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Why are there more non-synonymous SNPs than synonymous SNPs in the 1000 genomes data?
I have downloaded SNP data from the 1000 genomes project through Biomart and UCSC genome browser. These SNP data are annotated as being synonymous or non-synonymous (missense). In all textbooks it is said the the number of synonymous mutations should be much higher than non-synonymous mutations. Then why is it that I consistently observe higher number of non-synonymous SNPs for the human genome? Do you think there might be a mistake in annotating these SNPs or there is something else that I am missing?
This question generated a lot of discussion. And one of the key aspects is that you have to really pay attention to how the annotation features are provided in a database. Have a look at the chatter over there about various aspects of SNP annotations.