diff --git a/R/plot_residualError_QualityScoreCovariate.R b/R/plot_residualError_QualityScoreCovariate.R
index 7b3c166bf..92fe439d0 100644
--- a/R/plot_residualError_QualityScoreCovariate.R
+++ b/R/plot_residualError_QualityScoreCovariate.R
@@ -39,7 +39,9 @@ outfile = paste(input, ".quality_emp_hist.pdf", sep="")
 pdf(outfile, height=7, width=7)
 hst=subset(data.frame(e$Qempirical, e$nBases), e.nBases != 0)
 hst2=subset(data.frame(f$Qempirical, f$nBases), f.nBases != 0)
-plot(hst$e.Qempirical, hst$e.nBases, type="h", lwd=4, xlim=c(0,40), ylim=c(0,max(hst$e.nBases)), main="Empirical quality score histogram", xlab="Empirical quality score", ylab="Number of Bases",yaxt="n")
+percentBases=hst$e.nBases / sum(as.numeric(hst$e.nBases))
+entropy = -sum(log2(percentBases)*percentBases)
+plot(hst$e.Qempirical, hst$e.nBases, type="h", lwd=4, xlim=c(0,40), ylim=c(0,max(hst$e.nBases)), main=paste("Empirical quality score histogram, entropy = ",round(entropy,digits=3)), xlab="Empirical quality score", ylab="Number of Bases",yaxt="n")
 points(hst2$f.Qempirical, hst2$f.nBases, type="h", lwd=4, col="maroon1")
 axis(2,axTicks(2), format(axTicks(2), scientific=F))
 dev.off()
@@ -52,7 +54,7 @@ outfile = paste(input, ".quality_rep_hist.pdf", sep="")
 pdf(outfile, height=7, width=7)
 hst=subset(data.frame(e$Qreported, e$nBases), e.nBases != 0)
 hst2=subset(data.frame(f$Qreported, f$nBases), f.nBases != 0)
-plot(hst$e.Qreported, hst$e.nBases, type="h", lwd=4, xlim=c(0,40), ylim=c(0,max(hst$e.nBases)), main="Reported quality score histogram", xlab="Reported quality score", ylab="Number of Bases",yaxt="n")
+plot(hst$e.Qreported, hst$e.nBases, type="h", lwd=4, xlim=c(0,40), ylim=c(0,max(hst$e.nBases)), main=paste("Reported quality score histogram, entropy = ",round(entropy,digits=3)), xlab="Reported quality score", ylab="Number of Bases",yaxt="n")
 points(hst2$f.Qreported, hst2$f.nBases, type="h", lwd=4, col="maroon1")
 axis(2,axTicks(2), format(axTicks(2), scientific=F))
 dev.off()