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Please Help Me Understand GWAS Results

Hi there,

It's my first time working with GWAS so please bare with me. I've used both GAPIT and rMVP to run some GWAS analysis. My phenotype is categorical ordinal, (ie. a 1 to 5 scale). I've gotten significant SNPs but I don't quite understand how to interpret the results. How do I know if it is significant because it had higher associations to a rating of '1' vs '5'?

rmvp gwas gapit
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written by chloek88 • chloek88

Post a result example. Not sure if this description is going to be sufficient for people to give you an answer. You can redact gene names/sample info if you are worried about that.

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written by GenoMax GenoMax

Example of my phenotypic data input

Phenotype Data

Example of the results table

Results table

The phenotypic data + genomic data (.vcf) were used as the inputs for the analysis in rMVP.

Thank you.

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written by chloek88 • chloek88

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