Description

This track shows the S score (Z-score +- variance) for positive selection in humans within a 100 kb window surrounding each polymorphic position in the five modern human sequences and the human reference genome as described in Green et al., Supplemental Online Material Text 13, Burbano et al.. A positive score indicates more derived alleles in Neandertal than expected, given the frequency of derived alleles in human. A negative score indicates fewer derived alleles in Neandertal, and may indicate an episode of positive selection in early humans.

To view the polymorphic sites on which the S score was computed, open the S SNPs track.

Methods

Green et al. identified single-base sites that are polymorphic among five modern human genomes of diverse ancestry (in the Modern Human Seq track) plus the human reference genome. CpG sites were excluded because of the higher mutation rate at CpG sites. The ancestral or derived state of each single nucleotide polymorphism (SNP) was determined by comparison with the chimpanzee genome. The SNPs are displayed in the S SNPs track. The fact that SNPs with higher frequencies of the derived allele in modern humans were more likely to show the derived allele in Neandertals was used to calculate the expected number of derived alleles in Neandertal within a given region of the human genome. The observed numbers of derived alleles were compared to the expected numbers to identify regions where the Neandertals carry fewer derived alleles than expected given the human allelic states. The score assigned to each SNP is the z-score of the observed and expected counts relative to the variance in the number of the expected counts of derived alleles within the 100,000-base window around the SNP.

Note: In order to display both the score and the variance within the same track in the UCSC Genome Browser, the scores were modified as follows: at the SNP position, the value displayed is the score plus the variance. At the position following the SNP position, the score minus the variance is displayed. When viewing large regions (at least 100,000 bases), the default mean+whiskers condensation of the scores provides an indication of the range covered by the variance.

Reference

Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH et al. A draft sequence of the Neandertal genome. Science. 2010 May 7;328(5979):710-22. PMID: 20448178