Why does GRM give the incorrect number of SNPs?

I did this:


plink --bfile filename --geno 0.01 --hwe 0.001 --maf 0.05 --autosome --rel-cutoff 0.025 --make-bed --out cleaned


And then got 304,259 variants after.

But the number of variants (i.e., the N) differed when I created a GRM:


./gcta64 --bfile cleaned --make-grm --out cleanedgrm


In particular, when I did this:


# R script to read the GRM binary file

ReadGRMBin=function(prefix, AllN=F, size=4){

sum_i=function(i){

return(sum(1:i))

}

BinFileName=paste(prefix,".grm.bin",sep="")

NFileName=paste(prefix,".grm.N.bin",sep="")

IDFileName=paste(prefix,".grm.id",sep="")

id = read.table(IDFileName)

n=dim(id)[1]

BinFile=file(BinFileName, "rb");

grm=readBin(BinFile, n=n*(n+1)/2, what=numeric(0), size=size)

NFile=file(NFileName, "rb");

if(AllN==T){

N=readBin(NFile, n=n*(n+1)/2, what=numeric(0), size=size)

}

else N=readBin(NFile, n=1, what=numeric(0), size=size)

i=sapply(1:n, sum_i)

return(list(diag=grm, off=grm[-i], id=id, N=N))

}



A = ReadGRMBin(prefix = 'cleanedgrm')


A$N


A$N was 304,172. Isn't it supposed to be the original number of variants, which is 304,259?