Fig. 4

Effect of designs on ASB detection (cont). a–b Aligned reads at two SNPs with design-specific ASB for CTCF. chr3:157828322 exhibits ASB only under PE50v1 but not SE101v2, and vice versa for chrX:143648273. The vertical lines indicate the SNP location on the reference genome. Yellow rectangles are the reads that are properly mapped and cover the SNP under both designs. Blue rectangles are the reads that are mapped only under one design, or are mapped under both designs, but only cover the SNP under one design, but not the other. The two ends of the same fragments are connected via horizontal lines for the PE design. In each figure, the PE and SE reads labeled with the same number are from the same fragment. If one number only appears under one design, this read must have been filtered out or could not have been mapped under the other design. The reads assigned to the maternal allele are above the long horizontal line, and those assigned to the paternal allele are below the horizontal line. AlleleSeq only counts the reads overlapping with the SNP (the vertical line) when testing the allelic imbalance. c–d Numbers of SNPs with ASB and ASOC in favor of the same allele (TP) and different alleles (FP) for CTCF and BHLHE40 datasets, respectively. e Numbers of ASCB and BiASB of CTCF and BHLHE40 datasets