{ "type": "genome", "identifier": "GCF_024181585.1", "organism": "Treponema socranskii subsp. buccale", "title": "Treponema socranskii subsp. buccale", "description": "na", "data type": "Genome sequencing and assembly", "organization": "The University of Hong Kong", "publication": [ {} ], "properties": { "assembly_accession": "GCF_024181585.1", "bioproject": "PRJNA224116", "biosample": "SAMN15042362", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "69713", "species_taxid": "53419", "organism_name": "Treponema socranskii subsp. buccale", "infraspecific_name": "strain=ATCC 35534", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/07/07", "asm_name": "ASM2418158v1", "asm_submitter": "The University of Hong Kong", "gbrs_paired_asm": "GCA_024181585.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/024/181/585/GCF_024181585.1_ASM2418158v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2805741", "genome_size_ungapped": "2805741", "gc_percent": "49.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_024181585.1-RS_2024_07_16", "annotation_date": "2024-07-16", "total_gene_count": "2522", "protein_coding_gene_count": "2435", "non_coding_gene_count": "60", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-07-07", "dateModified": "2022-07-07", "datePublished": "2022-07-07", "_annotation": { "sample_count": 1, "sample_organism": [ "Treponema socranskii subsp. buccale" ], "sample_taxid": [ "69713" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China" ], "sample_host_location_id": [], "data_size": "0.778 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)": "2805741", "Number of Sequences": "1", "Longest Sequences (bp)": "2805741", "N50 (bp)": "2805741", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "49.0", "Number of CDSs": "2463", "Average Protein Length": "335.1", "Coding Ratio (%)": "88.3", "Number of rRNAs": "9", "Number of tRNAs": "48", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Treponema maltophilum", "strain": "strain=ATCC 51939", "accession": "GCA_000413055.1", "taxid": 51160, "species_taxid": 51160, 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"num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014334325.1", "gtdb_species": "s__Treponema_D sp014334325", "ani": 90.1572, "matched_fragments": 678, "total_fragments": 935, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.62", "min_intra_species_ani": "95.62", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.82", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000413055.1", "gtdb_species": "s__Treponema_C maltophilum", "ani": 82.2168, "matched_fragments": 153, "total_fragments": 935, "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_002399405.1", "gtdb_species": "s__Treponema_D sp002399405", "ani": 76.7123, "matched_fragments": 136, "total_fragments": 935, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.20", "min_intra_species_ani": "98.20", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000212415.1", "gtdb_species": "s__Treponema_F brennaborense", "ani": 76.4045, "matched_fragments": 72, "total_fragments": 935, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_F", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.21", "min_intra_species_ani": "99.21", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.796, "cell_length": 0.778, "doubling_h": 0.49, "growth_tmp": 37.0, "optimum_tmp": 37.0, "optimum_ph": 7.183, "genome_size": 2779234.5, "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", "socranskii", "subsp.", "buccale" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }