I am working with WGBS Data. I got a list of differentially methylated CpGs. I have done the annotation. I have downloaded ref file from UCSC and then merged it with my output file, which had coordinates. Now I got list of differentially methylated CpGs with coordinates and identifier (like NM or NR etc)

Now my problem is

1) After doing whole genome analysis, I am getting only a handful of coordinates (~50) which are matching to BED reference file. I have done with hg38 and hg19 both, but more or less same result.

So what can be the reason for that?