Human chr6 also has the MHC region which shows a DAF peak

Human chr6 has another prominent peak of DAF, corresponding to the MHC region. Flanked by the genes MOG and COL11A2, it spans from approximately 29624758 to 33145670 in the hg19 assembly. Below figure shows the MHC region in blue with the flanking genes in brown. The number of CNV's also jumps up in this region. 

 chr <- "chr6";    
 jpeg(paste("DAF.",chr,".jpeg",sep=""),width=1420)    
 par(mfrow=c(2,1))    
 read.table(file=paste("h.",chr,".mean.bed",sep=""),header=F,stringsAsFactors=F)->M    
 plot(as.numeric(M$V2),as.numeric(M$V4),xlab="Position along chromosome",ylab="Mean derived allele Frequency",main=chr)    
 lines(c(58830166,61830166),c(0.2,0.2),col="red",lwd=5)    
 text(63830166, 0.25,labels="Centromere",col="red")    
 lines(c(171105067,171115067),c(0.3,0.3),col="blue",lwd=5)    
 text(171105067, 0.35,labels="Telomere",col="blue")    
 lines(c(0,10000),c(0.3,0.3),col="blue",lwd=5)    
 text(0, 0.35,labels="Telomere",col="blue")    
 lines(c(57182422,57513376),c(0.25,0.25),col="brown",lwd=5)    
 text(57182422, 0.3,labels="PRIM2 gene",col="brown")    
 M[M$V2>57182422 & M$V3<57513376,]->N   
 points(N$V2,N$V4,pch=13,col="blue")   
 lines(c(33130469,33145670),c(0.35,0.35),col="brown",lwd=5)    
 text(39945670, 0.35,labels="COL11A2 gene",col="brown")    
 lines(c(29624758,29638656),c(0.35,0.35),col="brown",lwd=5)    
 text(25000000, 0.35,labels="MOG gene",col="brown")    
 lines(c(29624758,33145670),c(0.38,0.38),col="blue",lwd=5)    
 text(29624758, 0.42,labels="MHC",col="blue")    
 read.table(file=paste("h.",chr,".countdgv.bed",sep=""),header=FALSE)->C    
 plot(C$V2,C$V4,xlab="Position along chromosome",ylab="Count of known structural variants",main=chr)    
 cor.test(as.numeric(M$V4),C$V4,method="spearman")    
 dev.off()