Currently I am working with deepSNV and realized that the bam2R output results with A T C G X and N. I am aware of N stands for the reads that did not meet the threshold of quality, but I could not figure out what X stands for? I check the manual and the other information about it might be it stands for '-', but the insertion and deletion are provided in  (INS)ertions, (DEL)etions columns. So what does X means in bam2R result?

When I run the program I get the following column names in the output from bam2R

   A    T    C    G  -   N  INS DEL HEAD TAIL   QUAL

The "-" represents gaps (so it may be present for spliced alignments; e.g. introns). 

My guess is you converted the output to a data.frame which renamed that column to "X.".