{ "type": "genome", "identifier": "GCF_014202035.1", "organism": "Treponema rectale", "title": "Treponema rectale", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014202035.1", "bioproject": "PRJNA224116", "biosample": "SAMN14908544", "wgs_master": "JACHFR000000000.1", "refseq_category": "reference genome", "taxid": "744512", "species_taxid": "744512", "organism_name": "Treponema rectale", "infraspecific_name": "strain=DSM 103679", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/08/14", "asm_name": "ASM1420203v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_014202035.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/202/035/GCF_014202035.1_ASM1420203v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2869177", "genome_size_ungapped": "2868889", "gc_percent": "39.000000", "replicon_count": "0", "scaffold_count": "6", "contig_count": "6", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014202035.1-RS_2024_05_05", "annotation_date": "2024-05-05", "total_gene_count": "2459", "protein_coding_gene_count": "2398", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-08-14", "dateModified": "2020-08-14", "datePublished": "2020-08-14", "_annotation": { "sample_count": 1, "sample_organism": [ "Treponema rectale" ], "sample_taxid": [ "744512" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "0.800 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)": "2869177", "Number of Sequences": "6", "Longest Sequences (bp)": "1051090", "N50 (bp)": "1039330", "Gap Ratio (%)": "0.010038", "GCcontent (%)": "39.2", "Number of CDSs": "2405", "Average Protein Length": "365.2", "Coding Ratio (%)": "91.8", "Number of rRNAs": "3", "Number of tRNAs": "43", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Treponema rectale", "strain": "strain=DSM 103679", "accession": "GCA_014202035.1", "taxid": 744512, "species_taxid": 744512, "relation_to_type": "suspected-type", "validated": true, "ani": 100.0, "matched_fragments": 953, "total_fragments": 953, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Treponema succinifaciens", "strain": "strain=DSM 2489", "accession": "GCA_000195275.1", "taxid": 167, "species_taxid": 167, "relation_to_type": "type", "validated": true, "ani": 77.8846, "matched_fragments": 122, "total_fragments": 953, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Treponema porcinum", "strain": "strain=ATCC BAA-908", "accession": "GCA_900167145.1", "taxid": 261392, "species_taxid": 261392, "relation_to_type": "type", "validated": true, "ani": 77.3579, "matched_fragments": 75, "total_fragments": 953, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Treponema peruense", "strain": "strain=RCC2812", "accession": "GCA_016117655.1", "taxid": 2787628, "species_taxid": 2787628, "relation_to_type": "type", "validated": true, "ani": 77.1753, "matched_fragments": 144, "total_fragments": 953, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014202035.1", "gtdb_species": "s__Treponema_D rectale", "ani": 100.0, "matched_fragments": 953, "total_fragments": 953, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.45", "min_intra_species_ani": "97.19", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_900113965.1", "gtdb_species": "s__Treponema_D bryantii_A", "ani": 78.0474, "matched_fragments": 112, "total_fragments": 953, "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": "-" }, { "accession": "GCF_000195275.1", "gtdb_species": "s__Treponema_D succinifaciens", "ani": 77.8568, "matched_fragments": 123, "total_fragments": 953, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.40", "min_intra_species_ani": "98.24", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_016294035.1", "gtdb_species": "s__Treponema_D sp016294035", "ani": 77.7666, "matched_fragments": 120, "total_fragments": 953, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.69", "min_intra_species_ani": "98.66", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_016293645.1", "gtdb_species": "s__Treponema_D sp016293645", "ani": 77.6522, "matched_fragments": 92, "total_fragments": 953, "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": "-" }, { "accession": "GCA_016297415.1", "gtdb_species": "s__Treponema_D sp016297415", "ani": 77.6437, "matched_fragments": 81, "total_fragments": 953, "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": "-" }, { "accession": "GCF_900167025.1", "gtdb_species": "s__Treponema_D berlinense", "ani": 77.5586, "matched_fragments": 88, "total_fragments": 953, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.85", "min_intra_species_ani": "98.81", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_002395155.1", "gtdb_species": "s__Treponema_D sp002395155", "ani": 77.4561, "matched_fragments": 101, "total_fragments": 953, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.78", "min_intra_species_ani": "97.65", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.82", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_017534445.1", "gtdb_species": "s__Treponema_D sp017534445", "ani": 77.3586, "matched_fragments": 68, "total_fragments": 953, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.88", "min_intra_species_ani": "96.88", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_017392945.1", "gtdb_species": "s__Treponema_D sp017392945", "ani": 77.3463, "matched_fragments": 101, "total_fragments": 953, "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": "-" }, { "accession": "GCA_018384055.1", "gtdb_species": "s__Treponema_D sp018384055", "ani": 77.2405, "matched_fragments": 122, "total_fragments": 953, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.95", "min_intra_species_ani": "98.78", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_017614655.1", "gtdb_species": "s__Treponema_D sp017614655", "ani": 77.1824, "matched_fragments": 126, "total_fragments": 953, "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": "-" }, { "accession": "GCF_016117655.1", "gtdb_species": "s__Treponema_D sp900541995", "ani": 77.1794, "matched_fragments": 143, "total_fragments": 953, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.86", "min_intra_species_ani": "98.78", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_017614295.1", "gtdb_species": "s__Treponema_D sp017614295", "ani": 77.1558, "matched_fragments": 72, "total_fragments": 953, "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": "-" }, { "accession": "GCA_902789325.1", "gtdb_species": "s__Treponema_D sp902789325", "ani": 77.1312, "matched_fragments": 87, "total_fragments": 953, "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": "-" }, { "accession": "GCA_902797305.1", "gtdb_species": "s__Treponema_D sp902797305", "ani": 76.9432, "matched_fragments": 74, "total_fragments": 953, "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": "-" }, { "accession": "GCA_902766125.1", "gtdb_species": "s__Treponema_D sp902766125", "ani": 76.9382, "matched_fragments": 102, "total_fragments": 953, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.55", "min_intra_species_ani": "99.55", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900769985.1", "gtdb_species": "s__Treponema_D sp900769985", "ani": 76.8387, "matched_fragments": 91, "total_fragments": 953, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.33", "min_intra_species_ani": "98.33", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_002396325.1", "gtdb_species": "s__Treponema_D sp002396325", "ani": 76.837, "matched_fragments": 50, "total_fragments": 953, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.85", "min_intra_species_ani": "97.87", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.82", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCA_017476165.1", "gtdb_species": "s__Treponema_D sp017476165", "ani": 76.8258, "matched_fragments": 56, "total_fragments": 953, "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": "-" }, { "accession": "GCA_016282455.1", "gtdb_species": "s__Treponema_D sp016282455", "ani": 76.8138, "matched_fragments": 83, "total_fragments": 953, "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": "-" }, { "accession": "GCA_017550685.1", "gtdb_species": "s__Treponema_D sp017550685", "ani": 76.7042, "matched_fragments": 75, "total_fragments": 953, "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": "-" }, { "accession": "GCA_002373205.1", "gtdb_species": "s__Treponema_D sp002373205", "ani": 76.6819, "matched_fragments": 64, "total_fragments": 953, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.79", "min_intra_species_ani": "96.03", "mean_intra_species_af": "0.78", "min_intra_species_af": "0.67", "num_clustered_genomes": 16, "status": "-" }, { "accession": "GCA_017548565.1", "gtdb_species": "s__Treponema_D sp017548565", "ani": 76.6395, "matched_fragments": 86, "total_fragments": 953, "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": "-" }, { "accession": "GCA_902772975.1", "gtdb_species": "s__Treponema_D sp902772975", "ani": 76.6219, "matched_fragments": 73, "total_fragments": 953, "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": "-" }, { "accession": "GCA_017395545.1", "gtdb_species": "s__Treponema_D sp017395545", "ani": 75.9642, "matched_fragments": 60, "total_fragments": 953, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.59, "cell_length": 0.834, "doubling_h": 0.49, "growth_tmp": 35.047, "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": 0.055, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.055, "spiral_cell_shape": 0.888 }, "_genome_taxon": [ "Treponema", "rectale" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }