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Our support for structural variations is currently fairly limited, but here is what we have so far. Note that these require the "Stack Paired-end" option to be enabled. Click the gear menu in the upper left of the pileup plot, and then click "Stack Paired-end".

Mated Pairs:

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Nearby alignments from the same read pair are connected with a thin gray line.

Distant Mated Pairs:

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If a mated pair is separated by more than 1000bp, then they will not be connected with a line. Instead, they will have a small arrow pointing in the direction of their mate. Clicking on the alignment will show a detailed report in the data console which includes more information on the mate. This 1000bp limit exists mostly for technical reasons (pileups get very large and unwieldy with lots of long mated pairs). However, future versions of GenomeBrowse might allow the 1000bp limit to be user-modified.

Chromosome-Spanning Mated Pairs:

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If an alignment's mate is on another chromosome, then a double-headed arrow is drawn pointing in the direction of the mate.

There's been a lot of interest among our users regarding structural rearrangements, so we welcome any suggestions for improvement you might have!