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. 2012 Jan 16;14(2):203–212. doi: 10.1093/bib/bbr073

Figure 2:

Figure 2:

The filter options for sequence reads. A mapping quality cut-off (MAPQ) can be applied and reads can be explicitly filtered in or out based on their flag. The filter shown will hide all unmapped reads and only show the reads that are defined as a proper pair.