I wonder what is the relationship between Plink .tped and .ped files. From what I observe, it seems it is more complicated than a simple transpose.

For example, in Section 4.1.1 of this manual, there is an example as following:

1     1     0     0     1     1     1     1     G     G
1     2     0     0     2     1     0     0     A     G
1     3     0     0     1     1     1     1     A     G
1     4     0     0     2     1     2     1     A     A

is transposed as

1     snp1     0     10001     1     1     0     0     1     1     2     1
1     snp2     0     20001     G     G     G     A     G     A     A     A
#                                          ^     ^     ^     ^

but instead of, what I thought should be:

1     snp1     0     10001     1     1     0     0     1     1     2     1
1     snp2     0     20001     G     G     A     G     A     G     A     A
#                                          ^     ^     ^     ^

Why there is a reverse relationship here?

And I think this reverse is not guaranteed to happen, for the reasons that in example of Section 3.4 of the same manual, it's hard to tell if there is any pattern for whether should be reversed or not.

(I am quite new to this area, and I hope the reason is not something very superficial as common sense in this domain)