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I am curious if the line estimation shown in the history window for pileup
generation is at all accurate.  I am using the pileup files to generate
expression data from bwa mapping for looking at differential expression, but
I am having some trouble understanding the line estimates.  For example, for
one pileup file, when I cut the reference id column and the number of hits
column (columns 1 and 4), the number of lines in the cut file is about 25%
that of the pileup file, and for another file it will be 5000%.   How can
the number of lines grow 50x when I am just cutting columns from the file?
Shouldnt the line estimate be the same?

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