Chapter 3. Interpreting PyPop output

Alex Lancaster

Diogo Meyer

Richard M. Single

Last updated: $Date: 2007/08/17 05:14:11 $ by $Author: alancast $

Table of Contents

3.1. Population summary
3.2. Single locus analyses
3.2.1. Basic allele count information
3.2.2. Chi-square test for deviation from Hardy-Weinberg proportions (HWP).
3.2.3. Exact test for deviation from HWP
3.2.4. The Ewens-Watterson homozygosity test of neutrality
3.3. Multi-locus analyses
3.3.1. All pairwise LD
3.3.2. Haplotype frequency estimation

3.1. Population summary

A Population Summary is generated for each dataset analyzed. This summary provides basic demographic information and summarizes information about the sample size.

Sample output:

Example 3.1. Population summary sample output

Population Summary
==================
Population Name: UchiTelle
       Lab code: USAFEL
  Typing method: 12th Workshop SSOP
      Ethnicity: Telle
      Continent: NW Asia
Collection site: Targen Village
       Latitude: 41 deg 12 min N
      Longitude: 94 deg 7 min E

Population Totals
_________________
Sample Size (n): 47
Allele Count (2n): 94
Total Loci in file: 9
Total Loci with data: 8