Fine-scale recombination rate profile at DNA repeat elements

This site accompanies the article "A fine-scale chimpanzee genetic map from population sequencing".

Overview. The plot on the left depicts the recombination-influencing activity of repeat element families in Western Chimpanzees and humans (HapMap). The value reported is the ratio of the peak rate to background rate, as estimated from the robust genetic map after fitting a Gaussian profile using maximum likelihood. Repeat elements were required to have (1) greater than 150 thinned instances, (2) a profile fit with R-squared greater than 0.65 in at least one species, and (3) a relative difference less than 0.15 between the fold enrichment for the chimpanzee map and for the robust map.

All the fold-enrichment data is displayed by default. You may remove DNA repeat element classes by clicking the 'X' on the dashboard. Removed classes can be redisplayed using the drop down menu.

You can click on points to in the left-hand image to display the average recombination rate profile around each feature (bottom right-hand-side). Legend indicates the number of repeat elements used to generate each profile (after thinning so that no two repeats are within 10kb). Note that elements for chimpanzee profiles were identified from panTro2, and human profiles from hg18.

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