Figure 4

Base call content and quality bias. This figure demonstrates CHANCE output for base call content and quality bias module. (a,b) Plot of nucleotide frequency as a function of base position. (c,d) Plot of the frequency of uncallable bases as a function of base position. (e,f) Heat maps of Phred quality scores, where the x-axis corresponds to base position and the y-axis to Phred quality score. The color of a given (x,y) pair gives 1 minus the cumulative density of reads with a quality score of y or less. That is, it gives the fraction of reads with a quality score of y or more; so, the redder, the better. (a,c,e) H3K27ac IP in mouse whole limb from the Ahituv lab at UCSF. These samples show a marked drop in quality, a rise in uncallable bases, and an abrupt change in nucleotide frequencies for positions 22 to 24, indicating potential problems with the sequencing. For comparison, (b,d,f) show results for H3K4me3 IP from mouse NSCs from the Lim lab at UCSF, which exhibit relatively low bias.