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How to explain my QQ-plot result

Hello dear,

I am a beginner in exome-seq and have tried to get a threshold of p-value for significant mutations using QQ-plot. However, I couldn't because my QQ-plot looked very weird.

I couldn't figure it out whether it is a something wrong or not, and how I can explain or fix it.

can you help me with this?

Kakao-Talk-20190128-102101242

snp
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updated by zx8754 zx8754 • written by khlee02 • khlee02

Are these the results of an association analysis? It seems that your p-values are inflated, which can arise due to different reasons, more commonly due to unaccounted populations structure. There is a lot of literature on interpreting GWAS results. Maybe start with this? https://www.nature.com/articles/nrg1916

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written by GabrielMontenegro GabrielMontenegro

I really appreciate your kind comment. I am going to start with it. Is there any good tutorials for basic exome seq?

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written by khlee02 • khlee02

I am sorry for lack of information. I have done my exome-sequencing in tumor tissue and adjacent normal tissues, and got the p-value from fisher exact test between normal and cancer on each variation. The QQ plot was depicted by qqman in R

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written by khlee02 • khlee02

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