The column 7 in the mapping file format is designed to show the number of
mismatches of the alignments when output the "Best" or "Unique" mapping.
When -A option is specified, that is, users want to output ALL alignments
in the specified the threshold, the column (in version 0.2.9.4 or before)
currently print the "Minimum number of mismatches for that read) instead of
the number of mismatches.
For example, if read R mapped exactly to position P1, and mapped to
position P2 with one mismatches, currently the column 7 will print
universally "0" for in column 7 for both alignments, instead of print 0 in
first alignment and 1 in the second alignment. The output is a misleading
so it has scheduled to be changed in the future released.
Original issue reported on code.google.com by sorrychen@gmail.com on 24 May 2010 at 2:48
Original issue reported on code.google.com by
sorrychen@gmail.comon 24 May 2010 at 2:48