{ "type": "genome", "identifier": "GCF_017893965.1", "organism": "Treponema parvum", "title": "Treponema parvum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "The University of Hong Kong", "publication": [ {} ], "properties": { "assembly_accession": "GCF_017893965.1", "bioproject": "PRJNA224116", "biosample": "SAMN15062831", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "138851", "species_taxid": "138851", "organism_name": "Treponema parvum", "infraspecific_name": "strain=ATCC 700770", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/04/09", "asm_name": "ASM1789396v1", "asm_submitter": "The University of Hong Kong", "gbrs_paired_asm": "GCA_017893965.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/017/893/965/GCF_017893965.1_ASM1789396v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2658287", "genome_size_ungapped": "2658287", "gc_percent": "44.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_017893965.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "2340", "protein_coding_gene_count": "2273", "non_coding_gene_count": "56", "pubmed_id": "34236225" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-04-09", "dateModified": "2021-04-09", "datePublished": "2021-04-09", "_annotation": { "sample_count": 1, "sample_organism": [ "Treponema parvum" ], "sample_taxid": [ "138851" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "0.749 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)": "2658287", "Number of Sequences": "1", "Longest Sequences (bp)": "2658287", "N50 (bp)": "2658287", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "44.0", "Number of CDSs": "2295", "Average Protein Length": "346.7", "Coding Ratio (%)": "89.8", "Number of rRNAs": "6", "Number of tRNAs": "47", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Treponema parvum", "strain": "strain=ATCC 700770", "accession": "GCA_017893965.1", "taxid": 138851, "species_taxid": 138851, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 886, "total_fragments": 886, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Treponema maltophilum", "strain": "strain=ATCC 51939", "accession": "GCA_000413055.1", "taxid": 51160, "species_taxid": 51160, "relation_to_type": "type", "validated": true, "ani": 79.6432, "matched_fragments": 76, "total_fragments": 886, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_017893965.1", "gtdb_species": "s__Treponema_D parvum", "ani": 100.0, "matched_fragments": 886, "total_fragments": 886, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "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_017893945.1", "gtdb_species": "s__Treponema_D parvum_A", "ani": 94.8626, "matched_fragments": 767, "total_fragments": 886, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.67", "min_intra_species_ani": "97.67", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000413055.1", "gtdb_species": "s__Treponema_C maltophilum", "ani": 79.5756, "matched_fragments": 77, "total_fragments": 886, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_C", "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": "GCA_000413015.1", "gtdb_species": "s__Treponema_D paredis", "ani": 78.795, "matched_fragments": 105, "total_fragments": 886, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.58", "min_intra_species_ani": "95.58", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.222, "cell_length": 1.079, "doubling_h": 0.49, "growth_tmp": 36.0, "optimum_tmp": 33.75, "optimum_ph": 7.183, "genome_size": 2974429.677, "gc_content": 43.752, "coding_genes": 2837.944, "rRNA16S_genes": 2.285, "tRNA_genes": 45.166, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "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": [ "Treponema", "parvum" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }