- Sequence class variant effect score (nucleosome-occupancy-adjusted): For variants only. Computed as alt - ref of the raw sequence class scores **adjusted for nucleosome occupancy, i.e. histone normalized**. To better represent predicted variant effects on histone marks, it is necessary to normalize for nucleosome occupancy (for example, a LoF mutation near the TSS can decrease H3K4me3 modification level while increasing nucleosome occupancy, resulting in an overall increase in observed H3K4me3 quantity). Therefore, for variant effect computation, we used the sum of all histone profile predictions as an approximation to nucleosome occupancy and adjusted all histone mark predictions to remove the impact of nucleosome occupancy change (nonhistone mark predictions are unchanged). See manuscript methods for more detail.
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