qq-plot not start from the 0

Question

[ubs717]

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.

https://www.dropbox.com/s/7b1eo4flefb3q10/QQ_plot_Leaf_GWAS%20_%20miR396e-5p%20_%20length_specific_boxcox_transform_5genetic_2Latent.jpg?dl=0

Please, any suggestion?

Best, Shu-Yun Chen

Answer 1

[theobroma22]

It makes sense to me - guessing from your plot it shows that your pvalues range from 0.15 to 1E-7, right? If so, -log of 0.15 = 0.82 and -log of 1E-7 = 7. If you thought it should start from 0 means you have pvalues equal 1, cause -log of 1 = 0. Do you have pvalues equal to 1??