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I am working in the filtering steps, all my plots looks similar to your plots here, but the QD values are the opposite of what I am expecting, the most of the SNPs have values around 30. This means that I have the double of reads that support the heterozygous calls right? Is this normal? I am working with a mix of maize landraces and inbreed lines. I expect that some of them would be highly heterozygous, meanwhile others must to be highly homozygous. Do you think that this could be causing a problem?
Attached is my plot