To demonstrate the effectiveness of our signal adjustment procedure in reducing genomic waves, we examined the GCWF values for the 1444 genotyped samples before and after signal adjustment. The distribution of GCWF values after adjustment was much tighter around zero, indicating overall lower magnitude of positive and negative waves (Supplementary Figure 3). Before adjustment, the 5th and 95th percentile of GCWF values were −0.0869 and 0.0770, respectively; after adjustment these measures narrowed to −0.0062 and 0.0157. To give some concrete examples, we plotted the signal intensity patterns after wave adjustment for the two samples used in Figure 2, indicating that genomic waves are reduced for both samples with positive and negative waves (Supplementary Figure 4).
