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The picture below shows a fully expanded BAM file, showing the difficulty of seeing any details. The second picture shows just the depth graph (*BAM *track is 'hidden') with the tool tip showing the number of reads aligned onto that specific genomic location.

Mismatch Graph

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 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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