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?

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