Moreover, we compared the types of splicing events that are found to be significant by both methods (Figure S5) and observed that there are differences between the two methods. The majority (66%) of the signal that Altrans captures is due to exon skipping events followed by alternative 5′ and 3′ UTRs (15% and 11%, respectively). In comparison, Cufflinks has a more uniform distribution of significant event types, with the most common being alternative 5′ UTR (23%), followed by exon skipping (15%) and alternative first exons (14%). This difference in types of significant splicing events each method finds highlights their relative merits in identifying different types of splicing events and is one of the reasons for method-specific significant results. We have tested whether the exon skipping events identified by Altrans replicate between CEU discovery and remaining Europeans, and across populations, and we achieve high π1 values of 98% for CEU discovery replicated in remaining Europeans (Figure S4B), 70% for Europeans replicated in Africans, and 96% in Africans replicated in Europeans, which confirms that these events are enriched for true positives.