Tajima's D SNPs Track Settings
 
Tajima's D SNPs (from Human May 2004 assembly)   (All Variation and Repeats tracks)

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 SNPs AD  SNPs from African Descent used for Tajima's D (from Human May 2004 assembly)   Schema 
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 SNPs ED  SNPs from European Descent used for Tajima's D (from Human May 2004 assembly)   Schema 
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 SNPs XD  SNPs from Chinese Descent used for Tajima's D (from Human May 2004 assembly)   Schema 

Description

This track shows the SNPs that were used in the calculation of Tajima's D (Tajima, 1989), a measure of nucleotide diversity, estimated from the Perlegen data set (Hinds et al., 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. The original SNP coordinates were from the Human May 2004 assembly; they were transformed to this assembly using UCSC's liftOver program.

Methods

See the Tajima's D track or Carlson et al. for more details on the use of this track.

Credits

This track was created at the University of Washington using gfetch from the Nickerson Laboratory and the R statistical software package.

References

Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 1989 Nov;123(3):585-95.

Carlson CS, Thomas DJ, Eberle M, Livingston R, Rieder M, Nickerson DA. Genomic regions exhibiting positive selection identified from dense genotype data. Genome Res 2005 Nov;15(11):1553-65.