diff --git a/R/plot_residualError_OtherCovariate.R b/R/plot_residualError_OtherCovariate.R
index a85149061..ba187036e 100644
--- a/R/plot_residualError_OtherCovariate.R
+++ b/R/plot_residualError_OtherCovariate.R
@@ -54,8 +54,12 @@ pdf(outfile, height=7, width=7)
 hst=subset(data.frame(e$Covariate, e$nBases), e.nBases != 0)
 hst2=subset(data.frame(f$Covariate, f$nBases), f.nBases != 0)
 if( is.numeric(c$Covariate) ) {
-	plot(hst$e.Covariate, hst$e.nBases, type="h", lwd=2, main=paste(covariateName,"histogram"), xlab=covariateName, ylab="Count",yaxt="n",xlim=c(min(c$Covariate),max(c$Covariate)))
-	points(hst2$f.Covariate, hst2$f.nBases, type="h", lwd=2, col="cornflowerblue")
+    if( length(hst$e.Covariate) == 0 ) {
+        plot(hst2$f.Covariate, hst2$f.nBases, type="h", lwd=2, col="cornflowerblue", main=paste(covariateName,"histogram"), xlab=covariateName, ylab="Count",yaxt="n",xlim=c(min(c$Covariate),max(c$Covariate)))
+    } else {
+	    plot(hst$e.Covariate, hst$e.nBases, type="h", lwd=2, main=paste(covariateName,"histogram"), xlab=covariateName, ylab="Count",yaxt="n",xlim=c(min(c$Covariate),max(c$Covariate)))
+	    points(hst2$f.Covariate, hst2$f.nBases, type="h", lwd=2, col="cornflowerblue")
+	}
 	axis(2,axTicks(2), format(axTicks(2), scientific=F))
 } else { # Dinuc (and other non-numeric covariates) are different to make their plots look nice
 	hst=subset(data.frame(c$Covariate, c$nBases), c.nBases != 0)
diff --git a/R/plot_residualError_QualityScoreCovariate.R b/R/plot_residualError_QualityScoreCovariate.R
index 8dfaf0b3d..7dc885205 100644
--- a/R/plot_residualError_QualityScoreCovariate.R
+++ b/R/plot_residualError_QualityScoreCovariate.R
@@ -21,7 +21,7 @@ e <- rbind(d.good, d.1000, d.10000)
 rmseGood = sqrt(sum((d.good$Qempirical-d.good$Qreported)^2 * d.good$nBases) / sum(d.good$nBases) )
 rmseAll = sqrt(sum((e$Qempirical-e$Qreported)^2 * e$nBases) / sum(e$nBases) )
 theTitle = paste("RMSE_good = ", round(rmseGood,digits=3), ", RMSE_all = ", round(rmseAll,digits=3))
-if (length(t$nBases) == length(d.good$nBases) ) {
+if( length(t$nBases) - length(f$nBases) == length(d.good$nBases) ) {
 	theTitle = paste("RMSE = ", round(rmseAll,digits=3));
 }
 plot(d.good$Qreported, d.good$Qempirical, type="p", col="blue", main=theTitle, xlim=c(0,40), ylim=c(0,40), pch=16, xlab="Reported quality score", ylab="Empirical quality score")