Alastair
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Alastair
I came across a similar solution in [this](https://groups.google.com/forum/#!searchin/sga-users/duplicate$20read$20id%7Csort:relevance/sga-users/lTsVuNjUa1M/58QNWFrn2kAJ) google groups thread. It was the secondary/supplementary alignments causing the problem.