This track shows Rat quantitative trait loci (QTLs) from the Rat Genome Database (RGD) that have been coarsely mapped by UCSC to the $Organism genome using stringently filtered cross-species alignments. A quantitative trait locus (QTL) is a polymorphic locus that contains alleles which differentially affect the expression of a continuously distributed phenotypic trait. Usually a QTL is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci.
For a comprehensive review of QTL mapping techniques in the rat, see Rapp, J.P. (2000) in the References section below.
To map the Rat QTLs to $Organism, UCSC's chained and netted blastz alignments of Rat to $Organism were filtered to retain only those with high chain scores (>=500,000). This removed many valid-but-short alignments and in general retained only very long chains (>10,000, usually >100,000 bp), so that only large regions could be mapped. This choice was made because QTLs in general are extremely large and approximate regions. After the alignment filtering, UCSC's liftOver program was used to map Rat regions to $Organism via the filtered alignments.
To get a sense of how many genomic rearrangments between Rat and $Organism are in the region of a particular Rat QTL, you may want to view the $Organism Nets track in the Rat $o_date genome browser. In the position/search box, enter the name of the Rat QTL of interest.
Thanks to the RGD for providing the Rat QTLs. RGD is funded by grant HL64541 entitled "Rat Genome Database", awarded to Dr. Howard J Jacob, Medical College of Wisconsin, from the National Heart Lung and Blood Institute (NHLBI) of the National Institutes of Health (NIH).
Rapp JP. Genetic analysis of inherited hypertension in the rat. Physiol Rev. 2000 Jan;80(1):135-72.