Question: Is it normal that there are more non-synonymous SNPs Than synonymous SNPs in mouse cell lines?
gravatar for zhaoyang198691
3.4 years ago by
zhaoyang1986910 wrote:

I analyzed whole exome seq data from 5 mouse cell lines without matched normal. I used bwa -> GATK realignment -> GATK recalibration -> Varscan2 -> annovar for variant calling. I used GRCm38 as the reference genome. Three of these cell lines have much more (almost twice) non-synonymous SNPS than synonymous SNPs. Is that normal? I would expect more synonymous SNP in the data. The remaining two cell lines have more synonymous SNPs.

Thank you so much.

ADD COMMENTlink written 3.4 years ago by zhaoyang1986910

It is very much normal !

ADD REPLYlink written 3.4 years ago by poisonAlien2.8k
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