{ "type": "genome", "identifier": "GCF_000170955.2", "organism": "Borreliella valaisiana VS116", "title": "Borreliella valaisiana VS116", "description": "na", "data type": "Genome sequencing and assembly", "organization": "J. Craig Venter Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000170955.2", "bioproject": "PRJNA224116", "biosample": "SAMN02436326", "wgs_master": "ABCY00000000.2", "refseq_category": "reference genome", "taxid": "445987", "species_taxid": "62088", "organism_name": "Borreliella valaisiana VS116", "infraspecific_name": "strain=VS116", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2009/03/04", "asm_name": "ASM17095v2", "asm_submitter": "J. Craig Venter Institute", "gbrs_paired_asm": "GCA_000170955.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/170/955/GCF_000170955.2_ASM17095v2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1258864", "genome_size_ungapped": "1258864", "gc_percent": "27.500000", "replicon_count": "12", "scaffold_count": "12", "contig_count": "12", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000170955.2-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "1261", "protein_coding_gene_count": "1158", "non_coding_gene_count": "40", "pubmed_id": "22207749" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2009-03-04", "dateModified": "2009-03-04", "datePublished": "2009-03-04", "_annotation": { "sample_count": 1, "sample_organism": [ "Borreliella valaisiana VS116" ], "sample_taxid": [ "445987" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.337 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)": "1258864", "Number of Sequences": "12", "Longest Sequences (bp)": "913294", "N50 (bp)": "913294", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "27.5", "Number of CDSs": "1243", "Average Protein Length": "289.4", "Coding Ratio (%)": "85.7", "Number of rRNAs": "5", "Number of tRNAs": "33", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Borreliella valaisiana", "strain": "strain=VS116", "accession": "GCA_000170955.2", "taxid": 62088, "species_taxid": 62088, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 413, "total_fragments": 413, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Borreliella yangtzensis", "strain": "strain=DSM 24625", "accession": "GCA_014201775.1", "taxid": 683292, "species_taxid": 683292, "relation_to_type": "type", "validated": true, "ani": 94.3807, "matched_fragments": 359, "total_fragments": 413, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Borreliella garinii", "strain": "strain=CIP 103362", "accession": "GCA_001922545.1", "taxid": 29519, "species_taxid": 29519, "relation_to_type": "type", "validated": true, "ani": 91.9807, "matched_fragments": 354, "total_fragments": 413, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Borreliella garinii", "strain": "strain=20047", "accession": "GCA_003814405.1", "taxid": 29519, "species_taxid": 29519, "relation_to_type": "type", "validated": true, "ani": 91.8472, "matched_fragments": 364, "total_fragments": 413, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Borreliella afzelii", "strain": "strain=DSM 10508", "accession": "GCA_014202295.1", "taxid": 29518, "species_taxid": 29518, "relation_to_type": "type", "validated": true, "ani": 91.5676, "matched_fragments": 360, "total_fragments": 413, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Borreliella japonica", "strain": "strain=ATCC 51557", "accession": "GCA_900099615.1", "taxid": 34095, "species_taxid": 34095, "relation_to_type": "type", "validated": true, "ani": 91.375, "matched_fragments": 354, "total_fragments": 413, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Borreliella lanei", "strain": "strain=DSM 17992", "accession": "GCA_014205895.1", "taxid": 373540, "species_taxid": 373540, "relation_to_type": "type", "validated": true, "ani": 91.2075, "matched_fragments": 347, "total_fragments": 413, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Borreliella mayonii", "strain": "strain=MN14-1420", "accession": "GCA_001945665.1", "taxid": 1674146, "species_taxid": 1674146, "relation_to_type": "type", "validated": true, "ani": 91.0021, "matched_fragments": 370, "total_fragments": 413, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Borreliella burgdorferi", "strain": "strain=FDAARGOS_196", "accession": "GCA_002083055.2", "taxid": 139, "species_taxid": 139, "relation_to_type": "type", "validated": true, "ani": 90.7431, "matched_fragments": 367, "total_fragments": 413, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Borreliella bissettiae", "strain": "strain=DN127", "accession": "GCA_000222305.1", "taxid": 64897, "species_taxid": 64897, "relation_to_type": "type", "validated": true, "ani": 90.5517, "matched_fragments": 360, "total_fragments": 413, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000170955.2", "gtdb_species": "s__Borreliella valaisiana", "ani": 100.0, "matched_fragments": 413, "total_fragments": 413, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.52", "min_intra_species_ani": "99.04", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 14, "status": "conclusive" }, { "accession": "GCF_014201775.1", "gtdb_species": "s__Borreliella yangtzensis", "ani": 94.276, "matched_fragments": 361, "total_fragments": 413, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella", "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_001922545.1", "gtdb_species": "s__Borreliella garinii", "ani": 91.977, "matched_fragments": 354, "total_fragments": 413, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.97", "min_intra_species_ani": "96.83", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.85", "num_clustered_genomes": 112, "status": "-" }, { "accession": "GCF_014202295.1", "gtdb_species": "s__Borreliella afzelii", "ani": 91.5424, "matched_fragments": 360, "total_fragments": 413, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.29", "min_intra_species_ani": "99.08", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.92", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_900099615.1", "gtdb_species": "s__Borreliella japonica", "ani": 91.375, "matched_fragments": 354, "total_fragments": 413, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella", "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_008828755.2", "gtdb_species": "s__Borreliella turdi", "ani": 91.3062, "matched_fragments": 353, "total_fragments": 413, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.10", "min_intra_species_ani": "99.04", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 3, "status": "-" }, { "accession": 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"ani": 90.6767, "matched_fragments": 376, "total_fragments": 413, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella", "ani_circumscription_radius": 96.6606, "mean_intra_species_ani": "99.04", "min_intra_species_ani": "98.60", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.83", "num_clustered_genomes": 102, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.699, "cell_length": 0.602, "doubling_h": 0.602, "growth_tmp": 33.166, "optimum_tmp": 30.0, "optimum_ph": null, "genome_size": 1045928.0, "gc_content": 25.988, "coding_genes": 901.0, "rRNA16S_genes": 1.0, "tRNA_genes": 32.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 0.0, "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": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 1.0 }, "_genome_taxon": [ "Borreliella", "valaisiana", "VS116" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }