{ "type": "genome", "identifier": "GCF_000413035.1", "organism": "Treponema medium ATCC 700293", "title": "Treponema medium ATCC 700293", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Broad Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000413035.1", "bioproject": "PRJNA224116", "biosample": "SAMN02596986", "wgs_master": "ATFE00000000.1", "refseq_category": "na", "taxid": "1125700", "species_taxid": "58231", "organism_name": "Treponema medium ATCC 700293", "infraspecific_name": "strain=ATCC 700293", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/06/21", "asm_name": "Trep_medi_ATCC_700293_V1", "asm_submitter": "Broad Institute", "gbrs_paired_asm": "GCA_000413035.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/413/035/GCF_000413035.1_Trep_medi_ATCC_700293_V1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2727508", "genome_size_ungapped": "2715791", "gc_percent": "44.500000", "replicon_count": "0", "scaffold_count": "1", "contig_count": "19", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000413035.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "2384", "protein_coding_gene_count": "2289", "non_coding_gene_count": "56", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-06-21", "dateModified": "2013-06-21", "datePublished": "2013-06-21", "_annotation": { "sample_count": 1, "sample_organism": [ "Treponema medium ATCC 700293" ], "sample_taxid": [ "1125700" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.768 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)": "2727508", "Number of Sequences": "1", "Longest Sequences (bp)": "2727508", "N50 (bp)": "2727508", "Gap Ratio (%)": "0.429586", "GCcontent (%)": "44.3", "Number of CDSs": "2313", "Average Protein Length": "338.5", "Coding Ratio (%)": "86.1", "Number of rRNAs": "5", "Number of tRNAs": "49", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Treponema medium", "strain": "strain=ATCC 700293", "accession": "GCA_000413035.1", "taxid": 58231, "species_taxid": 58231, "relation_to_type": "type", "validated": true, "ani": 99.9999, "matched_fragments": 907, "total_fragments": 909, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Treponema medium", "strain": "strain=ATCC 700293", "accession": "GCA_017161265.1", "taxid": 58231, "species_taxid": 58231, "relation_to_type": "type", "validated": true, "ani": 99.9776, "matched_fragments": 906, "total_fragments": 909, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Treponema putidum", "strain": "strain=OMZ 758", "accession": "GCA_000755145.1", "taxid": 221027, "species_taxid": 221027, "relation_to_type": "type", "validated": true, "ani": 80.9815, "matched_fragments": 109, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Treponema putidum", "strain": "strain=ATCC 700334", "accession": "GCA_007830595.1", "taxid": 221027, "species_taxid": 221027, "relation_to_type": "type", "validated": true, "ani": 80.8225, "matched_fragments": 108, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Treponema 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"d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.95", "min_intra_species_ani": "97.95", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.59, "cell_length": 0.834, "doubling_h": 0.49, "growth_tmp": 37.0, "optimum_tmp": 33.75, "optimum_ph": 7.183, "genome_size": 2715791.0, "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", "medium", "ATCC", "700293" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }