Mismatch summary. An example of a mismatch summary plot, with associatedvariant calls. The top track shows a barchart of reference counts in gray andmismatched counts colored by the nucleotide. The middle track shows SNPs asletters, color coded also by nucleotide. There is one mismatch, 'T', that isdifferent for all of the reads from the 'A' in the reference genome (bottomletter plot).