We detected an average of ~1900 genes with Altrans, and ~250 with sQTLseekeR, with at least one cis-sQTL per tissue (FDR = 0.05; table S9). The greater genomic window tested around the TSS for Altrans, and the capacity to detect novel splicing events, explains the much larger number of sQTLs detected by Altrans than by sQTLseekeR (about 70% of Altrans sQTLs correspond to novel events, and only about 10% map within 5 kb of annotated genes). Despite the difference, Altrans and sQTLseekeR show strong complementarity, detecting variants that are associated with very different types of alternative splicing events. Most of the splice events detected by Altrans (80%) are exon-skipping events, while 60% of those detected by sQTLseekeR correspond to complex splice events, such as mutually exclusive exons (Fig. 5B and fig. S23). If we consider only sQTLs associated with exon-skipping events, the overlap in sQTLs identified by both methods is substantial (36% of sQTLseekeR are also found by Altrans, P = 0.004) (figs. S23 to S25). An example of an sQTL that we identified with potential biological relevance is shown in Fig. 5A (further examples are in fig. S26).
