d2a02f56a0e84d51213d44955b694ce7daace230 jnavarr5 Fri May 31 11:41:50 2019 -0700 Updating redirected links for hg18, uiLinks cronjob. diff --git src/hg/makeDb/trackDb/human/ntSssTop5p.html src/hg/makeDb/trackDb/human/ntSssTop5p.html index f44ef60..4ed0cb4 100644 --- src/hg/makeDb/trackDb/human/ntSssTop5p.html +++ src/hg/makeDb/trackDb/human/ntSssTop5p.html @@ -1,65 +1,65 @@ <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:ed@soe.ucsc.edu" title="ed@soe.ucsc.edu" 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