Alignment was performed with tophat v2.0.6 (http://tophat.cbcb.umd.edu). Alignments were processed using SAMtools v0.1.2, which generates site-specific allele frequencies using overlapping reads (read pileup). Allele specific expression was quantified by determining whether or not each overlapping read at mutant site matched the reference or the alternative allele. These summed counts represented our measures of relative allelic abundance at that site. Any deviation from equal allelic abundance was reflected allelic imbalance.
