Hi Ha,
The mapper application uses a combo of flow signals info quality scores, and difference type information to determine if a variant is of high quality. The HCDiffs file contains variants that have at least 3 non-duplicate reads relative to the reference or to other reads at that specific location.
I also found another thread that discusses uppercase and lower case and maybe helpful.
http://seqanswers.com/forums/showthread.php?t=1948