d2a02f56a0e84d51213d44955b694ce7daace230
jnavarr5
  Fri May 31 11:41:50 2019 -0700
Updating redirected links for hg18, uiLinks cronjob.

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 <H2>Description</H2>
 <P>
 This track shows regions of the human genome with a strong signal for depletion
 of Neandertal-derived alleles (regions from the 
 <A HREF="/cgi-bin/hgTrackUi?&c=chr1&g=ntSssZScorePMVar">Sel Swp Scan 
 (S)</A> track with S scores in the lowest 5%),
 which may indicate an episode of positive selection in early
 humans.</P>
 
 <H2>Display Conventions and Configuration</H2>
 <P>
 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).
 </P>
 
 <H2>Methods</H2>
 <P>
 Green <em>et al.</em> identified single-base sites that are
 polymorphic among five modern human genomes of diverse ancestry
 (in the 
 <A HREF="/cgi-bin/hgTrackUi?&c=chr1&g=ntModernHumans">Modern Human 
 Seq</A> 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 
 <A HREF="/cgi-bin/hgTrackUi?&c=chr1&g=ntSssSnps">S SNPs</A> 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 
 <A HREF="/cgi-bin/hgTrackUi?&c=chr1&g=ntSssZScorePMVar">Sel Swp Scan 
 (S)</A> 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.
 </P>
 <P>
 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 <em>et al.</em>.
 </P>
 
 <H2>Credits</H2>
 <P>
 This track was produced at UCSC using data generated by
 <A HREF="mailto:&#101;&#100;&#64;&#115;&#111;e.&#117;&#99;s&#99;.&#101;&#100;&#117;"
 title="&#101;&#100;&#64;&#115;&#111;e.&#117;&#99;s&#99;.&#101;&#100;&#117;" rel="nofollow"
 TARGET=_BLANK>Ed Green</a>.
 </P>
 
 <H2>References</H2>
 <p>
 Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH
 <em>et al</em>.
-<a href="http://science.sciencemag.org/content/328/5979/710.long" target="_blank">
+<a href="https://science.sciencemag.org/content/328/5979/710" target="_blank">
 A draft sequence of the Neandertal genome</a>.
 <em>Science</em>. 2010 May 7;328(5979):710-22.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/20448178" target="_blank">20448178</a>
 </p