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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 13 regions of the human genome in which there is
 considerably more haplotype diversity among non-African genomes than
 within African genomes.  A prediction of Neandertal-to-modern human
 gene flow is that these deeply divergent haplotypes which exist only in
 non-African populations entered the human gene pool from Neandertals.
 Of the 12 candidate gene flow regions with tag SNP data, there are 10
 regions in which Neandertals match the deep haplotype clade unique to
 non-Africans (out of Africa, OOA) instead of the cosmopolitan
 haplotype clade shared by Africans and non-Africans (cosmopolitan,
 COS).
 </P>
 <P>
 The table below was copied from Table 5, &quot;Non-African haplotypes 
 match Neandertal at an unexpected rate&quot;, from Green <em>et al.</em>:
 <BLOCKQUOTE><TABLE BORDER=1 CELLPADDING=4 BORDERCOLOR="#aaaaaa">
 <TR><TD>Region</TD><TD>Genomic Size</TD><TD>S<sub>T</sub></TD>
 <TD>Average<BR>Frequency<BR>in OOA</TD><TD>AM</TD><TD>DM</TD><TD>AN</TD><TD>DN</TD>
 <TD>Qualitative<BR>Assessment</TD></TR>
 <TR><TD><A HREF="../cgi-bin/hgTracks?db=$db&position=chr1:168,110,001-168,220,000&ntOoaHaplo=pack">chr1:168,110,001-168,220,000</A></TD><TD>110,000</TD><TD>2.9</TD><TD>6.3%</TD><TD>5</TD><TD>10</TD><TD>1</TD><TD>0</TD><TD>OOA</TD></TR>
 <TR><TD><A HREF="../cgi-bin/hgTracks?db=$db&position=chr1:223,760,001-223,910,000&ntOoaHaplo=pack">chr1:223,760,001-223,910,000</A></TD><TD>150,000</TD><TD>2.8</TD><TD>6.3%</TD><TD>1</TD><TD>4</TD><TD>0</TD><TD>0</TD><TD>OOA</TD></TR>
 <TR><TD><A HREF="../cgi-bin/hgTracks?db=$db&position=chr4:171,180,001-171,280,000&ntOoaHaplo=pack">chr4:171,180,001-171,280,000</A></TD><TD>100,000</TD><TD>1.9</TD><TD>5.2%</TD><TD>1</TD><TD>2</TD><TD>0</TD><TD>0</TD><TD>OOA</TD></TR>
 <TR><TD><A HREF="../cgi-bin/hgTracks?db=$db&position=chr5:28,950,001-29,070,000&ntOoaHaplo=pack">chr5:28,950,001-29,070,000</A></TD><TD>120,000</TD><TD>3.8</TD><TD>3.1%</TD><TD>16</TD><TD>16</TD><TD>6</TD><TD>0</TD><TD>OOA</TD></TR>
 <TR><TD><A HREF="../cgi-bin/hgTracks?db=$db&position=chr6:66,160,001-66,260,000&ntOoaHaplo=pack">chr6:66,160,001-66,260,000</A></TD><TD>100,000</TD><TD>5.7</TD><TD>28.1%</TD><TD>6</TD><TD>6</TD><TD>0</TD><TD>0</TD><TD>OOA</TD></TR>
 <TR><TD><A HREF="../cgi-bin/hgTracks?db=$db&position=chr9:32,940,001-33,040,000&ntOoaHaplo=pack">chr9:32,940,001-33,040,000</A></TD><TD>100,000</TD><TD>2.8</TD><TD>4.2%</TD><TD>7</TD><TD>14</TD><TD>0</TD><TD>0</TD><TD>OOA</TD></TR>
 <TR><TD><A HREF="../cgi-bin/hgTracks?db=$db&position=chr10:4,820,001-4,920,000&ntOoaHaplo=pack">chr10:4,820,001-4,920,000</A></TD><TD>100,000</TD><TD>2.6</TD><TD>9.4%</TD><TD>9</TD><TD>5</TD><TD>0</TD><TD>0</TD><TD>OOA</TD></TR>
 <TR><TD><A HREF="../cgi-bin/hgTracks?db=$db&position=chr10:38,000,001-38,160,000&ntOoaHaplo=pack">chr10:38,000,001-38,160,000</A></TD><TD>160,000</TD><TD>3.5</TD><TD>8.3%</TD><TD>5</TD><TD>9</TD><TD>2</TD><TD>0</TD><TD>OOA</TD></TR>
 <TR><TD><A HREF="../cgi-bin/hgTracks?db=$db&position=chr10:69,630,001-69,740,000&ntOoaHaplo=pack">chr10:69,630,001-69,740,000</A></TD><TD>110,000</TD><TD>4.2</TD><TD>19.8%</TD><TD>2</TD><TD>2</TD><TD>0</TD><TD>1</TD><TD>OOA</TD></TR>
 <TR><TD><A HREF="../cgi-bin/hgTracks?db=$db&position=chr15:45,250,001-45,350,000&ntOoaHaplo=pack">chr15:45,250,001-45,350,000</A></TD><TD>100,000</TD><TD>2.5</TD><TD>1.1%</TD><TD>5</TD><TD>6</TD><TD>1</TD><TD>0</TD><TD>OOA</TD></TR>
 <TR><TD><A HREF="../cgi-bin/hgTracks?db=$db&position=chr17:35,500,001-35,600,000&ntOoaHaplo=pack">chr17:35,500,001-35,600,000</A></TD><TD>100,000</TD><TD>2.9</TD><TD>(no tags)</TD><TD>n/a</TD><TD>n/a</TD><TD>n/a</TD><TD>n/a</TD><TD>n/a</TD></TR>
 <TR><TD><A HREF="../cgi-bin/hgTracks?db=$db&position=chr20:20,030,001-20,140,000&ntOoaHaplo=pack">chr20:20,030,001-20,140,000</A></TD><TD>110,000</TD><TD>5.1</TD><TD>64.6%</TD><TD>0</TD><TD>0</TD><TD>10</TD><TD>5</TD><TD>COS</TD></TR>
 <TR><TD><A HREF="../cgi-bin/hgTracks?db=$db&position=chr22:30,690,001-30,820,000&ntOoaHaplo=pack">chr22:30,690,001-30,820,000</A></TD><TD>130,000</TD><TD>3.5</TD><TD>4.2%</TD><TD>0</TD><TD>2</TD><TD>5</TD><TD>2</TD><TD>COS</TD></TR>
 </TABLE>
 <BR>
 S<sub>T</sub> = estimated ratio of OOA/African gene tree depth.<BR>
 Average Frequency in OOA = average (across tag SNPs in the region) of the population frequency in the 48 OOA individuals of the OOA-only allele for each tag SNP.<BR>
 AM = Neandertal has ancestral allele and matches OOA-specific clade.<BR>
 DM = Neandertal has derived allele and matches OOA-specific clade.<BR>
 AN = Neandertal has ancestral allele and does not match OOA-specific clade.<BR>
 DN = Neandertal has derived allele and does not match OOA-specific clade.
 </P></BLOCKQUOTE>
 
