7
$\begingroup$

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?

$\endgroup$
5
  • $\begingroup$ 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
    Aug 13 '17 at 20:01
  • $\begingroup$ Does Figure 4A help? nature.com/nature/journal/v491/n7422/fig_tab/… $\endgroup$ Aug 14 '17 at 8:04
  • $\begingroup$ You might be able to calculate yourself the stats you want if you download the data. $\endgroup$
    – llrs
    Aug 14 '17 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 $\endgroup$ Oct 31 '17 at 20:36
  • $\begingroup$ An important clarifying question: Do you only care about this information in the context of humans? $\endgroup$
    – conchoecia
    Feb 15 '18 at 23:46
1
$\begingroup$

This dbsnp github repo seems to offer that information.

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

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.