With CRISPAltRations™, the software behind the rhAmpSeq CRISPR Analysis Tool, we analyzed the editing in three experimental replicates of 20 paired, treated, and control Cas9-edited loci. The treated samples had known indel editing levels (0.05, 0.10, 0.20, 0.50, 1.0, 2.0, and 3.4%), while the control samples had noise signals ranging from 0–0.4%.
Using the Fisher’s Exact Test (with a threshold of p<0.5), we show that 95% sensitivity and specificity were obtained for detecting indels down to 0.5%. This analysis assumed that there were:
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