{ "type": "genome", "identifier": "GCF_003987595.1", "organism": "Vagococcus entomophilus", "title": "Vagococcus entomophilus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Centers for Disease Control and Prevention", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003987595.1", "bioproject": "PRJNA224116", "biosample": "SAMN06609013", "wgs_master": "NGJZ00000000.1", "refseq_category": "reference genome", "taxid": "1160095", "species_taxid": "1160095", "organism_name": "Vagococcus entomophilus", "infraspecific_name": "strain=DSM 24756", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/12/17", "asm_name": "ASM398759v1", "asm_submitter": "Centers for Disease Control and Prevention", "gbrs_paired_asm": "GCA_003987595.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/987/595/GCF_003987595.1_ASM398759v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2444868", "genome_size_ungapped": "2444868", "gc_percent": "36.500000", "replicon_count": "0", "scaffold_count": "7", "contig_count": "7", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003987595.1-RS_2024_05_04", "annotation_date": "2024-05-04", "total_gene_count": "2367", "protein_coding_gene_count": "2276", "non_coding_gene_count": "65", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-12-17", "dateModified": "2018-12-17", "datePublished": "2018-12-17", "_annotation": { "sample_count": 1, "sample_organism": [ "Vagococcus entomophilus" ], "sample_taxid": [ "1160095" ], "sample_host_organism": [ "Vespula vulgaris" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Czech Republic: Prague" ], "sample_host_location_id": [], "data_size": "0.688 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)": "2444868", "Number of Sequences": "7", "Longest Sequences (bp)": "1260240", "N50 (bp)": "1260240", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "36.5", "Number of CDSs": "2339", "Average Protein Length": "303.7", "Coding Ratio (%)": "87.2", "Number of rRNAs": "5", "Number of tRNAs": "51", "Number of CRISPRs": "5" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Vagococcus entomophilus", "strain": "strain=DSM 24756", "accession": "GCA_003987595.1", "taxid": 1160095, "species_taxid": 1160095, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 812, "total_fragments": 812, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Enterococcus lactis", "strain": "strain=CCM 8412", "accession": "GCA_015751045.1", "taxid": 357441, "species_taxid": 357441, "relation_to_type": "type", "validated": true, "ani": 78.3596, "matched_fragments": 58, "total_fragments": 812, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus hirae", "strain": "strain=ATCC 9790", "accession": "GCA_000271405.2", "taxid": 1354, "species_taxid": 1354, "relation_to_type": "type", "validated": true, "ani": 78.3043, "matched_fragments": 59, "total_fragments": 812, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus hirae", "strain": "strain=DSM 20160", "accession": "GCA_001885955.1", "taxid": 1354, "species_taxid": 1354, "relation_to_type": "type", "validated": true, "ani": 78.2535, "matched_fragments": 60, "total_fragments": 812, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus hirae", "strain": "strain=FDAARGOS_1123", "accession": "GCA_016766815.1", "taxid": 1354, "species_taxid": 1354, "relation_to_type": "type", "validated": true, "ani": 78.2131, "matched_fragments": 58, "total_fragments": 812, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus hirae", "strain": "strain=ATCC 9790", "accession": "GCA_000393835.1", "taxid": 1354, "species_taxid": 1354, "relation_to_type": "type", "validated": true, "ani": 78.1772, "matched_fragments": 58, "total_fragments": 812, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus hirae", "strain": "strain=ATCC 9790", "accession": "GCA_000407425.1", "taxid": 1354, "species_taxid": 1354, "relation_to_type": "type", "validated": true, "ani": 78.1218, "matched_fragments": 58, "total_fragments": 812, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus ureasiticus", "strain": "strain=DSM 23328", "accession": "GCA_001730285.1", "taxid": 903984, "species_taxid": 903984, "relation_to_type": "type", "validated": true, "ani": 78.0045, "matched_fragments": 80, "total_fragments": 812, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus thailandicus", "strain": "strain=NBRC 101867", "accession": "GCA_007989705.1", "taxid": 417368, "species_taxid": 417368, "relation_to_type": "type", "validated": true, "ani": 77.992, "matched_fragments": 80, "total_fragments": 812, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus thailandicus", "strain": "strain=DSM 21767", "accession": "GCA_001886265.1", "taxid": 417368, "species_taxid": 