Dear All,

How do I interpret the results from PLINK2.0 when generating haplotype frequencies for three variants?

plink2 --bfile mydata --ld 12439 12340 --out gene_12439_12340 

This generates the following results:

  Solution #3 (best likelihood):
      r^2 = 0.624219    D' = 1

        Frequencies      :              12439
  (expectations under LE)          MAJOR       MINOR
                                 ----------  ----------
                           MAJOR  0.599307    0
                                 (0.422837)  (0.176470)
                  12340 
                           MINOR  0.106236    0.294457
                                 (0.282706)  (0.117987)

      Major alleles are in phase with each other.

Specifically, I obtained three solutions with different D' and R-squared values, where the first and third solutions had D' = 1, while the second had D' = 0.593841. Similarly, the R-squared values also varied.

Although I understand that an R-squared value of 0.624219 suggests moderate correlation between the two SNPs, and a D' value of 1 indicates perfect LD.

I am still struggling to interpret the frequencies given for the major and minor alleles in the 2X2 table. Additionally, I do not understand why these three solutions have different D' and R-squared values. Can anyone provide guidance on how to interpret these results?