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 <H2>Description</H2>
 <P>
 
 This track shows Tajima's D (Tajima, 1989), a measure of nucleotide
 diversity, estimated from the Perlegen data set (Hinds <em>et al.</em>, 2005).
 Tajima's D is a statistic used to compare an observed nucleotide
 diversity against the expected diversity under the assumption that all
 polymorphisms are selectively neutral and constant population size.
 
 <H2>Methods</H2>
 
 Tajima's D was estimated in 100 kbp sliding windows across the
 autosomal genome, reporting the Tajima's D measure at the central 10
 kbp of the window and stepping by 10 kbp.  Thus, the Tajima's D for
 the window chr1:100,001-200,000 is reported at coordinates
 chr1:145,001-155,000, the Tajima's D for the window
 chr1:110,001-210,000 is reported at coordinates chr1:155,001-165,000,
 and so forth.
 <P>
 The theoretical distribution of Tajima's D (95% c.i. between -2 and
 +2) assumes that polymorphism ascertainment is independent of allele
 frequency. High values of Tajima's D suggest an excess of common
 variation in a region, which can be consistent with balancing
 selection, population contraction.  Negative values of Tajima's D, on
 the other hand, indicate an excess of rare variation, consistent with
 population growth, or positive selection.  Population admixture can
 lead to either high or low Tajima's D values in theory.  Demographic
 parameters would be expected to affect the genome more evenly than
 selective pressures, so previous analyses have suggested that using
 the empiric distribution of Tajima's D from a collection of regions
 across the genome provides advantages in assessing whether selection
 or demography might explain an observed deviation from
 expectation. Because of the ascertainment bias toward common
 polymorphism in the Perlegen data set, positive Tajima's D values are
 difficult to interpret, and modeling ascertainment is difficult.
 However, given that the ascertainment bias raises the mean of the
 distribution, extreme negative values in extended regions can be
 useful in qualitatively identifying interesting regions for full
 resequencing and more rigorous theoretical analysis of nucleotide
 diversity.  For further discussion, see Carlson <em>et al.</em> (2005).
 <P>
 In full display mode, this track shows the nucleotide diversity across
 three human populations: 23 individuals of African American Descent
 (AD), 24 individuals of European Descent (ED) and 24 individuals of
 Chinese Descent (XD), as well as the polymorphic sites within each
 population used to estimate nucleotide diversity.  Only SNPs observed
 to be polymorphic within each subpopulation were used in the Tajima's
 D calculation.  Nucleotide diversity is shown in dense display mode
 using a grayscale density gradient, with light colors indicating low
 diversity.
 
 <H2>Credits</H2>
 <P>
 This track was created at the University of Washington using gfetch
 from the Nickerson Laboratory and the 
 <A HREF="http://www.r-project.org/" 
 TARGET=_blank>R statistical software package</A>.</P>
 
 <H2>References</H2>
 <P>
 Tajima, F. 
-<A HREF="http://www.genetics.org/content/123/3/585"
+<A HREF="https://www.genetics.org/content/123/3/585"
 TARGET=_blank>Statistical method for testing the neutral mutation hypothesis 
 by DNA polymorphism</A>. 
 <em>Genetics</em> <B>123</B>, 585-595 (1989).</P>
 <P>
 Carlson, C.S., Thomas, D.J., Eberle, M., Livingston, R., Rieder, M. 
 Nickerson, D.A. 
 <A HREF="https://genome.cshlp.org/content/15/11/1553.abstract"
 TARGET=_blank>Genomic regions exhibiting positive selection identified from 
 dense genotype data</A>. 
 <em>Genome Res</em> <B>15</B>, 1553-65 (2005).</P>