[galaxy-user] Extracting reads mapped from bwa mapping

Hello,

I recently figured out how to filter the output bwa SAM file for flag type in order to determine the number of reads that were successfully mapped. My question is, I previously thought I could generate a pileup, then sum the number of counts for each base of the reference, and divide this number by the length of the reads (not exact if some reads are hanging over the edge of the reference sequence, but should be close?). But when I compare these methods, I get drastically different results. What am I missing?

Thanks, Austin