{ "type": "genome", "identifier": "GCA_938042225.1", "organism": "Treponema socranskii", "title": "Treponema socranskii", "description": "derived from metagenome; fragmented assembly; genome length too small", "data type": "Genome sequencing and assembly", "organization": "European Bioinformatics Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCA_938042225.1", "bioproject": "PRJEB51075", "biosample": "SAMEA14084590", "wgs_master": "CALIRW000000000.1", "refseq_category": "na", "taxid": "53419", "species_taxid": "53419", "organism_name": "Treponema socranskii", "infraspecific_name": "", "isolate": "ERR589380_bin.94_CONCOCT_v1.1_MAG", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2023/01/10", "asm_name": "ERR589380_bin.94_CONCOCT_v1.1_MAG", "submitter": "European Bioinformatics Institute", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/938/042/225/GCA_938042225.1_ERR589380_bin.94_CONCOCT_v1.1_MAG", "excluded_from_refseq": "derived from metagenome; fragmented assembly; genome length too small", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2023-01-10", "dateModified": "2023-01-10", "datePublished": "2023-01-10", "_annotation": { "sample_count": 1, "sample_organism": [ "Treponema socranskii" ], "sample_taxid": [ "53419" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China" ], "sample_host_location_id": [], "data_size": "0.572 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 92.33, "contamination": 4.55, "strain_heterogeneity": 50.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2009512", "Number of Sequences": "777", "Longest Sequences (bp)": "21333", "N50 (bp)": "2973", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "50.7", "Number of CDSs": "1259", "Average Protein Length": "303.1", "Coding Ratio (%)": "57.0", "Number of rRNAs": "0", "Number of tRNAs": "22", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [], "cc_result": { "completeness": 92.33, "contamination": 4.55, "strain_heterogeneity": 50.0 }, "gtdb_result": [ { "accession": "GCF_000468115.1", "gtdb_species": "s__Treponema_D socranskii", "ani": 95.1848, "matched_fragments": 244, "total_fragments": 262, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "inconclusive" }, { "accession": "GCF_014334325.1", "gtdb_species": "s__Treponema_D sp014334325", "ani": 95.0337, "matched_fragments": 247, "total_fragments": 262, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.62", "min_intra_species_ani": "95.62", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.82", "num_clustered_genomes": 2, "status": "inconclusive" }, { "accession": "GCF_902983995.1", "gtdb_species": "s__Treponema_D buccale", "ani": 93.92, "matched_fragments": 241, "total_fragments": 262, "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_000413015.1", "gtdb_species": "s__Treponema_D paredis", "ani": 92.7326, "matched_fragments": 239, "total_fragments": 262, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.58", "min_intra_species_ani": "95.58", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_017940005.1", "gtdb_species": "s__Treponema_D sp017940005", "ani": 76.4093, "matched_fragments": 61, "total_fragments": 262, "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": -0.796, "cell_length": 0.778, "doubling_h": 0.49, "growth_tmp": 37.0, "optimum_tmp": 37.0, "optimum_ph": 7.183, "genome_size": 2779234.5, "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 }, "_gtdb_taxon": [ "d__Bacteria", "p__Spirochaetota", "c__Spirochaetia", "o__Treponematales", "f__Treponemataceae", "g__Treponema_D", "s__Treponema_D socranskii" ], "_genome_taxon": [ "Treponema", "socranskii", "d__Bacteria", "p__Spirochaetota", "c__Spirochaetia", "o__Treponematales", "f__Treponemataceae", "g__Treponema_D", "s__Treponema_D socranskii", "Bacteria", "Spirochaetota", "Spirochaetia", "Treponematales", "Treponemataceae", "Treponema", "D", "Treponema", "D", "socranskii" ], "_meo": [ { "id": "MEO_0000054", "label": "feces" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }