Analysing neutral SNPs = everything makes sense from a population genetic structure point of view. When analysing the outlier SNPs (that come from the same pool of SNPs called using STACKS) sites that were closer in the plates during sequencing, group together.
I believe if it was cross-contamination, I would expect to see the same grouping pattern when using the neutral data set too, which I do not.
Any ideas?
Cheers,
G
Are you assembling your loci de novo or based on a reference genome?
Have you explored the chance that the data is correct and the distribution of outliers' genetic variation is associated with non-neutral processes?
Cheers
Hi Jose Alberto Lopez-Aleman thanks for your reply.
I have called the SNPs de novo as the mapping rate of my short reads against the closest genome available was 27% (quite low). I thought about that, but there is a very clear cut between the two groups corresponding to the samples on the plates and it does not make sense geographically at all. I have environmental data too but it appears a bit too much of a coincidence to me..
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