Fig. 2
Gene-proximal haplotype predictions in low coverage single-cell sequencing data. Pictured is a screen capture of the haplotype data in Fig. 1 zoomed in to the BRCA2 gene locus (±2 Mb) on chromosome 13. Maternal and paternal haplotypes are each depicted in “prediction” and “marginal” plots for each child, with alternating clear and gray background shading distinguishing the plots of one child from that of neighboring children above and below. The “prediction” plot indicates the hidden Markov model (HMM) haplotype prediction in each child relative to child 1. Dark red and dark blue shaded segments indicate child 1 matching maternal and paternal haplotypes (containing V1 and V2 BRCA2 variants), respectively. Lighter shading indicates wild type haplotypes that are not present in child 1. The “marginal” plot indicates the degree of confidence with which the HMM is reporting a certain haplotype prediction. A marginal value of 1 means a high confidence prediction of a child 1 matching haplotype. A marginal value of 0 means high confidence prediction of a child 1 mismatching haplotype. We call sites with marginal values between 0.01 and 0.99 low confidence. These sites often appear near meiotic recombination sites. The marginal plots also depict the SNP sites (red/blue dots) on the arrays that were used to phase the parental haplotypes and were also successfully sequenced. Note that children 2, 3, and 4 exhibit an identical paternal recombination event ~1 Mb downstream of the BRCA2 gene (demarcated by purple arrow and dashed vertical line). This strongly suggests that child 1 is recombinant at this site. Array data from children 2, 3, and 4 confirmed these high resolution findings (see also the inset of Fig. 1).
