Concordance of shared and private SNPs in P1 and P2 datasets
P1 and P2 SNPs that are shared with the corresponding P1+P2 dataset have
much higher levels of concordance than private SNPs in the P1 and P2
datasets (Figure 5). In addition, these shared SNPs show the expected
increase in concordance with increasing sequence depth, similar to P1+P2
SNPs, whereas private SNPs show the unexpected increase in concordance
at low sequencing depth previously noted in Figure 3. This phenomenon
could be due to enrichment with homeo-SNPs, which are truly heterozygous
in all individuals but may appear as homozygous when sequencing depth is
limited. One limitation of our reduced representation library
preparation protocol is that alleles underlying a locus may have
different fragment sizes, leading to amplification bias (Davey et al.,
2011). In samples with very low sequencing depth, under-represented
reads from the larger fragment may be entirely absent, leading to higher
concordance at low depth in the private SNPs.