Supplementary Figure 5: Site stratification by calling and filtering status across cohorts.

On the x-axis we show the number of studies a variant was called in (out of 20) and on the y-axis we show the number of times it was filtered out by the cohort-specific internal QC pipelines. The color shows the percentage of variants in each such cell (red means more than 10% of variants lie in that cell while blue means less than 0.1%). The number to the top right of each cell denotes the Ts/Tv ratio for all sites in that cell. Cells higher in the plot have been filtered out relatively often and usually represent poor variants, as is also seen from the low Ts/Tv ratio. All variants above the red line were filtered out (which excludes all cells which had been filtered independently by more than 4 studies or have Ts/Tv ratio less than 1.7)