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The Mismatch graph is specific to short read alignment files, such as BAM. The graph shows only the number of mismatched nucleotides across all reads at a specific genomic location, which can be very helpful in the detection of allelic variation, SNP identification and also error checking. Right click in the label to access the menu; choose Make choose Track Operations > Mismatch Graph. This function requires that the genomic sequence be loaded; if it is not loaded, IGB will load the sequence for you.
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In the Mismatch Pileup, you have the Depth portion represented as a dark gray graph, with the Mismatch overlayed . Further, the mismatches are color coded to in the matching nucleotide colors. The colors show which and how many of each nucleotide(s) are present at each mismatch position. The Mismatch Pileup graph, like the Mismatch graph, is also specific to short read alignment files, such as BAM. Right click in the label to access the menu; choose Make choose Track Operations > Mismatch Pileup Graph. This function requires that the genomic sequence be loaded; if it is not loaded, IGB will load the sequence for you.
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