I am only getting started with learning how to process genomics data, therefore I need some help making sense of the output of the Michigan imputation server. So, I imputated my genotypes, run QC and then extracted the dosage matrix, however now the output looks like this containing a variety of numbers ranging from 0 to 2:
id Sam1 Sam2 Sam3 Sam4
rs12238997 0.013 0.479 0.005 0.002
rs12029736 0.603 0.96 1.629 0.95
rs4951859 1.741 0.911 1.797 1.814
while I was expecting something like AA AC CC?
Maybe it has something to do with the reference?
Thank you in advance for your time!