{"database": "WtMTA-db", "private": false, "path": "/WtMTA-db-25eb725", "size": 160895049728, "tables": [{"name": "genomes", "columns": ["taxonomy_id", "species", "common_name", "group", "phylum", "order", "family", "u12_status", "n_minor_introns", "percent_minor_introns", "u12_density_percentile", "n_u12_all", "n_major_introns", "motif_category", "z_excess", "hc_u12_cds", "hc_u12_exon", "snrna_status", "minor_snrnas", "n_minor_snrna", "u11_E", "u12_E", "u4atac_E", "u6atac_E", "total_genes", "total_introns_scored", "genome_size_bp", "gc_content", "coding_gc_content", "n_contigs", "assembly_n50", "assembly_l50", "busco_score", "accession", "genome_version", "source", "assembly_url", "ncbi_taxonomy_url", "wikipedia_url", "common_name_level", "taxonomy", "genome_path", "annotation_path"], "primary_keys": ["taxonomy_id"], "count": 2634, "hidden": false, "fts_table": "genomes_fts", "foreign_keys": {"incoming": [{"other_table": "transcripts", "column": "taxonomy_id", "other_column": 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"transcripts", "columns": ["id", "taxonomy_id", "transcript_id", "gene_id", "chromosome", "strand", "start", "end", "coding_length", "introns_per_kbp_cds", "n_introns", "n_minor_introns", "proportion_minor_introns"], "primary_keys": ["id"], "count": 51752125, "hidden": false, "fts_table": "transcripts_fts", "foreign_keys": {"incoming": [{"other_table": "introns", "column": "id", "other_column": "transcript_id"}, {"other_table": "minor_introns", "column": "id", "other_column": "transcript_id"}], "outgoing": [{"other_table": "genomes", "column": "taxonomy_id", "other_column": "taxonomy_id"}]}, "private": false}, {"name": "_build_progress", "columns": ["species_key", "taxonomy_id", "n_introns", "n_transcripts", "status", "ts"], "primary_keys": ["species_key"], "count": 2780, "hidden": true, "fts_table": null, "foreign_keys": {"incoming": [], "outgoing": []}, "private": false}, {"name": "genomes_fts", "columns": ["species", "common_name", "phylum", "order", "family", "genomes_fts", "rank"], "primary_keys": [], "count": 2634, "hidden": true, "fts_table": "genomes_fts", "foreign_keys": {"incoming": [], "outgoing": []}, "private": false}, {"name": "genomes_fts_config", "columns": ["k", "v"], "primary_keys": ["k"], "count": 1, "hidden": true, "fts_table": null, "foreign_keys": {"incoming": [], "outgoing": []}, "private": false}, {"name": "genomes_fts_data", "columns": ["id", "block"], "primary_keys": ["id"], "count": 42, "hidden": true, "fts_table": null, "foreign_keys": {"incoming": [], "outgoing": []}, "private": false}, {"name": "genomes_fts_docsize", "columns": ["id", "sz"], "primary_keys": ["id"], "count": 2634, "hidden": true, "fts_table": null, "foreign_keys": {"incoming": [], "outgoing": []}, "private": false}, {"name": "genomes_fts_idx", "columns": ["segid", "term", "pgno"], "primary_keys": ["segid", "term"], "count": 40, "hidden": true, "fts_table": null, "foreign_keys": {"incoming": [], "outgoing": []}, "private": false}, {"name": "intron_stats", "columns": ["taxonomy_id", "is_minor", "cds", "longest_iso", "metric", "total_n", "bins_json"], "primary_keys": ["taxonomy_id", "is_minor", "cds", "longest_iso", "metric"], "count": 89390, "hidden": true, "fts_table": null, "foreign_keys": {"incoming": [], "outgoing": []}, "private": false}, {"name": "motif_pwm", "columns": ["taxonomy_id", "is_minor", "cds", "longest_iso", "motif", "n_introns", "counts_json"], "primary_keys": ["taxonomy_id", "is_minor", "cds", "longest_iso", "motif"], "count": 