Concordance between genotype calls from replicate samples by method. Boxplots of the replicate concordance for 10 samples from the MS-GWAS which were analyzed using DNA derived from both saliva and blood. High concordance between replicates calls (> 98.5% agreement) is the norm. The 8th sample is an exception, due to poor quality of one of the replicates (Figure 5). For this pair of samples, the concordance values are 16.6%, 15.6% and 40.8% for GenCall, Illuminus and CRLMM respectively (values not plotted as they are off the scale). GenoSNP did not produce calls for one of the samples (Figure 5B), so concordance could not be calculated for this replicate pair.