This track displays the conservation between the mouse and human genomes for 50 bp 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 50 bp 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 50 bp windows.
Genome-wide alignments between mouse and human were produced by
blastz. A set of 50 bp 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
The track filter can be used to configure some of the display characteristics of the track.
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. Thanks to the Mouse Genome Sequencing Consortium for providing the mouse sequence data.