Pedigree Verification Lines (parental contribution)ΒΆ

This analysis provides several key statistics to determine whether a sampled line is a progeny of the expected, or designated, parents.

In addition to this help page, you can also read the Pedigree Verification - Lines (parental contribution) Tutorial, which runs through the process of running the analysis and viewing the results with a sample dataset.

PedVerF1sKnownParentsDialog

Using the Pedigree Verification - Lines (parental contribution) dialog you can select the two parental lines that you are comparing sampled lines against.

The following statistics are provided;

  • Data count - the number of markers with non-missing values.
  • % Data - the number of markers with non-missing values as a percent of the total markers for a sample.
  • Het count - the number of markers with heteozygous genotypes (i.e. alleles that differ) for a sample.
  • % Het - the number of markers with heteozygous genotypes as a percent of the total markers for a sample.
  • % Allele Match to P1 - alleles in the sampled line that match an allele in P1, as a percentage of non-missing data in both the sampled line and P1, across all markers for a sample. e.g. Sampled line = A/T C/C and P1 = A/T C/T is a 75% match.
  • % Allele Match to P2 - alleles in the sampled line that match an allele in P2, as a percentage of non-missing data in both the sampled line and P2, across all markers for a sample. e.g. Sampled line = A/A C/T and P2 = A/T C/T is a 100% match.
  • % Allele Match to P1 / P2 - alleles in the sampled line that match an allele in EITHER P1 OR P2, as a percentage of non-missing data in both the sampled line and either parent, across all markers for a sample. e.g. Sampled line = A/T C/C, P1 = T/T A/A and P2 = A/A T/T is a 25% match.

These statistics can be used to filter results;

  • Data Count and % Data - since for many pedigree tests a small number of markers are used, the results can first be filtered by Data Count or % Data to eliminate potentially skewed results.
  • % Het - % het data can be used to assess whether the expected generation has been sampled eg if sampling is on fixed lines, and a sampled line has unexpectedly high hets, this line could be filtered out from being selected.