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IGB displays insertions, deletions and mismatches as follows:

• Insertions - residues Residues flanking insertion site appear are shown in white black with a black backgroundwhite background by default (purple on white here); triangular shapes between them point to the location of the inserted base(s) present in the aligned sequence but not in the reference. 

  • Select an insertion and the Selection Info tab to display the sequence of inserted bases

• Deletions - residues Residues deleted in the aligned sequenced relative to the reference appear as horizontal lines that are of the same color and connect flanking residues.
• Mismatches - residues Residues in the aligned sequence that do not match the corresponding base in the reference appear as highlighted bases. To highlight mismatches, click Load Sequence

Use the zoom stripe (shown in gray) as a guide to compare mismatches, deletions, and insertions between different read alignments and the reference.
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Insertions, Deletions, and Mismatches in IGB

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To re-create this scene in IGB:

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