Could you please help me to understand my qqplot of TASSEL. I am looking to make association using MLM at TASSEL. I have total 71 samples in my vcfs and have 52K markers per traits. I have a total 5 data columns. If I use these traits as data, I do not get any significant SNPs but once I add factor column in phenotype file, I get some significant SNPs. However the qqplot seems different.