I need to prove that a given region on the genome maintains has the same base composition proportions (20% A, 15% T, 19% C, etc…) of that genome. I thought about doing Chi-squared test of independence since I deal with exact counts. As a result, I found $p<0.05$ suggests that they are independent so I say the base composition was changed. I just wanted to get a review of my action.
mydf: hg19 AR A 854963149 705448 T 856055361 705519 G 593325228 482498 C 592966724 479646 N 239850802 2806685
Pearson's Chi-squared test
data: mydf X-squared = 15718000, df = 4, p-value < 2.2e-16
Is this method valid ?