text: user12135: We were looking for genetic diversity in the exon level of an MHC transcript and analysing the data under ANGSD (Analysis of next generation Sequencing Data) written in C++
  We used ANGSD to calculate Thetas and Tajima D neutrality tests and one of the thetas was a pairwise theta, however I am unsure what this means and how it differs from Tajima's D?
  http://www.popgen.dk/angsd/index.php/Thetas,Tajima,Neutrality_tests
  We then divided the tP over length of each exon to find genetic diversity in the exon level. However, as I am very interested in statistics, if someone could explain what the tP statistic means exactly it would be highly appreciated.
  
  user2907: While I can't explain it to you directly, you might check out the section on theta estimators in Korneliussen et al. (2013) which is cited on the above ANGSD wiki page. The equation for this estimator in this paper traces back to the original Tajima (1989).
  
original_text: 12135: <p>We were looking for genetic diversity in the exon level of an MHC transcript and analysing the data under <a href="http://www.popgen.dk/angsd/index.php/ANGSD" rel="nofollow noreferrer">ANGSD</a> (Analysis of next generation Sequencing Data) written in C++</p>
  <p>We used ANGSD to calculate Thetas and Tajima D neutrality tests and one of the thetas was a pairwise theta, however I am unsure what this means and how it differs from Tajima's D?</p>
  <p><a href="http://www.popgen.dk/angsd/index.php/Thetas,Tajima,Neutrality_tests" rel="nofollow noreferrer">http://www.popgen.dk/angsd/index.php/Thetas,Tajima,Neutrality_tests</a></p>
  <p>We then divided the tP over length of each exon to find genetic diversity in the exon level. However, as I am very interested in statistics, if someone could explain what the tP statistic means exactly it would be highly appreciated.</p>
   2907: <p>While I can't explain it to you directly, you might check out the section on theta estimators in <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-289" rel="nofollow noreferrer">Korneliussen et al. (2013)</a> which is cited on the above ANGSD wiki page. The equation for this estimator in this paper traces back to the <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1203831/pdf/ge1233585.pdf" rel="nofollow noreferrer">original Tajima (1989).</a></p>
  