825, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus hermanniensis", "strain": "strain=DSM 17122", "accession": "GCA_001885945.1", "taxid": 249189, "species_taxid": 249189, "relation_to_type": "type", "validated": true, "ani": 79.9513, "matched_fragments": 401, "total_fragments": 825, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_005405345.1", "gtdb_species": "s__Enterococcus_A viikkiensis", "ani": 100.0, "matched_fragments": 819, "total_fragments": 825, "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": "conclusive" }, { "accession": "GCF_001885905.1", "gtdb_species": "s__Enterococcus_A devriesei", "ani": 91.7632, "matched_fragments": 731, "total_fragments": 825, "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": "-" }, { "accession": "GCF_000407185.1", "gtdb_species": "s__Enterococcus_A malodoratus", "ani": 80.7226, "matched_fragments": 484, "total_fragments": 825, "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_018917525.1", "gtdb_species": "s__Enterococcus_A raffinosus_A", "ani": 80.6081, "matched_fragments": 453, "total_fragments": 825, "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_005405485.1", "gtdb_species": "s__Enterococcus_A hulanensis", "ani": 80.5507, "matched_fragments": 489, "total_fragments": 825, "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_001886185.1", "gtdb_species": "s__Enterococcus_A raffinosus", "ani": 80.5254, "matched_fragments": 434, "total_fragments": 825, "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_005405225.1", "gtdb_species": "s__Enterococcus_A dongliensis", "ani": 80.4986, "matched_fragments": 286, "total_fragments": 825, "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_017315985.1", "gtdb_species": "s__Enterococcus_A sp017315985", "ani": 80.4774, "matched_fragments": 428, "total_fragments": 825, "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": 80.4598, "matched_fragments": 397, "total_fragments": 825, "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_000406965.1", "gtdb_species": "s__Enterococcus_A avium", "ani": 80.3589, "matched_fragments": 458, "total_fragments": 825, "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": "-" }, { "accession": "GCF_001885945.1", "gtdb_species": "s__Enterococcus_A hermanniensis", "ani": 79.9378, "matched_fragments": 402, "total_fragments": 825, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.04, "cell_length": -0.019, "doubling_h": -0.346, "growth_tmp": 37.0, "optimum_tmp": 30.0, "optimum_ph": 8.805, "genome_size": 2545311.0, "gc_content": 40.262, "coding_genes": 2937.768, "rRNA16S_genes": 5.5, "tRNA_genes": 60.871, "gram_stain": 1.0, "sporulation": 0.062, "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": 0.031, "coccus_cell_shape": 0.812, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.156, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Enterococcus", "viikkiensis" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }