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. 2010 Jan 13;5(1):e8219. doi: 10.1371/journal.pone.0008219

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This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.

This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration, which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.

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The 470K SNP set is enriched with SNPs identified from the ends of reads. Panel A demonstrates that this read position bias can be eliminated by applying a Q score threshold. Panel B demonstrates that the genotypic contingency test also improves SNP calling.