I am using PLINK2 to create a profile score and am confused to what the output represent:
My score file has ~84k SNPs and my profile output looks like this
FID IID PHENO CNT CNT2 SCORE 00 1 1 173748 83462 0.017818 01 1 1 173740 83216 0.017095 02 2 1 173728 83738 0.017375
CNT -Number of non-missing SNPs used for scoring CNT2 -The number of named alleles
It seems to me that plink might have interchanged CNT and CNT2 column but I do not understand what "number of named alleles" mean ? Also, the scoring is such, all my individuals are scored in the range of 0.017095 to 0.017999, isn't that a bit strange ?