Fig. 3

Examples of read pileups. Pileups corresponding to correctly genotyped repeats: A both repeat alleles are short; B one allele is expanded; and C both alleles are expanded. Pileups corresponding to incorrectly genotyped repeats (problem areas are marked with an exclamation sign): D expanded allele is supported by just one read suggesting that its size is overestimated; E 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; F the short allele is supported by just one spanning read suggesting that this allele is not real and that both alleles are expanded