6254a2f3273acb0889ba875ffab273f0099cea16 galt Tue May 21 00:17:23 2019 -0700 Fixe problems found by htmlCheck validate and hgNearTest robot diff --git src/hg/makeDb/trackDb/human/humMusL.html src/hg/makeDb/trackDb/human/humMusL.html index 15e973b..cfd0e35 100644 --- src/hg/makeDb/trackDb/human/humMusL.html +++ src/hg/makeDb/trackDb/human/humMusL.html @@ -21,31 +21,31 @@ by scanning the sequence, sliding 5 bases at a time, and only those windows with at least 15 aligned bases were kept. For each window, a conservation score defined by <br><br> <center> S = sqrt(n/m(1-m))(p-m) </center> <br> was calculated, where n is the number of aligning bases in the window, p is the percent identity between human and mouse for these aligning bases, and m is the average percent identity for aligned neutrally evolving bases in a larger region surrounding the 50 bp window being scored. Neutral bases were taken from ancestral repeat sequences, which are relics of transposons that were inserted before the human-mouse split. To transform S into an L-score, the empirical - cumulative distribution function CDF(S) = P(x < S) + cumulative distribution function CDF(S) = P(x < S) is computed from the scores of all windows genome-wide, and the L-score is defined as <br><br> <center> L = -log_10(1 - CDF(S)). </center> <br> <br> The L-score provides a frequentist confidence assessment. A Bayesian calculation of the probability that a window is under selection can also be made using a mixture decomposition of the empirical density of the scores for all windows genome-wide into a neutral and a selected component. Details are given in a manuscript in preparation. The results are