We wanted to assess how discoveries of one method compared to the other. For each significant variant-link pair in one population by one method, we calculated the p value of the same variant-link pair in the same population based on quantifications by the other method. For this we had to select common links identified by each method, and therefore many genes are not being tested for replication across methods. From these p value distributions, we calculated the π1 statistic, which indicates the proportion of true positives (Figure S6). We estimate that 94% of Altrans asQTLs in Europeans and 90% Altrans asQTLs in Africans are replicated by Cufflinks quantifications in the corresponding population, for the common links between the two methods. In contrast, replication in the other direction, Cufflinks asQTLs in Altrans, is lower: 57% and 51% for Europeans and Africans, respectively. When we are testing Altrans results in Cufflinks, we are testing 507 and 77 genes for Europeans and Africans, respectively, and when testing Cufflinks in Altrans, these values are 1,260 and 230, respectively. We then multiply the corresponding π1 values with these number of genes tested to get an estimate of the number of genes that replicate across methods and divide these with the corresponding number of asQTL genes found in the original discovery (e.g., for European Cufflinks in Altrans: 1,260 × 0.57 / 1,737 = 41%). In doing so we estimate the percentage of genes that are “discoverable” by the other method. This percentage is similar across methods and is in the Europeans 33% and 41% for Altrans and Cufflinks, respectively. In the Africans these values are 42% and 39%. This is due to the different space of alternative splicing that each method is best at quantifying and is another confirmation of the complementary nature of these methods.