grouping of maf results in GWAS

Question

[joanfitz5]

In my GWAS output I am getting groups of SNPs with exactly the same maf. My sample size is 5345. Is sample size causing this or is there another reason.

All the best Joan

Edit:

Thank you for getting back to me. I am doing a linear analysis in plink2 (covariates not included) on a sample of 5346 induviduals using a cognitive phenotype and the following command ./plink2 pfile XXX --glm cols=+a1 --pheno phenocog -- out XXX. My QC has a maf of .001 and an info score of 0.9

1   31015397    rs1484840     T   C   C   0.00415369   ADD   5345   -1054.79   234.319   -4.50153   6.88998e-06
1   31048487    rs114685975   C   T   T   0.003274     ADD   5345   -1116.13   254.996   -4.37707   1.2258e-05
1   31050995    rs138406068   C   T   T   0.003274     ADD   5345   -1116.13   254.996   -4.37707   1.2258e-05
1   31052680    rs112644260   C   G   G   0.003274     ADD   5345   -1116.13   254.996   -4.37707   1.2258e-05
1   31056654    rs112145079   C   T   T   0.003274     ADD   5345   -1116.13   254.996   -4.37707   1.2258e-05
1   88211845    rs112901772   C   T   T   0.0348179    ADD   5345   366.968    84.3818   4.3489     1.39366e-05

[Nicolas Rosewick]

could you describe a little bit more your experiment design, the tools you used and put some of your results here ? Without that it will be difficult to help you.

Answer 1

[chrchang523]

By itself, this is nothing to worry about. If you have no missing genotypes, there are only 5335 possible minor allele frequencies, corresponding to the fractions 11/10690, 12/10690, 13/10690, ..., and 5345/10690. And the smallest fractions are a lot more frequent than the rest.