Plink automatically sets A2 as the major allele and then tests A1 (minor allele) for the purposes of regression. You could switch these through the use of the --a1-allele / --a2-allele flags.

Kevin

Use plink 2.0 --glm for this; it gives you a lot more flexibility re: what columns are included in the output, and by default both alleles are shown (and there's a third column indicating which allele is currently being regressed on).