Fig. 3. Cryptic donor activation is influenced by relative strength.

a–e Assessment of algorithmic scores of splice-site strength for AM-variants. NNS NNSplice, MES MaxEntScan, SAI SpliceAI, DF Donor Frequency. Categories such as weaker by >50% are assigned based on how the score has been impacted by the variant (i.e., more than halved). a Proportion of variants with annotated-donor Δ scores (Annotated_VAR/Annotated_REF) in each of the categories shown in the figure key. Most AM-variants weaken the annotated-donor by >50% (dark blue). See supplementary Fig. 2 for full plots. b Example variant showing the Donor Frequency (DF) scores (see supplementary Fig. 1) for the cryptic-donor (DF = 0.77), versus the reference (REF = 0.34) and variant (VAR = 0.05) annotated-donor, as well as surrounding decoys not used. Vertical dotted lines indicate position of annotated- and cryptic-donors. Donors coloured according to the figure key. c Percent of cryptic-donors stronger than the annotated_VAR. d Percent of cryptic-donors that are not the strongest donor splice-site within 250 nt. e Percent of AM-variant activated cryptic-donors that are not recognised by each algorithm (i.e., score of 0). f–h Strength measures for CM-variants. f Proportion of variants with cryptic-donor Δ scores (Cryptic_VAR/Cryptic_REF) in each of the categories shown in legend. Most CM-variants strengthen the cryptic-donor by >10% (dark yellow). See supplementary Fig. 2 for full plots. g As in b. h As in c. i, j Strength measures for AM/CM-variants. i As in a. j As in f. k As in b. l As in c. m, n Pearson correlation of strength measures. m Δ Annotated (VAR/REF) for AM & AM/CM-variants (all variants which affect the annotated-donor). n Cryptic difference (VAR – REF) for CM & AM/CM-variants (all variants which affect the cryptic-donor).