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. 2011 Nov 14;12:557. doi: 10.1186/1471-2164-12-557

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Copyright ©2011 Zhan et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Heterozygous SNPs called on chromosome 9. Chromosome 9 contains the largest identical by descent (IBD) region detected in the genome of the sequenced animal. The lower minimum allele percentage of heterozygous calls in the IBD region by both the Mosaik+GigaBayes and CLC pipelines, indicates that even a few false alignments can introduce higher false positive rates (FPRs) compared to the FPRs using the BWA and SMALT pipelines. bwa denotes BWA+SAMtools, clc denotes CLC Genomics Workbench, giga denotes Mosaik+GigaBayes, smalt denotes SMALT+SAMtools.