{ "type": "genome", "identifier": "GCF_004792515.1", "organism": "Vagococcus xieshaowenii", "title": "Vagococcus xieshaowenii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Chinese Center for Disease Control and Prevention", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004792515.1", "bioproject": "PRJNA224116", "biosample": "SAMN11283524", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2562451", "species_taxid": "2562451", "organism_name": "Vagococcus xieshaowenii", "infraspecific_name": "strain=CF-49", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/04/14", "asm_name": "ASM479251v1", "asm_submitter": "Chinese Center for Disease Control and Prevention", "gbrs_paired_asm": "GCA_004792515.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/792/515/GCF_004792515.1_ASM479251v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2071287", "genome_size_ungapped": "2071287", "gc_percent": "35.500000", "replicon_count": "3", "scaffold_count": "3", "contig_count": "3", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004792515.1-RS_2024_04_30", "annotation_date": "2024-04-30", "total_gene_count": "2023", "protein_coding_gene_count": "1908", "non_coding_gene_count": "84", "pubmed_id": "32195646" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-04-14", "dateModified": "2019-04-14", "datePublished": "2019-04-14", "_annotation": { "sample_count": 1, "sample_organism": [ "Vagococcus xieshaowenii" ], "sample_taxid": [ "2562451" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Tibet Plateau,Qinghai" ], "sample_host_location_id": [], "data_size": "0.578 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)": "2071287", "Number of Sequences": "3", "Longest Sequences (bp)": "1983513", "N50 (bp)": "1983513", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "35.5", "Number of CDSs": "1959", "Average Protein Length": "308.3", "Coding Ratio (%)": "87.5", "Number of rRNAs": "22", "Number of tRNAs": "58", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Vagococcus xieshaowenii", "strain": "strain=personal::cf-49", "accession": "GCA_004792515.1", "taxid": 2562451, 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"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": 77.7942, "matched_fragments": 97, "total_fragments": 690, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus haemoperoxidus", "strain": "strain=DSM 15920", "accession": "GCA_001885985.1", "taxid": 155618, "species_taxid": 155618, "relation_to_type": "type", "validated": true, "ani": 77.6311, "matched_fragments": 84, "total_fragments": 690, "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": 77.4751, "matched_fragments": 56, "total_fragments": 690, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus ureilyticus", "strain": "strain=CCUG 48799", "accession": "GCA_002806915.1", "taxid": 1131292, "species_taxid": 1131292, "relation_to_type": "type", "validated": true, "ani": 77.4172, "matched_fragments": 69, "total_fragments": 690, "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": 77.3569, "matched_fragments": 74, "total_fragments": 690, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus rivorum", "strain": "strain=LMG 25899", "accession": "GCA_001742285.1", "taxid": 762845, "species_taxid": 762845, "relation_to_type": "type", "validated": true, "ani": 77.0596, "matched_fragments": 74, "total_fragments": 690, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004792515.1", "gtdb_species": "s__Vagococcus_A sp004792515", "ani": 100.0, "matched_fragments": 690, "total_fragments": 690, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_005145005.1", "gtdb_species": "s__Vagococcus_A zengguangii", "ani": 83.0014, "matched_fragments": 415, "total_fragments": 690, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.48", "min_intra_species_ani": "99.48", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": 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"vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Vagococcus", "xieshaowenii" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }