This track displays the conservation between the mouse and human genomes for 50bp windows in the mouse genome that have at least 15 bp aligned to human. The score for a window reflects the probability that the level of observed conservation in that 50bp region would occur by chance under neutral evolution. It is given on a logarithmic scale, and thus it is called the "L-score". An L-score of 1 means there is a 1/10 probability that the observed conservation level would occur by chance, an L-score of 2 means a 1/100 probability, an L-score of 3 means a 1/1000 probability, etc. The L-scores display as "mountain ranges". Clicking on a mountain range, a detail page is displayed from which you can access the base level alignments, both for the whole region and for the individual 50bp windows.
Genome-wide alignments between mouse and human were produced by
Blastz. A set of 50bp windows in the mouse genome were determined
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
L-score Frequentist probability Bayesian probability of this L-score or greater that window with this given neutral evolution L-score is under selection ------------------------------------------------------------------ 1 0.1 0.32 2 0.01 0.75 3 0.001 0.94 4 0.0001 0.97 5 0.00001 0.98 6 0.000001 0.99 7 0.0000001 >0.99 8 0.00000001 >0.99
Thanks to Webb Miller and Scott Schwartz for creating the Blastz alignments, Jim Kent for post-processing them, and Mark Diekhans for scoring the windows and selecting out the ancestral repeats. Krishna Roskin created S-scores for these windows. Ryan Weber computed the CDF for these S-scores, and created the remaining track display functions.