I am performing a GWAS analysis and try to understand the influence of the minor allele count filter.Setting the filter to 1 % gave me this plot and I am confused about the same -log10 pvalues around ~ 3.8 which shows a strange pattern (many dots in one line with same value).
If I increase the filter to 6 % the dots in a line disappear but I loose also some significant SNPs:
Sample are about 77000 SNP positions (barley), unimputed from GWAS (all NaNs removed). GWAS was performed with 200 phenotype samples.
How to interpret the dots in a line?