38310, "hidden": true, "fts_table": null, "foreign_keys": {"incoming": [], "outgoing": []}, "private": false}, {"name": "sqlite_stat1", "columns": ["tbl", "idx", "stat"], "primary_keys": [], "count": 37, "hidden": true, "fts_table": null, "foreign_keys": {"incoming": [], "outgoing": []}, "private": false}, {"name": "transcripts_fts", "columns": ["transcript_id", "gene_id", "transcripts_fts", "rank"], "primary_keys": [], "count": null, "hidden": true, "fts_table": "transcripts_fts", "foreign_keys": {"incoming": [], "outgoing": []}, "private": false}, {"name": "transcripts_fts_config", "columns": ["k", "v"], "primary_keys": ["k"], "count": 1, "hidden": true, "fts_table": null, "foreign_keys": {"incoming": [], "outgoing": []}, "private": false}, {"name": "transcripts_fts_data", "columns": ["id", "block"], "primary_keys": ["id"], "count": 449484, "hidden": true, "fts_table": null, "foreign_keys": {"incoming": [], "outgoing": []}, "private": false}, {"name": "transcripts_fts_docsize", "columns": ["id", "sz"], "primary_keys": ["id"], "count": 51752125, "hidden": true, "fts_table": null, "foreign_keys": {"incoming": [], "outgoing": []}, "private": false}, {"name": "transcripts_fts_idx", "columns": ["segid", "term", "pgno"], "primary_keys": ["segid", "term"], "count": 248918, "hidden": true, "fts_table": null, "foreign_keys": {"incoming": [], "outgoing": []}, "private": false}], "hidden_count": 14, "views": [], "queries": [{"title": "BED-format introns (by taxid + adjusted_score band)", "params": ["taxid", "min_score", "max_score"], "sql": "select\n  chromosome,\n  start,\n  \"end\",\n  id,\n  adjusted_score,\n  strand\nfrom introns\nwhere taxonomy_id = :taxid\n  and adjusted_score >= :min_score\n  and adjusted_score <= :max_score\norder by chromosome, start", "name": "bed_format", "private": false}, {"title": "Minor (U12-type) introns for one genome", "params": ["taxid"], "sql": "select\n  id, chromosome, start, \"end\", strand, length,\n  dinucleotide_pair, adjusted_score, rel_score,\n  is_high_confidence_minor, motif_category, transcript_id\nfrom minor_introns\nwhere taxonomy_id = :taxid\norder by adjusted_score desc", "name": "minor_introns_by_genome", "private": false}, {"title": "Most U12-like introns for one genome (ranked by raw motif score)", "description_html": "The strongest U12-motif introns in one genome by <code>p_motif</code> \u2014 the raw motif-model\nprobability, independent of the per-species call gate \u2014 whether or not they cleared the U12\nthreshold. Useful for genomes with minor-snRNA machinery but few or no calls. The\n<code>type_id</code>/<code>adjusted_score</code> columns show which (if any) were actually called.\nParameters: <code>?tax=&lt;taxonomy_id&gt;&amp;n=&lt;N&gt;</code>.\n", "params": ["tax", "n"], "sql": "select\n  id, transcript_id, chromosome, start, \"end\", strand, length, phase, in_cds,\n  dinucleotide_pair, type_id, adjusted_score, rel_score, p_motif, svm_score, motif_category,\n  exon5_flank, five_ss_seq, bps_seq, three_ss_seq, exon3_flank\nfrom introns\nwhere taxonomy_id = cast(:tax as integer)\norder by p_motif desc\nlimit cast(:n as integer)", "name": "top_motif_introns", "private": false}], "allow_execute_sql": true, "query_ms": 49.37646817415953, "source": "Larue & Roy, 2023", "source_url": "https://doi.org/10.1101/2022.09.24.509304", "license": "ODbL", "license_url": "https://opendatacommons.org/licenses/odbl/"}