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Thousands of significant SNPs

Hi,

I have performed a GWAS between two genetically diverse bacterial populations and I found about 3000 significant SNP (p-value < 5e-8), I also found 120 SNPs with a p-value close to zero. About 500 genes harbor these significant SNPs. How to analyze these significant SNPs? Any suggestions for the downstream analysis?

Thanks!

gwas snp bacteria

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updated 6.1 years ago by Asaf

• written 6.1 years ago by arash.iranzadeh1980 •

Does the QQ plot looks ok? Are you trying to select SNPs for Stage-2 GWAS?

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written 6.1 years ago by gabi •

Many thanks. QQ plot shows a great deviation. Please see below. I think it should be ok! What do you think? Any suggestions?

https://ibb.co/Rgdxd05

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written 6.1 years ago by arash.iranzadeh1980 •

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