{ "type": "genome", "identifier": "GCF_003814425.1", "organism": "Borreliella bavariensis PBi", "title": "Borreliella bavariensis PBi", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Bavarian Health and Food Safety Authority", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003814425.1", "bioproject": "PRJNA224116", "biosample": "SAMN08918524", "wgs_master": "na", "refseq_category": "na", "taxid": "290434", "species_taxid": "664662", "organism_name": "Borreliella bavariensis PBi", "infraspecific_name": "strain=PBi", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/11/23", "asm_name": "ASM381442v1", "asm_submitter": "Bavarian Health and Food Safety Authority", "gbrs_paired_asm": "GCA_003814425.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/814/425/GCF_003814425.1_ASM381442v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1279859", "genome_size_ungapped": "1279859", "gc_percent": "28.000000", "replicon_count": "12", "scaffold_count": "12", "contig_count": "12", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003814425.1-RS_2024_09_13", "annotation_date": "2024-09-13", "total_gene_count": "1301", "protein_coding_gene_count": "1179", "non_coding_gene_count": "41", "pubmed_id": "30586413" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-11-23", "dateModified": "2018-11-23", "datePublished": "2018-11-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Borreliella bavariensis PBi" ], "sample_taxid": [ "290434" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [ "Lyme borreliosis" ], "sample_host_disease_id": [], "sample_host_location": [ "Germany" ], "sample_host_location_id": [], "data_size": "0.344 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)": "1279859", "Number of Sequences": "12", "Longest Sequences (bp)": "905817", "N50 (bp)": "905817", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "27.8", "Number of CDSs": "1257", "Average Protein Length": "291.6", "Coding Ratio (%)": "85.9", "Number of rRNAs": "6", "Number of tRNAs": "33", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Borreliella garinii subsp. bavariensis", "strain": "strain=PBi", "accession": "GCA_003814425.1", "taxid": 664662, "species_taxid": 29519, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 420, "total_fragments": 422, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Borreliella garinii subsp. bavariensis", "strain": "strain=PBi", "accession": "GCA_000196215.1", "taxid": 664662, "species_taxid": 29519, "relation_to_type": "type", "validated": true, "ani": 99.9532, "matched_fragments": 328, "total_fragments": 422, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Borreliella garinii", "strain": "strain=CIP 103362", "accession": "GCA_001922545.1", "taxid": 29519, "species_taxid": 29519, "relation_to_type": "type", "validated": true, "ani": 96.9443, "matched_fragments": 364, "total_fragments": 422, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Borreliella garinii", "strain": "strain=20047", "accession": "GCA_003814405.1", "taxid": 29519, "species_taxid": 29519, "relation_to_type": "type", "validated": true, "ani": 96.8438, "matched_fragments": 367, "total_fragments": 422, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Borreliella afzelii", "strain": "strain=DSM 10508", "accession": "GCA_014202295.1", "taxid": 29518, "species_taxid": 29518, "relation_to_type": "type", "validated": true, "ani": 92.3936, "matched_fragments": 377, "total_fragments": 422, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Borreliella valaisiana", "strain": "strain=VS116", "accession": "GCA_000170955.2", "taxid": 62088, "species_taxid": 62088, "relation_to_type": "type", "validated": true, "ani": 91.7501, "matched_fragments": 364, "total_fragments": 422, "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": 91.7119, "matched_fragments": 369, "total_fragments": 422, "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": 91.5679, "matched_fragments": 357, "total_fragments": 422, "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": 91.2546, "matched_fragments": 377, "total_fragments": 422, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001922545.1", "gtdb_species": "s__Borreliella garinii", "ani": 96.9443, "matched_fragments": 364, "total_fragments": 422, "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": "conclusive" }, { "accession": "GCF_014202295.1", "gtdb_species": "s__Borreliella afzelii", "ani": 92.353, "matched_fragments": 378, "total_fragments": 422, "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_008828755.2", "gtdb_species": "s__Borreliella turdi", "ani": 91.9418, "matched_fragments": 348, "total_fragments": 422, "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": "GCF_000170955.2", "gtdb_species": "s__Borreliella valaisiana", "ani": 91.703, "matched_fragments": 365, "total_fragments": 422, "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": "-" }, { "accession": "GCF_001945665.1", "gtdb_species": "s__Borreliella mayonii", "ani": 91.6256, "matched_fragments": 371, "total_fragments": 422, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella", "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_014201705.1", "gtdb_species": "s__Borreliella spielmanii", "ani": 91.5846, "matched_fragments": 354, "total_fragments": 422, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.52", "min_intra_species_ani": "98.52", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900099615.1", "gtdb_species": "s__Borreliella japonica", "ani": 91.5679, "matched_fragments": 357, "total_fragments": 422, "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_014205895.1", "gtdb_species": "s__Borreliella lanei", "ani": 91.499, "matched_fragments": 345, "total_fragments": 422, "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_000181875.2", "gtdb_species": "s__Borreliella finlandensis", "ani": 91.2635, "matched_fragments": 364, "total_fragments": 422, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella", "ani_circumscription_radius": 96.6606, "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_000222305.1", "gtdb_species": "s__Borreliella bissettiae", "ani": 91.1817, "matched_fragments": 376, "total_fragments": 422, "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_000008685.2", "gtdb_species": "s__Borreliella burgdorferi", "ani": 91.1534, "matched_fragments": 379, "total_fragments": 422, "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": "-" }, { "accession": "GCF_014201775.1", "gtdb_species": "s__Borreliella yangtzensis", "ani": 90.6995, "matched_fragments": 365, "total_fragments": 422, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.699, "cell_length": 0.602, "doubling_h": 0.602, "growth_tmp": 33.166, "optimum_tmp": 32.817, "optimum_ph": null, "genome_size": 1097921.458, "gc_content": 26.989, "coding_genes": 1026.214, "rRNA16S_genes": 1.033, "tRNA_genes": 31.833, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.666, "range_salinity": 0.0, "facultative_respiration": 0.0, "anaerobic_respiration": 0.125, "aerobic_respiration": 0.875, "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", "bavariensis", "PBi" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }