Measures of sample quality for the MS-GWAS by genotyping method. Samples from different batches (from 1 to 6) are plotted in different colors. For GenCall and Illuminus, the per sample no call rate (%) is used to measure sample quality. The GenoSNP per sample quality measure is the average posterior probability of all calls within a sample, with higher values (closer to 1) indicative of higher quality. In CRLMM a signal-to-noise score which measures separation between the 3 major clusters in each sample (Figure 5A) is calculated. For this measure, higher scores represent higher quality. Despite the differences in scale, all methods appear to assign the most extreme quality scores (highest values in the case of GenCall and Illuminus, and lowest for GenoSNP and CRLMM) to the same samples.