The meaning of "X" in the intermediate files

[Miffy-yan]

In the intermediate files which contain extracted SNP info for each SNP location, it's obvious that "N" would be given to a SNP of it is not covered by the read. However, sometimes, I will also get "X" for some SNP sites, what's the meaning of the "X" here?

A fake example could be:

AATTCCXXTTCCNNN

What do the two "X" in between mean?

[ngthomas]

Hi Miffy-yan. I apologize for the late response. "X" normally represents deletion.