Table 3 MethylToSNP predictions in the southern African data set
From: MethylToSNP: identifying SNPs in Illumina DNA methylation array data
Description | Probes tested (#) | # SNP predictions in dataset | Overlap with dbSNP 142 (#) | Overlap with dbSNP 146 (#) | Potential novel SNPs (#) | Sites lost by filtering all dbSNP 142 positions (#)b | Sites lost by filtering all dbSNP 146 positions (#)b | Median reliability scores of predicted SNPs | # novel SNPs with reliability scores ≥ 0.5 |
|---|---|---|---|---|---|---|---|---|---|
All probe sites | 473,767 | 2296 | 1249 | 1402 | 894 | 101,558 | 144,569 | 0.979 | 827 |
Differential methylationc | 12,613 | 23 | 19 | 19 | 4 | 2143 | 3081 | 0.395 | 2 |
Top 5% differential methylationa,c | 400 | 1 | 0 | 0 | 1 | 0 | 48 | 0.779 | 1 |