Additional file 4.

Figure S2 - examples of false read mapping. False read mapping occurs when a sequenced read is incorrectly aligned to its reference sequence (that is, to the incorrect location in the genome). This is most likely to occur in the presence of closely related sequences existing in replicate in the reference sequence and can result from either (a) SNP occurrence or (b) base-call sequencing error in the sample genome, such that the similarity between reads containing a variant (or false) allele and the reference genome decreases at one locus and increases at another (false) locus. Instances of false mapping consequently decrease the chance of a SNP call at a true locus and increase the chance of a false SNP call at the wrong locus.

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Simola and Kim Genome Biology 2011 12:R55   doi:10.1186/gb-2011-12-6-r55