Problem about ClonalFrame

[wurensh]

hi, all. In one of our projects, we use ClonalFrame to remove SNPs caused by recombination. However, when I process the output of ClonalFrame, I faced one problem:

In the poly part of the output, I think the number should be continual, however, there appear some zeros in the sequence, such as,
# poly
...
659
701
0
0
0
0
0
728
733
734
735

I don't know these zeros mean. Can anyone here help me? Many thanks.

[wurensh]

Thanks to Xavier, I have solved this problem.

According to Xavier, these zeros mean that the site can't be found in the first genome. In my input data of clonalFrame, these sites use - instead of ATCG.