Fig. 2.

SNP-ChIP is robust to variation in both sequencing depth and amount of spike-in cells. a Number of aligned reads in SNP-ChIP as a function of total size of raw read sample. Systematic raw read subsamples of size 1 to 10 million were obtained for each sample and mapped to the hybrid SK1-S288c genome. b Distribution of spike-in normalization factors computed using all 10,000 possible combinations of read subsamples in (a). The inset is a zoom-in on a narrow window of the x axis where all values are located. c Percentage of reads aligning to the spike-in genome in the input sample versus the immunoprecipitated sample (ChIP) for wild type and red1-pG162A strains. Note: In contrast to red1_ycs4S, which contains an introgressed region with dozens of SNP surrounding the RED1 locus, the red1-pG162A mutant only carries the causative promoter mutation. d Resulting wild type-normalized spike-in normalization factor (equivalent to Red1 amount) in the red1-pG162A strain after performing SNP-ChIP with percentages of added spike-in cells ranging from 5 to 30%. The results suggest that spike-in material proportions of 15% and higher are appropriate for SNP-ChIP