417368, "relation_to_type": "type", "validated": true, "ani": 77.8903, "matched_fragments": 80, "total_fragments": 812, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus quebecensis", "strain": "strain=LMG 26306", "accession": "GCA_001730365.1", "taxid": 903983, "species_taxid": 903983, "relation_to_type": "type", "validated": true, "ani": 77.8213, "matched_fragments": 69, "total_fragments": 812, "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": 77.7773, "matched_fragments": 68, "total_fragments": 812, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vagococcus silagei", "strain": "strain=2B-2", "accession": "GCA_004795745.1", "taxid": 2508885, "species_taxid": 2508885, "relation_to_type": "type", "validated": true, "ani": 77.7465, "matched_fragments": 65, "total_fragments": 812, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus cecorum", "strain": "strain=ATCC 43198", "accession": "GCA_000492155.1", "taxid": 44008, "species_taxid": 44008, "relation_to_type": "type", "validated": true, "ani": 77.6967, "matched_fragments": 59, "total_fragments": 812, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vagococcus coleopterorum", "strain": "strain=HDW17A", "accession": "GCA_011303955.1", "taxid": 2714946, "species_taxid": 2714946, "relation_to_type": "type", "validated": true, "ani": 77.6877, "matched_fragments": 52, "total_fragments": 812, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vagococcus salmoninarum", "strain": "strain=NCFB 2777", "accession": "GCA_003987495.1", "taxid": 2739, "species_taxid": 2739, "relation_to_type": "type", "validated": true, "ani": 77.6654, "matched_fragments": 55, "total_fragments": 812, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus quebecensis", "strain": "strain=DSM 23327", "accession": "GCA_001886145.1", "taxid": 903983, "species_taxid": 903983, "relation_to_type": "type", "validated": true, "ani": 77.5661, "matched_fragments": 68, "total_fragments": 812, "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": 77.5359, "matched_fragments": 56, "total_fragments": 812, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vagococcus allomyrinae", "strain": "strain=BWB3-3", "accession": "GCA_017829975.1", "taxid": 2794353, "species_taxid": 2794353, "relation_to_type": "type", "validated": true, "ani": 77.4478, "matched_fragments": 61, "total_fragments": 812, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus cecorum", "strain": "strain=DSM 20682", "accession": "GCA_000379745.1", "taxid": 44008, "species_taxid": 44008, "relation_to_type": "type", "validated": true, "ani": 77.432, "matched_fragments": 55, "total_fragments": 812, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus ratti", "strain": "strain=DSM 15687", "accession": "GCA_001886195.1", "taxid": 150033, "species_taxid": 150033, "relation_to_type": "type", "validated": true, "ani": 77.4181, "matched_fragments": 69, "total_fragments": 812, "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": 77.3821, "matched_fragments": 55, "total_fragments": 812, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus canintestini", "strain": "strain=DSM 21207", "accession": "GCA_001885735.1", "taxid": 317010, "species_taxid": 317010, "relation_to_type": "type", "validated": true, "ani": 77.3162, "matched_fragments": 62, "total_fragments": 812, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vagococcus carniphilus", "strain": "strain=ATCC BAA-640", "accession": "GCA_014397115.1", "taxid": 218144, "species_taxid": 218144, "relation_to_type": "type", "validated": true, "ani": 77.2515, "matched_fragments": 76, "total_fragments": 812, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003987595.1", "gtdb_species": "s__Vagococcus_E entomophilus", "ani": 100.0, "matched_fragments": 812, "total_fragments": 812, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_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": "conclusive" }, { "accession": "GCA_000271405.2", "gtdb_species": 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"matched_fragments": 63, "total_fragments": 812, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.82", "min_intra_species_ani": "97.77", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001730315.1", "gtdb_species": "s__Enterococcus ureilyticus", "ani": 77.975, "matched_fragments": 78, "total_fragments": 812, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.76", "min_intra_species_ani": "99.29", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.94", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_001886265.1", "gtdb_species": "s__Enterococcus_B thailandicus", "ani": 77.935, "matched_fragments": 79, "total_fragments": 812, 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