We analyzed genotype fidelity using the genetic association software PLINK [13], with which we calculated identity-by-state pairwise distances for the 500 k combined array set and for each 250 k array separately.
This algorithm calculates identity values based on the percentage of identical residues among all ungapped positions between sequence pairs.
Using identity by state does not require prior knowledge of allele frequencies or pedigree information, and is more computationally tractable and is less affected by population stratification than calculating identity by descent probabilities.
tarsalis, we used their 5' promoter sequences to calculate identity by BLAST analysis (Table 1).
Duplicates were identified by calculating identity by state (IBS) values using PLINK and one sample from each duplicate pair was removed.
An alternative variant of GS uses genomic data to calculate identity-by-descent (IBD) relationships, and has led to promising results on real data [ 4].
A fast, partly recursive deterministic method for calculating Identity-by-Descent (IBD) probabilities was developed with the objective of using IBD in Quantitative Trait Locus (QTL) mapping.
†Full-length aa capsid sequence and partial (245-aa residues) RdRp at the at the C-terminus were used to calculate identities.
Further, the marker density on the consensus map is suitable for whole genome pedigree analysis, and calculating identity-by-descent through generations.
