Chapter 3. Interpreting PyPop output

Last updated: $Date: 2008/08/17 08:51:35 $ 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

As mentioned in Section 2.1.3, “What happens when you run PyPop?”, The XML file is the primary output created by PyPop and contains the complete set of results. The text output, generated from the XML file via XSLT, contains a human-readable summary of the XML results. Below we discuss the output contained in this text file.

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