Metadata for various molecular traits included in the eQTL Catalogue. Metadata files for the Leafcutter datasets can be found here. The tab-separated files contain the following columns: phenotype_id - ID of the molecular trait that has been quantified. This can be either the gene ID (RNA-eq eQTLs), probe ID (microarray eQTLs), transcript ID (full-length transcript usage QTLs), splice junction ID (Leafcutter), exon id (exon-level QTLs) or any other molecular trait that has been quantified. quant_id - Used to quantify relative transcript usage or relative transcriptional event usage (in txrevise). group_id - Used for transcript usage and splicing phenotypes. Overlapping phenotypes whose relative expression is quantified belong to the same group (e.g. alternative spliced exons form clusters in Leafcutter). QTLTools permutation p-values are calculated accross all phenotypes within a group and only the phenotype with the smallest permutation p-value is reported. gene_id - Ensembl gene id chromosome - Chromosome of the gene gene_start - End coordinate of the gene (GRCh38) gene_end - Start coordinate of the gene (GRCh38) strand - Strand of the gene gene_name - Gene name extracted from Ensembl biomart. gene_type - Gene type extracted from Ensembl biomart. gene_gc_content - Percentage GC content of the gene. Extracted from Ensembl biomart and used as a covariate in cqn normalisation. Calculated with bedtools nuc for exons. gene_version - Ensembl gene version phenotype_pos - Genomic position used to determine the centre point of the cis-window for QTL mapping. By default this is the beginning of the gene (either gene start or gene end, depending on the strand of the gene). phenotype_length - (optional) - Length of the gene or exon in basepairs. Required to properly normalise featureCounts quantification results with cqn.

April 2023 - Added metadata for SomaLogic aptamers.