{ "type": "genome", "identifier": "GCA_944390595.1", "organism": "uncultured Brachyspira sp.", "title": "uncultured Brachyspira sp.", "description": "derived from environmental source; derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "Institut National pour la Recherche Agronomique (FRANCE)", "publication": [ {} ], "properties": { "assembly_accession": "GCA_944390595.1", "bioproject": "PRJEB53581", "biosample": "SAMEA110136422", "wgs_master": "CALXRN000000000.1", "refseq_category": "na", "taxid": "221953", "species_taxid": "221953", "organism_name": "uncultured Brachyspira sp.", "infraspecific_name": "", "isolate": "E20__bin322", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/06/30", "asm_name": "E20__bin322", "submitter": "Institut National pour la Recherche Agronomique (FRANCE)", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/944/390/595/GCA_944390595.1_E20_bin322", "excluded_from_refseq": "derived from environmental source; derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-06-30", "dateModified": "2022-06-30", "datePublished": "2022-06-30", "_annotation": { "sample_count": 1, "sample_organism": [ "uncultured Brachyspira sp." ], "sample_taxid": [ "221953" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "France" ], "sample_host_location_id": [], "data_size": "0.820 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 85.27, "contamination": 6.25, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3020730", "Number of Sequences": "250", "Longest Sequences (bp)": "70924", "N50 (bp)": "18467", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "27.2", "Number of CDSs": "2621", "Average Protein Length": "311.8", "Coding Ratio (%)": "81.2", "Number of rRNAs": "0", "Number of tRNAs": "37", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Brachyspira alvinipulli", "strain": "strain=ATCC 51933", "accession": "GCA_000518245.1", "taxid": 84379, "species_taxid": 84379, "relation_to_type": "type", "validated": true, "ani": 94.1419, "matched_fragments": 794, "total_fragments": 880, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brachyspira hyodysenteriae", "strain": "strain=B78", "accession": "GCA_001013005.1", "taxid": 159, "species_taxid": 159, "relation_to_type": "type", "validated": true, "ani": 83.8543, "matched_fragments": 623, "total_fragments": 880, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brachyspira hyodysenteriae", "strain": "strain=B-78", "accession": "GCA_001676785.2", "taxid": 159, "species_taxid": 159, "relation_to_type": "type", "validated": true, "ani": 83.8064, "matched_fragments": 632, "total_fragments": 880, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brachyspira hyodysenteriae", "strain": "strain=B78", "accession": "GCA_000383255.1", "taxid": 159, "species_taxid": 159, "relation_to_type": "type", "validated": true, "ani": 83.7992, "matched_fragments": 628, "total_fragments": 880, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brachyspira suanatina", "strain": "strain=AN4859/03", "accession": "GCA_001049755.1", "taxid": 381802, "species_taxid": 381802, "relation_to_type": "type", "validated": true, "ani": 83.6074, "matched_fragments": 666, "total_fragments": 880, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brachyspira intermedia", "strain": "strain=PWS/A", "accession": "GCA_000223215.1", "taxid": 84377, "species_taxid": 84377, "relation_to_type": "type", "validated": true, "ani": 83.5565, "matched_fragments": 649, "total_fragments": 880, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brachyspira innocens", "strain": "strain=B256", "accession": "GCA_000384655.1", "taxid": 13264, "species_taxid": 13264, "relation_to_type": "type", "validated": true, "ani": 82.4623, "matched_fragments": 622, "total_fragments": 880, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brachyspira pilosicoli", "strain": "strain=P43/6/78", "accession": "GCA_000325665.1", "taxid": 52584, "species_taxid": 52584, "relation_to_type": "type", "validated": true, "ani": 79.9832, "matched_fragments": 448, "total_fragments": 880, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 85.27, "contamination": 6.25, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCF_000518245.1", "gtdb_species": "s__Brachyspira alvinipulli", "ani": 94.1419, "matched_fragments": 794, "total_fragments": 880, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira", "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_001676785.2", "gtdb_species": "s__Brachyspira hyodysenteriae", "ani": 83.7858, "matched_fragments": 635, "total_fragments": 880, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.16", "min_intra_species_ani": "98.93", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.95", "num_clustered_genomes": 58, "status": "-" }, { "accession": "GCF_000223215.1", "gtdb_species": "s__Brachyspira intermedia", "ani": 83.5535, "matched_fragments": 649, "total_fragments": 880, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira", "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_001049755.1", "gtdb_species": "s__Brachyspira suanatina", "ani": 83.5511, "matched_fragments": 672, "total_fragments": 880, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira", "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_002214805.1", "gtdb_species": "s__Brachyspira hampsonii", "ani": 82.4694, "matched_fragments": 657, "total_fragments": 880, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.94", "min_intra_species_ani": "99.90", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000384655.1", "gtdb_species": "s__Brachyspira innocens", "ani": 82.461, "matched_fragments": 623, "total_fragments": 880, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira", "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_002379365.1", "gtdb_species": "s__Brachyspira sp002379365", "ani": 82.1826, "matched_fragments": 641, "total_fragments": 880, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira", "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_000092845.1", "gtdb_species": "s__Brachyspira murdochii", "ani": 82.1793, "matched_fragments": 648, "total_fragments": 880, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.81", "min_intra_species_ani": "96.97", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_910578695.1", "gtdb_species": "s__Brachyspira sp910578695", "ani": 81.6311, "matched_fragments": 561, "total_fragments": 880, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira", "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_000325665.1", "gtdb_species": "s__Brachyspira pilosicoli", "ani": 79.973, "matched_fragments": 449, "total_fragments": 880, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.38", "min_intra_species_ani": "97.84", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 19, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.456, "cell_length": 0.738, "doubling_h": 0.477, "growth_tmp": 37.0, "optimum_tmp": 37.4, "optimum_ph": 7.1, "genome_size": 3148275.979, "gc_content": 27.312, "coding_genes": 2613.666, "rRNA16S_genes": 1.0, "tRNA_genes": 33.25, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.25, "anaerobic_respiration": 0.75, "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__Brachyspirae", "o__Brachyspirales", "f__Brachyspiraceae", "g__Brachyspira", "s__Brachyspira sp944390595" ], "_genome_taxon": [ "uncultured", "Brachyspira", "sp.", "d__Bacteria", "p__Spirochaetota", "c__Brachyspirae", "o__Brachyspirales", "f__Brachyspiraceae", "g__Brachyspira", "s__Brachyspira sp944390595", "Bacteria", "Spirochaetota", "Brachyspirae", "Brachyspirales", "Brachyspiraceae", "Brachyspira", "Brachyspira", "sp944390595" ], "_meo": [ { "id": "MEO_0000460", "label": "cecum" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }