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I'd like to know how common certain mutation types are in public data sets like the 1000 Genomes, ExAC, and ESP6500. Specifically, I'd like to know the distribution of stop-gains, stop-losses, frameshift, and other mutation types. For example, what is the median number of stop-gains observed across individuals in the ExAC population? I'd like to have the full distribution, but median values would work.

To be clear, I am not looking for allele frequencies.

I didn't find this kind of summary data when I looked at the respective websites. Is there a good source for these summary data?

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  • $\begingroup$ Are you looking for statistics on the most severe variant at each genomic location? It is possible for many different transcript variants to map to the same location, which can influence the results that come out of this. $\endgroup$
    – gringer ♦
    Commented Aug 13, 2017 at 20:01
  • $\begingroup$ Does Figure 4A help? nature.com/nature/journal/v491/n7422/fig_tab/… $\endgroup$
    – Chris_Rands
    Commented Aug 14, 2017 at 8:04
  • $\begingroup$ You might be able to calculate yourself the stats you want if you download the data. $\endgroup$
    – llrs
    Commented Aug 14, 2017 at 9:47
  • $\begingroup$ For some types of variant annotations, you can pull all the SNPs from dbSNP as they do in this paper. ncbi.nlm.nih.gov/pmc/articles/PMC3500177 $\endgroup$
    – eric_kernfeld
    Commented Oct 31, 2017 at 20:36
  • $\begingroup$ An important clarifying question: Do you only care about this information in the context of humans? $\endgroup$
    – conchoecia
    Commented Feb 15, 2018 at 23:46

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This dbsnp github repo seems to offer that information.

https://github.com/ncbi/dbsnp/tree/master/Build%20Announcements/151

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