FASTQ data files were analyzed using CLC Genomic Workbench software version 7.0.4 (CLC Bio) according to a previously described method (Carette et al., 2011a (link), b (link)). Briefly, after quality trimming and removal of the common LTR sequence, the 50–base pair reads were mapped onto the human genome (hg19). To exclude ambiguous alignments, mismatch reads were not allowed, and all nonspecific matched reads were ignored. To eliminate PCR amplification bias and determine the unique insertion sites, duplicate reads were removed and counted as one read (a unique insertion site). The independent insertion sites were further classified as being in the sense or antisense orientation compared with the gene. The total number of inactivating insertions, which consisted of all the sense or antisense orientations in the exons of the genes and the number of inactivating insertions per individual gene, were counted. The amount of enrichment of a particular gene in the screen was calculated by comparing the selected with the unselected population. For each gene, a p value and a p value corrected for the false-discovery rate (FDR) were calculated by the one-sided Fisher exact test using R software. A bubble plot was created using R software.