{ "type": "genome", "identifier": "GCA_004554075.1", "organism": "Treponema sp.", "title": "Treponema sp.", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "University of Alberta", "publication": [ {} ], "properties": { "assembly_accession": "GCA_004554075.1", "bioproject": "PRJNA494875", "biosample": "SAMN10183623", "wgs_master": "SFOB00000000.1", "refseq_category": "na", "taxid": "166", "species_taxid": "166", "organism_name": "Treponema sp.", "infraspecific_name": "", "isolate": "W3P1.029", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/04/01", "asm_name": "ASM455407v1", "submitter": "University of Alberta", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/004/554/075/GCA_004554075.1_ASM455407v1", "excluded_from_refseq": "derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-04-01", "dateModified": "2019-04-01", "datePublished": "2019-04-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Treponema sp." ], "sample_taxid": [ "166" ], "sample_host_organism": [ "Sus scrofa" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Canada: Edmonton" ], "sample_host_location_id": [], "data_size": "1.056 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 4.36, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3713748", "Number of Sequences": "331", "Longest Sequences (bp)": "178874", "N50 (bp)": "23790", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "40.1", "Number of CDSs": "2971", "Average Protein Length": "340.3", "Coding Ratio (%)": "81.7", "Number of rRNAs": "1", "Number of tRNAs": "39", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Treponema succinifaciens", "strain": "strain=DSM 2489", "accession": "GCA_000195275.1", "taxid": 167, "species_taxid": 167, "relation_to_type": "type", "validated": true, "ani": 83.406, "matched_fragments": 92, "total_fragments": 1050, "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": 78.0599, "matched_fragments": 72, "total_fragments": 1050, "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": 77.239, "matched_fragments": 97, "total_fragments": 1050, "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": 76.9853, "matched_fragments": 80, "total_fragments": 1050, "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": 76.8094, "matched_fragments": 92, "total_fragments": 1050, "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": 75.8584, "matched_fragments": 53, "total_fragments": 1050, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 4.36, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_004554075.1", "gtdb_species": "s__Treponema_D sp004554075", "ani": 100.0, "matched_fragments": 1041, "total_fragments": 1050, "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_000421345.1", "gtdb_species": "s__Treponema_D bryantii_B", "ani": 85.6702, "matched_fragments": 666, "total_fragments": 1050, "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_900113965.1", "gtdb_species": "s__Treponema_D bryantii_A", "ani": 84.0011, "matched_fragments": 634, "total_fragments": 1050, "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": 83.9326, "matched_fragments": 559, "total_fragments": 1050, "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", 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"mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_017940255.1", "gtdb_species": "s__Treponema_D sp017940255", "ani": 80.264, "matched_fragments": 349, "total_fragments": 1050, "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_002315375.1", "gtdb_species": "s__Treponema_D sp002315375", "ani": 77.2539, "matched_fragments": 146, "total_fragments": 1050, "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 }, "_gtdb_taxon": [ "d__Bacteria", "p__Spirochaetota", "c__Spirochaetia", "o__Treponematales", "f__Treponemataceae", "g__Treponema_D", "s__Treponema_D sp004554075" ], "_genome_taxon": [ "Treponema", "sp.", 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