Reads with Adapters : reads with sequencing adapters or reads two with poly A(read-through adpaters).
Reads too Short : reads with read length less than 20bp after trimming.
Reads Written : reads pass filtering.
Base Pairs Processed : total processed base pairs.
Base Pairs Quality-Trimmed : bases pairs removed from the end of the read whose quality is smaller than the given threshold
Base Pairs Written : base pairs pass filtering.