Greetings, we produced a track for Genome Browser that perhaps can be of any interest to other peoples. We computed the fixation index (FST) on the most up to date dataset available from HapMap. In particular, we computed the difference in the allelic frequencies of 3 populations, broadly reflecting a continental subdivision, by means of the Weir&Cockerham FST estimator. Data are from the last HapMap release (HapMap Public Release #27 merged II+III) and regards about 3.3 millions of SNPs. The detailed description of materials and methods can be found in the paper "Genome-Wide Scan for Signatures of Human Population Differentiation and Their Relationship with Natural Selection, Functional Pathways and Diseases" (PLoS ONE 4(11): e7927. doi:10.1371/journal.pone.0007927) available at the URL http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0007927 It is worth stressing that, in our opinion, the problem is of quite general interest. For example, we received many requests for the script we developed to compute the FST at a genome-wide level. We know that another track regarding FST is already present in the browser but some important differences exists. The most important ones are that HapMap data are very dense and also concerns X, Y and mitochondrial chromosomes. Moreover, the signal is base-wise and not smoothed, thus the actual value of selective pressure for each SNP is available (this can be of particular interest, for example, to those working on GWAS). The track is available at the URL
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr17&hgt.customText=http://www.geneticamedica.unina.it/FstTrack.bed.bz2 Track is BedGraph format and concerns hg18 database. If it can be of any relevance for you, all data (including heterozigosity and many other measures) are also stored in a local MySQL database. We will be pleased if you can consider to distribute this data by means of your browser. Looking forward for to hearing from you. Regards, Roberto Amato _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
