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
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).
Green et al. identified single-base sites that are
polymorphic among five modern human genomes of diverse ancestry
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..
This track was produced at UCSC using data generated by
Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH
A draft sequence of the Neandertal genome.
Science. 2010 May 7;328(5979):710-22.