Statistical detection of SNEPs. a Statistical tests applied to 39,961 matched well-positioned nucleosomes and UNRs (dots). The x-axis is the significance of a differential MNase-seq signal between the strains, which reflects different levels of nucleosome occupancy. The y-axis is the statistical significance of SNEP detection for H3K4me3, which corresponds to the null hypothesis of no interaction term in a generalized linear model implemented in DESeq (see “Methods” and ). Orange (black) dots correspond to nucleosomes for which the test was (was not) significant at the genome-wide level, respectively (FDR = 0.0001). Labels B, C and E indicate nucleosomes presented in the corresponding panels. b Count data for a nucleosome where an SNEP is detected. A differential H3K4me3 ChIP-seq value was observed, with no significant change in MNase-seq counts between the strains. c Count data for a nucleosome where an SNEP is detected, with differential MNase-seq values. Despite a lower abundance of the nucleosome in RM, the ChIP signal for this strain is comparable or even higher than that for BY. The trimethylation level therefore differs between strains after accounting for nucleosome abundance. d Coverage profile of the locus containing the SNEP presented in b. The figure was produced by prolonging the reads to a final length of 150 nucleotides and normalizing by the sample size factor (see “Methods”). Boxes below the profiles indicate six well-positioned nucleosomes (top BY, bottom RM), colored in violet for the one presented in b. x-axis: genomic coordinates (in nucleotides) on the BY genome. e Count data for a nucleosome where the differential ChIP signal is fully explained by differential occupancy. Variation at this nucleosome is therefore not an SNEP.