GWAS q-q plot showing lots of "1's" and a flat line with logistic regression
0
0
Entering edit mode
21 months ago
Vanish007 ▴ 40

Hi,

I have some RADseq sequencing data that I ran a gwas on. We ran these on zebrafish and for the case/control we had 25 controls and 17 cases, filtering out for MAF < 0.3. For the associative study, we went with a logistic regression model. However when I plot the q-q plot, I seem to have received a strange result with an over-abundance of 1's in my p-value. Here is what I got:

qqplot

histogram_p

Could this be mainly due to low quality reads? Is there anything else that could be causing this?

Thank you for the help.

gwas qqplot plink • 597 views
ADD COMMENT

Login before adding your answer.

Traffic: 1565 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6