wavy patterns in different samples, we refer to waves that have positive correlation with GC as positive waves (Figure 2A) and those with negative correlation as negative waves (Figure 2E). Table 1.Correlation of wave with genomic featuresGenomic featuresSample 1Sample 210 kb window100 kb window1 Mb window10 kb window100 kb window1 Mb windowGC percentage0.700.850.96−0.47−0.69−0.89Segmental duplication0.030.060.17−0.02−0.05−0.17Gene content0.070.130.34−0.03−0.09−0.31Exon content0.120.360.62−0.09−0.29−0.62Simple repeats0.180.210.19−0.12−0.23−0.27Conserved region0.040.160.26−0.01−0.12−0.24The list of correlation coefficients between median LRR values and several genomic features within nonoverlapping windows. Three different window sizes, including 10, 100 kb and 1 Mb, are examined. Two representative samples with opposite phases are included. The local GC content appears to be best correlated with median signal intensity in sliding windows of varying sizes.
