## Description

This track shows regions of the human genome with a strong signal for depletion of Neandertal-derived alleles (regions from the Sel Swp Scan (S) track with S scores in the lowest 5%), which may indicate an episode of positive selection in early humans.

## Display Conventions and Configuration

Grayscale shading is used as a rough indicator of the strength of the score; the darker the item, the stronger its negative score. The strongest negative score (-8.7011) is shaded black, and the shading lightens from dark to light gray as the negative score weakens (weakest score is -4.3202).

## 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, and determined ancestral or derived state of each single nucleotide polymorphism (SNP) by comparison with the chimpanzee genome. The SNPs are displayed in the S SNPs track. The human allele states were used to estimate an expected number of derived alleles in Neandertal in the 100,000-base window around each SNP, and a measure called the S score was developed, displayed in the Sel Swp Scan (S) track, to compare the observed number of Neandertal alleles in each window to the expected number. An S score significantly less than zero indicates a reduction of Neandertal-derived alleles (or an increase of human-derived alleles not found in Neandertal), consistent with the scenario of positive selection in the human lineage since divergence from Neandertals.

Genomic regions of 25,000 or more bases in which all polymorphic sites were at least 2 standard deviations below the expected value were identified, and S was recomputed on each such region. Regions with S scores in the lowest 5% (strongest negative scores) were prioritized for further analysis as described in Green et al..

## Credits

This track was produced at UCSC using data generated by Ed Green.

## References

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 7 May;328(5979):710-22.