Fig. 6

The effect of sequencing depth on capturing expressed genes, informative genes, DEGs, and variants. Each sequencing depth downsample consisted of ten repetitions (a cluster of 10 points from the downsampling subsets). Lilac lines are non-linear asymptotic regression models; each parameter was fit to a regression model independently. Turquoise dots represent the start of the plateau, defined by a slope of 0.0001, representing a gain of 1 gene/variant when increasing the sequencing depth by 10,000 reads per sample. (A) Number of expressed genes as a function of sequencing depth per sample. (B) Number of informative genes (expressed genes with at least 10 reads mapped to in at least 50% of the samples) as a function of sequencing depth per sample. (C) Number of differentially expressed genes (DEGs) as a function of sequencing depth per sample. (D) Number of SNPs called as a function of sequencing depth per sample. (E) Number of INDELs called as a function of sequencing depth per sample