Subtitle: This time… its correlated.
Previously I showed that with the default ML snp calling on GBS data, heterozygosity was higher with high and low amounts of data. I then took my data, fed it through a snp-recaller which looks for sites that were called as homozygous but had at least 5 reads that matched another possible base at that position (i.e. a base that had been called there in another sample). I pulled all that data together, and put it into a single table with all samples where I filtered by: