low quality samples were removed (p-value=9 × 10−4) and it varies significantly with the number of samples removed (p-value=2 × 10−4). However, the discordance is very low for both types of plates. The highest median discordance between original and recalled genotypes is 6 × 10−5 for an HPFS plate with five low quality samples. For comparison, the median discordance between 15 HapMap control samples from HPFS (all from plates with no low quality samples) and the external consensus reference is 1.4 × 10−4. Therefore, the effect of recalling after low quality sample removal (measured as discordance between original and recalled genotypes) is less than independent genotyping of the same sample.
