Hello,

I am new to bioinformatics. I am learning about SNPs and trying to use vcftool. In vcftool if i use the --012 option it generates a .012 file with 0,1,2 in it. Where "*Genotypes are represented as 0, 1 and 2, where the number represent that number of non-reference alleles.*"(Ref: Vcftool manual). So If for a snp position the reference allele is C the possible combinations are CC,CT,TC,TT where CC=0, CT/TC=1, TT=2 are the encodings. 

My first question is what does this CC mean ?? Does this mean at the particular position there is neocleotide C and it is paring with another neocleotide C on the other strand? 

If that so it is not following the [base-pair rule][1] . Is it ? 

Finally the generated files have very large number of 0's and 2's than that of number of 1's. Should not CT/TC be the common combination that CC and TT. 

If I am understanding completely wrong some helpful links will be appreciated.

  [1]: https://en.wikipedia.org/wiki/Chargaff%27s_rules

Thanks In Advance.
CC means homozygous for C. CT/TC would mean heterozygous and so on.