Examples of read pileups

Overview

Pileups corresponding to correctly genotyped repeats are characterized by a relatively even read coverage of both alleles (Figure 1, panels 1-3). At the typical whole-genome sequencing depths (30-60x), each position of a haplotype sequence is expected to be covered by many reads (15-30), although the coverage may dip in certain regions due to technical factors like GC bias. For repeats much shorter than the read length this implies the presence of multiple spanning reads (Figure 1, both alleles on panel 1 and short allele on panel 2). The repeats much larger than the read length are expected to contain multiple in-repeat reads (Figure 1, long allele on panel 1 and both alleles on panel 2). Here are real examples corresponding to panels 1, 2, and 3.

The table below describes the contents of panels 4-6.

Panel	Issue	Explanation	Examples
4	False expansion call	Sequencing depth inside the repeat is very low compared to surrounding reigon	4
5	False expansion call	Multiple indels in in-repeat reads suggest incorrect alignments
6	Missed double expansion	Short allele supported by very few reads; excess of flanking reads on long allele	6

Figure 1: Examples of read pileups. Pileups corresponding to correctly genotyped repeats: (1) both repeat alleles are short; (2) one allele is expanded; (3) both alleles are expanded. Pileups corresponding to incorrectly genotyped repeats: (4) expanded allele is supported by just one read suggesting that its size is overestimated; (5) expanded allele is supported by poorly aligning reads (each containing multiple indels) suggesting that the reads are incorrectly mapped and that size of the repeat is overestimated; (6) the short allele is supported by just one spanning read suggesting that this allele is not real and that both alleles are expanded.