 <H2>Display Conventions and Configuration</H2>
 <P>
 A region is colored green if its qualitative assessment is OOA, blue
 if COS, and gray if unknown (no tag SNPs in region).
 </P>
 
 <H2>Methods</H2>
 <P>
 Green <em>et al.</em> used 1,263,750 Perlegen Class A SNPs, identified
 in 71 individuals of diverse ancestry (see Hinds <em>et al.</em>), to
 identify 13 candidate gene flow regions (Supplemental Online Materials
 Text 17).
 24 individuals of European ancestry and 24 individuals of Han Chinese
 ancestry were used to represent the non-African population, and the
 remaining 23 individuals, of African American ancestry, were used to
 represent the African population.
 </P>
 <P>
 From the 1,263,750 Perlegen Class A SNPs, they identified 166 tag
 SNPs that separate (see below) 12 of the haplotype clades in
 non-Africans (OOA) from the cosmopolitan haplotype clades shared between
 Africans and non-Africans (COS) and for which they had data from the
 Neandertals. Of the 13 regions, one had no tag SNPs so could not be
 assessed, two were COS, and 10 were OOA (see final column Table 1).
 </P>
 <P>
 Overall, the Neandertals match the deep clade unique to non-Africans
 (OOA) at 133 of the 166 tag SNPs. They assessed the rate at which
 Neandertal matches each of these clades by further subdividing the 133
 tag SNPs based on their ancestral or derived status in
 Neandertal and whether they matched the OOA-specific clade or not.
 Candidate regions were qualitatively assessed to be OOA matches for 
 Neandertal when the proportion of tag SNPs matching the OOA-specific 
 clade is much more than 50%.
 </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" 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>
 
 <p>
 Hinds DA, Stuve LL, Nilsen GB, Halperin E, Eskin E, Ballinger DG, Frazer KA, Cox DR.
-<a href="http://science.sciencemag.org/content/307/5712/1072" target="_blank">
+<a href="https://science.sciencemag.org/content/307/5712/1072" target="_blank">
 Whole-genome patterns of common DNA variation in three human populations</a>.
 <em>Science</em>. 2005 Feb 18;307(5712):1072-9.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15718463" target="_blank">15718463</a>
 </p>