This track shows Mouse quantitative trait loci (QTLs) from Mouse Genome Informatics (MGI) at the Jackson Laboratory 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.
To map the Mouse QTLs to $Organism, UCSC's chained and netted blastz alignments of Mouse to $Organism were filtered to retain only those with minimum length of 20,000 bases in both Mouse and $Organism, and minimum score of 10,000. This removed many valid-but-short alignments. 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 Mouse regions to $Organism via the filtered alignments.
For the purpose of cross-species mapping, MGI QTLs were divided into two categories: QTLs whose genomic coordinates span the entire confidence interval (often several million bases), and QTLs for which only the STS marker with the peak score was given, resulting in genomic coordinates for very small regions (most less than 300 bases). QTLs in the latter set were so small as to make mapping impossible in many cases, so their coordinates were padded by 50,000 bases before and after, for a total size of approximately 100,000 bases, a conservative proxy for the unknown confidence interval. The two categories of QTL are displayed in subtracks: MGI Mouse QTL for the unmodified QTLs and MGI Mouse QTL Padded for the single-marker QTLs that were padded to 100,000 bases.
To get a sense of how many genomic rearrangments between Mouse and $Organism are in the region of a particular Mouse QTL, you may want to view the $Organism Nets track in the Mouse $o_date genome browser. In the position/search box, enter the name of the Mouse QTL of interest.
Thanks to MGI at the Jackson Laboratory, and Bob Sinclair in particular, for providing these data.