How many SNPs I should expect to see in a normal human embryonic stem cell (hESC) with WES analysis?

Question

[maria2019]

I have a normal human embryonic stem cell line (hESC) and the WES data analysis gives me 109313 SNP and 9943 Indel results. Are these numbers normal for a NORMAL cell line? I was thinking since this is a normal cell line it should not have many SNPs. For the SNP calling I used samtools and I did not do any special filtering ( like count of the reads covering the position of the SNP). Should I do some sort of special filtering?

[igor]

Yes. That is roughly normal. You expect to see millions of SNPs across the entire individual genome. The exome covers only about 2% of that, but that still leaves you with plenty.

You might find these previous discussion helpful:

• What is the expected rate of SNPs within a human exome sequencing with HiSeq?
• Finding True SNPs after hard filtering on GATK
• GATK Variant calling