An alternate CHRNA4 transcript (uc010 gke.1) encodes an additional exon (designated 4.1 in Supplementary Figure 1) located between exons 4 and 5 of the major transcript (uc002.yes.2). We used split read counts (reads crossing an exon:exon boundary) and a chi-square test to evaluate the relative efficiency of splicing events, which utilize the exon 4 splice donor and to query whether the efficiency varied by SNP genotype.
