Fig. 2

Simulations identity the optimal MapQ setting for accurate VSG-ES mapping. a. In silico reads generated from the ART program for a subset of VSG-ESs were aligned to the genome; only the VSG-ESs are shown on a linear scale. Varying the MapQ value (either no filter – 0, or incrementally > 1, > 10, > 40) to filter non-uniquely mapping reads improves the signal to noise ratio. mVSG, metacyclic VSGs. Beneath each panel is a schematic map for each locus. Boxes, coding sequences; arrowsheads, Pol-I promoters. Red reads BES1, Green reads BES5, Orange reads BES14, Blue reads BES15. b Analysis of all VSG-ESs using the ART method. Plots show reads derived from each contig, and aligned to the genome; only genes in VSG-ESs are shown. MapQ > 12 is the lowest value at which no noise is detected. Metacyclic VSGs are on the left