Boxplots of significant markers present also the missing data phenotype values.

[dosshra]

Hello
In the box-plots that show the distribution of phenotypic data by alleles (GAPIT.Phenotype.Distribution_Significantmarkers) there is a box-plot for N which represents missing data in the HapMap. I wonder if the missing data is also some how included in the GWAS itself?
Thank you

[jiabowang]

If there is missing genotype in your HapMap file, the GAPIT will consider them as heterozygotes.

[pkmnsandy]

Does that affect the overall result of the GWAS? I also saw a box plot for N and also Y.

[jiabowang]

@pkmnsandy If you impute those missing genotype using other software. The GWAS result should be different. We suggest imputation before GWAS.