Reports - Founder Metrics

Founder Metrics - Contribution Detail Report - listing the founders of a group of animals, showing the %contribution to the group, the %founder alleles retained, and the likelihood that each founders genes have only been passed down to at most one member of the group
Founder Metrics - Contribution Detail Report - listing the founders of a group of animals, showing the %contribution to the group, the %founder alleles retained, and the likelihood that each founders genes have only been passed down to at most one member of the group

 

Founder Metrics Contribution Detail Report - Matrix with founders in columns and group members in rows, giving the %contribution of each founder to each descendant
Founder Metrics Contribution Detail Report - Matrix with founders in columns and group members in rows, giving the %contribution of each founder to each descendant

PedScope can analyse the founders of a single animal, or a group of animals, and list various measures of genetic diversity associated with them. Typically this would be used to analyse the founders of a group of animals that make up a 'current population' or a group from which future breeding is to occur. In the description that follows, 'current population' means either the currently selected animal, or the group of tagged animals, whichever has been chosen for the report.

There are 3 separate founder metrics reports available to choose from the report selector (at the top of the report pane):

  • Summary
  • Contribution Detail
  • and Genome Uniqueness Detail

The Founder Metrics - Summary report lists the founders and for each founder it gives its:

  • Contribution - The proportion of the genes in the current population due to that founder.
  • Alleles Retained - The proportion of the genes of that founder that have probably been retained in the current population.
  • Founder Genome Uniqueness - The probability that genes from that founder are only present in, normally, 1 member of the current population. We say 'normally', because you can adjust the genome uniqueness threshold on the General tab of the Document Settings window.

As with all other tables in PedScope, you can sort the founders by clicking on the columns. It is therefore very easy indeed to work out which founders have had the main influence on any group of animals, and which have the least.

The other two founder metrics reports, Contribution Detail and Genome Uniqueness Detail, display matrices that give the contribution and genome uniqueness values between every member of the current population and every founder. The matrix columns hold the founders, and the rows the members of the current population. The top two matrix rows always contain the summary value (i.e. the contribution or genome uniqueness with respect to the whole group), and the alleles of each founder retained by the whole group - the same values as given in the summary table. The properties pane comprises two columns and contains the record details for the currently selected matrix cell.

All founder reports let you choose the depth of ancestry to be considered when building the report. PedScope searches the pedigrees of all animals in the current population to that depth to provide a list of ancestors, and then locates animals within that group that are founders with respect to the group. This is an important distinction; see Population Genetics - Founders.

All founder reports also include the following measures of genetic diversity, which are single values computed for the whole of the current population:

You can customize the definition of genome uniqueness. By default, a gene from a given founder is considered to be inherited uniquely when it is present in only one member of the current population. You can increase this threshold, e.g. you could choose to have PedScope treat the presence of the gene in at most 3 animals as meaning 'unique'.

The probability of alleles retained, and genome uniqueness, are computed using a gene drop analysis. You can customize the number of simulations used to compute these values.


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