text: user9278: 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?
  
  user492: This looks like genotyping failed for some samples. It's unclear from the op whether the genotyping data was controlled for quality, but I would recommend performing sample QC.
  On a side note: in human gwas with imputed snps, I would expect to see clusters of significant snps as a sign that the significant snps are not an artifact. In the op there are some single significant snps. This might be a sign that those significant snps are artifacts. There are also some snps that form clusters and therefore look more promising.
  
original_text: 9278: <p>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).</p>
  <p><a href="https://i.stack.imgur.com/w9x4I.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/w9x4I.png" alt="enter image description here" /></a></p>
  <p>If I increase the filter to 6 % the dots in a line disappear but I loose also some significant SNPs:</p>
  <p><a href="https://i.stack.imgur.com/4tMdD.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/4tMdD.png" alt="enter image description here" /></a></p>
  <p>Sample are about 77000 SNP positions (barley), unimputed from GWAS (all NaNs removed). GWAS was performed with 200 phenotype samples.</p>
  <p>How to interpret the dots in  a line?</p>
   492: <p>This looks like genotyping failed for some samples. It's unclear from the op whether the genotyping data was controlled for quality, but I would recommend performing sample QC.</p>
  <p>On a side note: in human gwas with imputed snps, I would expect to see clusters of significant snps as a sign that the significant snps are not an artifact. In the op there are some single significant snps. This might be a sign that those significant snps are artifacts. There are also some snps that form clusters and therefore look more promising.</p>
  