I am getting a significant marker trait association for traits. But understanding the allelic association is difficult; NN is the missing allele. Can anyone help me?
From the figure file shared, it is clear that it is a false association. You need to do data cleaning by removing minor alleles and missing data, both genotype-wise and marker-wise, with certain thresholds. Then impute the missing data points. I think you should get true associations with cleaned data.