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If you hover the Select tool (arrow cursor) over an individual bar of the graph, you will get a tool tip showing the total number of reads, and then the number of reads broken down by nucleotide. In the picture below, you can see that the total number of reads at the specified position is 260 (blue arrow). Of those reads, 257 at at 'T', which you can see is the matching nucleotide (purple arrows). 3 of those reads contain a 'G' instead; since G is a MISmatchmismatch, the graph shows a bar with height of 3 (red arrows).

Mismatch Pileup Graph

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