Supplementary Figure 1: The GIREMI method.

(a) Distribution of mutual information for editing sites and SNPs relative to any other types of mismatches. Upper: all editing sites or SNPs; lower: separated according to the type of regions harboring editing sites or SNPs (rep.: repetitive). The table (right) shows the number of sites involved in each category for the lower panel. (see details in Supplementary Note 1) (b) Flowchart of GIREMI, see Online Methods for details. (c) Distribution of the absolute difference between allelic ratios of the mismatches corresponding to RNA editing sites or known SNPs and the estimated allelic ratio of the gene by maximum likelihood. The data were derived using predicted editing sites by the mutual information test in GM12878 data. (d) Pictograms of the -1 and +1 nucleotides flanking an RNA editing site compared to those of a SNP, derived using the predicted editing sites by the mutual information test in the GM12878 data. (e) Types of sites that are harbored in the same pair of reads as known recoding sites identified by the mutual information step alone. These sites are separated into different types (SNPs, RNA editing sites or un-determined SNVs (see Supplementary Note 1)). All the RNA editing sites shown here were located in non-repetitive regions.