Fig. 1. Workflow of study and schematic demonstration of annotation groups.

The workflow depicts the processes involved in creation of the annotation with set parameters for each of the three groups of annotations generated and the processes involved in hypothesis-testing. CNC scores: constrained, non-conserved scores; CNCRs: constrained, non-conserved regions: CNCRs are defined as genomic regions that were first among the 12.5% most constrained, then with a CNC score of ≥1 (i.e. a twofold higher ranking in constraint than conservation). Constrained regions are defined as the regions within the 12.5% most constrained of the genome irrespective of conservation score. Non-conserved regions are defined as relatively non-conserved genomic regions with a conservation rank determined by the rank of the first quartile phastCons20 score at a CNC score of 1 (rank ≤ 25,623,592) (irrespective of constraint score). CDTS is the context-dependent tolerance score. Minus CDTS score is used as a lower score of CDTS corresponds to a more constrained region.