Howdy,
In the Methods paragraph in the description of "mapability", at
http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=wgEncodeMapability
the phrase "S=1 means exact match, S=0.5 is two matches" is
misleading. Reading the rest of the paragraph, what S=1 apparently
means is that the k-mer is unique in the genome at edit distance 2
(counting only mismatches). Similarly, S=2 means there are two k-mers
within edit distance 2-- the one at this position and one somewhere
else (and that one may or may not be a match).
It is easy to read "exact match" and think that no mismatches are
allowed.
Bob H
P.S. mapability should really have two ps, but it's probably too late
to correct that.
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