{ "type": "genome", "identifier": "GCA_022782005.1", "organism": "Spirochaetia bacterium", "title": "Spirochaetia bacterium", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "AAFC", "publication": [ {} ], "properties": { "assembly_accession": "GCA_022782005.1", "bioproject": "PRJNA629856", "biosample": "SAMN26525510", "wgs_master": "JALESD000000000.1", "refseq_category": "na", "taxid": "2053615", "species_taxid": "2053615", "organism_name": "Spirochaetia bacterium", "infraspecific_name": "", "isolate": "SUG286", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/04/01", "asm_name": "ASM2278200v1", "submitter": "AAFC", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/022/782/005/GCA_022782005.1_ASM2278200v1", "excluded_from_refseq": "derived from metagenome; genus undefined", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-04-01", "dateModified": "2022-04-01", "datePublished": "2022-04-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Spirochaetia bacterium" ], "sample_taxid": [ "2053615" ], "sample_host_organism": [ "Sus scrofa domesticus" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Canada:Lacombe" ], "sample_host_location_id": [], "data_size": "0.700 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 8.33, "strain_heterogeneity": 50.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2492399", "Number of Sequences": "282", "Longest Sequences (bp)": "69389", "N50 (bp)": "13878", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "37.1", "Number of CDSs": "1955", "Average Protein Length": "331.4", "Coding Ratio (%)": "78.0", "Number of rRNAs": "1", "Number of tRNAs": "45", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "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": 77.6181, "matched_fragments": 115, "total_fragments": 681, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Treponema berlinense", "strain": "strain=ATCC BAA-909", "accession": "GCA_900167025.1", "taxid": 225004, "species_taxid": 225004, "relation_to_type": "type", "validated": true, "ani": 77.3057, "matched_fragments": 74, "total_fragments": 681, "ani_threshold": 95, "status": "below_threshold" }, { "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": 76.8944, "matched_fragments": 84, "total_fragments": 681, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Treponema succinifaciens", "strain": "strain=DSM 2489", "accession": "GCA_000195275.1", "taxid": 167, "species_taxid": 167, "relation_to_type": "type", "validated": true, "ani": 76.2269, "matched_fragments": 57, "total_fragments": 681, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Treponema ruminis", "strain": "strain=DSM 103462", "accession": "GCA_014201975.1", "taxid": 744515, "species_taxid": 744515, "relation_to_type": "type", "validated": true, "ani": 76.0686, "matched_fragments": 60, "total_fragments": 681, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 8.33, "strain_heterogeneity": 50.0 }, "gtdb_result": [ { "accession": "GCA_017381365.1", "gtdb_species": "s__Treponema_D sp017381365", "ani": 98.4347, "matched_fragments": 578, "total_fragments": 681, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.14", "min_intra_species_ani": "97.14", "mean_intra_species_af": "0.75", "min_intra_species_af": "0.75", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCA_017392945.1", "gtdb_species": "s__Treponema_D sp017392945", "ani": 79.0693, "matched_fragments": 252, "total_fragments": 681, "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_017386165.1", "gtdb_species": "s__Treponema_D sp017386165", "ani": 78.4954, "matched_fragments": 165, "total_fragments": 681, "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_000260795.1", "gtdb_species": "s__Treponema_D sp000260795", "ani": 78.1138, "matched_fragments": 120, "total_fragments": 681, "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_000619925.1", "gtdb_species": "s__Treponema_D sp000619925", "ani": 78.0972, "matched_fragments": 126, "total_fragments": 681, "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_900541945.1", "gtdb_species": "s__Treponema_D sp900541945", "ani": 77.9353, "matched_fragments": 143, "total_fragments": 681, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.94", "min_intra_species_ani": "97.90", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_016297805.1", "gtdb_species": "s__Treponema_D sp016297805", "ani": 77.9249, "matched_fragments": 130, "total_fragments": 681, "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": 77.916, "matched_fragments": 161, "total_fragments": 681, "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_017390125.1", "gtdb_species": "s__Treponema_D sp017390125", "ani": 77.7923, "matched_fragments": 133, "total_fragments": 681, "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_900317625.1", "gtdb_species": "s__Treponema_D sp900317625", "ani": 77.7114, "matched_fragments": 170, "total_fragments": 681, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.21", "min_intra_species_ani": "99.03", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.87", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_016287815.1", "gtdb_species": "s__Treponema_D sp016287815", "ani": 77.6761, "matched_fragments": 78, "total_fragments": 681, "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_900769325.1", "gtdb_species": "s__Treponema_D sp900769325", "ani": 77.5552, "matched_fragments": 134, "total_fragments": 681, "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_002478955.1", "gtdb_species": "s__Treponema_D sp002478955", "ani": 77.5415, "matched_fragments": 161, "total_fragments": 681, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.79", "min_intra_species_ani": "97.79", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.82", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_018064905.1", "gtdb_species": "s__Treponema_D sp018064905", "ani": 77.4563, "matched_fragments": 102, "total_fragments": 681, "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_016290335.1", "gtdb_species": "s__Treponema_D sp016290335", "ani": 77.1694, "matched_fragments": 99, "total_fragments": 681, "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_017962965.1", "gtdb_species": "s__Treponema_D sp017962965", "ani": 76.8838, "matched_fragments": 83, "total_fragments": 681, "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_017622055.1", "gtdb_species": "s__Treponema_D sp017622055", "ani": 76.6555, "matched_fragments": 63, "total_fragments": 681, "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_014334335.1", "gtdb_species": "s__Treponema_D sp014334335", "ani": 76.5937, "matched_fragments": 64, "total_fragments": 681, "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_016283615.1", "gtdb_species": "s__Treponema_D sp016283615", "ani": 76.5503, "matched_fragments": 71, "total_fragments": 681, "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_gtdb_taxon": [ "d__Bacteria", "p__Spirochaetota", "c__Spirochaetia", "o__Treponematales", "f__Treponemataceae", "g__Treponema_D", "s__Treponema_D sp017381365" ], "_genome_taxon": [ "Spirochaetia", "bacterium", "d__Bacteria", "p__Spirochaetota", "c__Spirochaetia", "o__Treponematales", "f__Treponemataceae", "g__Treponema_D", "s__Treponema_D sp017381365", "Bacteria", "Spirochaetota", "Spirochaetia", "Treponematales", "Treponemataceae", "Treponema", "D", "Treponema", "D", "sp017381365" ], "_meo": [ { "id": "MEO_0000054", "label": "feces" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }