penalty was −250, the gap extension penalty was −100, Smith and Waterman minimum identical alignment threshold was 30.0%, while other SHRiMP parameters were left at default. Using these settings all mappings with a minimum overlap of 15 bases, or with 20 matches with one mismatch, or 30 matches with 2 mismatches, or full-length (50 bp) probe hybridizations with no more than 15 mismatches were accepted. Any trans-eQTL was discarded, if the expression probe had a mapping that was within 2 Mb of the SNP that showed the trans-eQTL effect. Once these potential false-positive trans-eQTLs had been removed from the real, non-permuted data, we repeated the multiple testing correction (again controlling the FDR at 0.05).
