Hi everyone, I did the GWAS analysis and got the result from TASSEL with GLM. Then I tried to make a qq-plot based on the p-value from GWAS output result. However, the qq-plot always started from y-axis 1 but not from 0 no matter how I modified the calculation. Following is the linkage for one of my qq-plot, please check it.

Please, any suggestion?

Best, Shu-Yun Chen