As far as I remember the output to stdout is a SAM pileup file including the positions of the mutations. http://samtools.sourceforge.net/pileup.shtml

The stdout looks like this

chrX    89985560        T       C       -
chrX    89990640        T       Y       +  
chrX    89991017        C       M       +
chrX    89991096        G       R       +
chrX    89994004        A       R       + 
chrX    89994987        A       W       +
chrX    89995790        A       R       +

Even when I generate 100 reads the stdout is 2,923,254 lines long. So is is just generating and outputting mutations for the whole genome and then generating reads indepently of these across the genome?

So where do I find out what the 'W's and 'R's etc mean? And also, what is the quickest way of finding out which of these mutations were incorporated into the actual reads I generated?