{ "type": "genome", "identifier": "GCF_014201975.1", "organism": "Treponema ruminis", "title": "Treponema ruminis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014201975.1", "bioproject": "PRJNA224116", "biosample": "SAMN14908472", "wgs_master": "JACHFQ000000000.1", "refseq_category": "reference genome", "taxid": "744515", "species_taxid": "744515", "organism_name": "Treponema ruminis", "infraspecific_name": "strain=DSM 103462", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/08/14", "asm_name": "ASM1420197v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_014201975.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/201/975/GCF_014201975.1_ASM1420197v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3323807", "genome_size_ungapped": "3323429", "gc_percent": "44.000000", "replicon_count": "0", "scaffold_count": "16", "contig_count": "16", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014201975.1-RS_2024_09_26", "annotation_date": "2024-09-26", "total_gene_count": "2858", "protein_coding_gene_count": "2785", "non_coding_gene_count": "61", "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 ruminis" ], "sample_taxid": [ "744515" ], "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": "0.939 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)": "3323807", "Number of Sequences": "16", "Longest Sequences (bp)": "624017", "N50 (bp)": "397985", "Gap Ratio (%)": "0.011373", "GCcontent (%)": "44.1", "Number of CDSs": "2779", "Average Protein Length": "368.0", "Coding Ratio (%)": "92.3", "Number of rRNAs": "3", "Number of tRNAs": "52", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Treponema ruminis", "strain": "strain=DSM 103462", "accession": "GCA_014201975.1", "taxid": 744515, "species_taxid": 744515, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1101, "total_fragments": 1101, "ani_threshold": 95, "status": "conclusive" }, { "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": 77.515, "matched_fragments": 127, "total_fragments": 1101, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_017161305.1", "gtdb_species": "s__Treponema_D ruminis", "ani": 99.9778, "matched_fragments": 890, "total_fragments": 1101, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCA_902785455.1", "gtdb_species": "s__Treponema_D sp902785455", "ani": 87.0574, "matched_fragments": 698, "total_fragments": 1101, "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_017430385.1", "gtdb_species": "s__Treponema_D sp017430385", "ani": 83.0324, "matched_fragments": 595, "total_fragments": 1101, "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_017469785.1", "gtdb_species": "s__Treponema_D sp017469785", "ani": 80.4078, "matched_fragments": 445, "total_fragments": 1101, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.36", "min_intra_species_ani": "97.36", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.82", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_017395545.1", "gtdb_species": "s__Treponema_D sp017395545", "ani": 80.1865, "matched_fragments": 334, "total_fragments": 1101, "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_002368605.1", "gtdb_species": "s__Treponema_D sp002368605", "ani": 80.0528, "matched_fragments": 422, "total_fragments": 1101, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.93", "min_intra_species_ani": "96.81", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.77", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_002393835.1", "gtdb_species": "s__Treponema_D sp002393835", "ani": 79.6314, "matched_fragments": 345, "total_fragments": 1101, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.83", "min_intra_species_ani": "96.83", "mean_intra_species_af": "0.78", "min_intra_species_af": "0.78", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_017484285.1", "gtdb_species": "s__Treponema_D sp017484285", "ani": 79.2181, "matched_fragments": 369, "total_fragments": 1101, "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_017464425.1", "gtdb_species": "s__Treponema_D sp017464425", "ani": 78.9489, "matched_fragments": 338, "total_fragments": 1101, "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_017449265.1", "gtdb_species": "s__Treponema_D sp017449265", "ani": 78.9339, "matched_fragments": 172, "total_fragments": 1101, "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_902803735.1", "gtdb_species": "s__Treponema_D sp902803735", "ani": 78.2443, "matched_fragments": 106, "total_fragments": 1101, "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_017449285.1", "gtdb_species": "s__Treponema_D sp017449285", "ani": 77.6576, "matched_fragments": 119, "total_fragments": 1101, "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", "ruminis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }