GWAS MAC filter Interpretation
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.