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. 2015 Aug 25;5:13443. doi: 10.1038/srep13443

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Copyright © 2015, Macmillan Publishers Limited

This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

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Read mapping (highlighted with red line) is identified as Scenario 2 and Scenario 3 by CADBURE and visualized in Tablet²⁶. Tablet shows reads mapped against the mouse reference genome. The same read (name shown in popup) is mapped differently to the genome by GSNAP and TopHat2 aligners. (a) GSNAP mapped the same 40 base read perfectly with no mismatches to Chromosome 2 from 152,318,712 to 152,318,751. (b) TopHat2 mapped the same read with a spliced alignment to Chromosome 2 with 1 base at 152,318,455, leaving a long gap for an intron (257 bp; from 152,318,456 to 152,318,712; displayed with ‘N’) and then (c) TopHat2 mapped 39 bases continuously from 152,318,713 to 152,318,751.