To investigate the relationships between variations in several local genomic features and variation in local signal intensities, we randomly chose two samples with opposite direction of genomic wave (Figure 2A and E, Table 1). We generated nonoverlapping windows across the entire genome, and calculated the median signal intensity in each of these windows. We then calculated the correlation coefficient of median signal intensities for each window with multiple genomic features in the same window, including the fraction of GC content, the fraction of bases with segmental duplication (14), the fraction of bases within RefSeq transcripts (15), the fraction of bases within exons of RefSeq transcripts (15), the fraction of bases within simple repeat region (16) and the fraction of bases within most conserved genomic regions in 28-way vertebrate multiple alignments (17). The analysis was repeated with a window size of 10, 100 kb and 1 Mb, respectively. Among all genomic features we examined, we found that local GC content is the most correlated factor with median signal intensities. In addition, for both samples, the magnitude of correlation between signal intensity
