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
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joanfitz5 •
2 answers
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.
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
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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.