Figure 3.

NA24143 read alignments to GRCh38. (A) Schematic showing the alignment of a subset of reads unmapped on GRCh37 to GRCh38. Reads align to GRCh38 at the position of components that were added to span a GRCh37 assembly gap (orange). (B) Graph showing counts of reads uniquely mapped to unchanged regions of GRCh37 that uniquely map to nonequivalent locations in GRCh38. (C) Chart describing the GRCh38 distribution of reads from B, categorized by sequence location (same or different chromosome/scaffold) and sequence type (centromeric versus noncentromeric): (OFFCEN) movement to centromeric sequence on a different chromosome; (OFF) movement to noncentromeric sequence on a different chromosome; (ONCEN) movement to centromeric sequence on the same chromosome; (ON) movement to noncentromeric sequence on the same chromosome; (TOSCAF) movement to a noncentromeric unlocalized or unplaced scaffold; (UNCEN) movement to an unplaced scaffold containing centromere-associated sequence.