Figure 4

Features of the filtering steps. (A) Number of hits per gene after Filter II. The majority of genes have less than five hits and there is no significant correlation between number of hits and gene length (Spearman r = 0.05 p-value = 0.124). In the insert: the genes with >5 hits are enriched for private variants. (B) Frequency across 100 replicates of genes that pass Filter I in resampling form a control population. Most genes are retained <5% of times (yellow) therefore are retained if found in the embryos. 1531 genes are instead retained in > 5% of replicates (blue) and therefore discarded if found in the embryos, under the assumption that they can be filtered by chance in healthy controls. (C) Despite comparable read depth between private and non-private variants After Filter III to control for possible artifacts due to scanty coverage, we further filter to remove hits that are private and with read depth outside the range found in non-private ones.