This track displays the conservation between the mouse (Feb. 2003, mm3 ) and rat (Jan. 2003, rn2) genomes for 50 bp windows in the mouse genome that have at least 15 bp aligned to rat. 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 rat 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
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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 Jim Kent for creating the blastz alignments and post-processing to create blastzBestRat track. Ryan Weber computed the windows s-scores, computed the CDF of these scores, and created the remaining track display functions. Mark Diekhans and Krishna Roskin created software used in this process. Mouse sequence data are provided by the Mouse Genome Sequencing Consortium.