Fig. 5: Analysis of the Sanger dataset from Project Score.

a Number and percentage of gRNAs in the Sanger library that have 0, 1, or more than 1 perfect targets (H0) in the human genome (hg38 assembly) or that have 0, 1, or more than 1 targets with a single hamming mismatch (H1). b Left, boxplots of z-scores of gRNA log₂FC for all Project Score screens across multiple H0 bins (i.e., increasing numbers of perfect targets). Right, boxplots of z-scores for gRNA log₂FC for all Project Score screens across multiple H1 bins (i.e., increasing numbers of targets with a single hamming mismatch) for gRNAs that have a single perfect targeting the genome (H0 = 1). Dashed lines indicate median depletion of specific gRNAs (H0 = 1, H1 = 0) targeting known non-essential (top) or essential (bottom) genes. One-sided Pearson correlation values between mean depletion and number of off-targets, as well as the significance of the correlation are shown below. n = 324. c As in b but plotting z-scores of gRNA log₂FC against GuideScan’s specificity bins. Specificity values correspond to highest value of each bin. Note how for 19-mer gRNAs there is no correlation between GuideScan’s score and depletion. One-sided Pearson correlation values between mean depletion and number of off-targets, as well as the significance of the correlation are shown below. n = 324. d Left, change in recall (5% FDR) for each Project Score screen after being corrected with CSC. On the right we show examples of precision-recall curves for screens showing increased recall (MCAS, second most improved) or decreased recall (OAW42, second most decreased) after correction. Dashed line highlights 0.95 precision value (which corresponds to a false discovery rate of 5%). Note how the improved recall in the MCAS screen is accompanied by an increase in the area under the curve (AUC). In contrast, the decreased recall in the OAW42 screen is accompanied by no change in the AUC. All boxplots show minimum, maximum, median, first, and third quartiles.