Fig. 4
From: Zea mays RNA-seq estimated transcript abundances are strongly affected by read mapping bias
Comparison of alignment criteria on cis-eQTL effect size. Each cis-eQTL for which the B73 allele increased a target gene’s expression was labelled “yes” if its effect estimated using the most relaxed alignment criteria was lower than its effect using the default alignment criteria. The proportion of “yes” genes was calculated. The cis-eQTL effect was estimated as the average of the mean expression of RILs with the B73 genotype minus the mean expression of RILs with the Mo17 genotype. A large proportion of B73 positive cis-eQTLs had greater effects using default alignment criteria (binomial test, P < 2.2e-16)