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Table 2 Summaries of sgRNA sequence alignments across four CRISPR knockout libraries

From: Multiple-gene targeting and mismatch tolerance can confound analysis of genome-wide pooled CRISPR screens

  Avana GeCKOv2 Brunello TKOv3
Reference [7] [25] [7] [26]
Number of unique guides 73,782 119,461 77,441 71,090
Number of unique NTC guides 995 1000 1000 0
Number of unique guides targeting miRNAs 0 6835 0 0
Number of unique guides targeting coding genes 72,787 111,626 76,441 70,948
Number of targeted coding genes 18,547 19,050 19,114 18,053
Average number of guides per gene 4 6 4 4
Number of guides with no on-targets 86 157 1 16
Number (%) of guides with 1 on-target 68,742 (94.4%) 108,368 (97.1%) 73,410 (96.0%) 68,872 (97.1%)
Number (%) of guides with 2 on-targets 2628 (3.6%) 1665 (1.5%) 1681 (2.2%) 1775 (2.5%)
Number (%) of guides with > 2 on-targets 1331(1.8%) 1436 (1.3%) 1349 (1.8%) 285 (0.4%)
Number (%) of guides with no SM off-targets 65,070 (89.4%) 104,965 (94.0%) 69,407 (90.8%) 67,584 (95.3%)
Number (%) of guides with 1 SM off-target 5079 (7.0%) 4168 (3.7%) 4352 (5.7%) 2984 (4.2%)
Number (%) of guides with 2 SM off-targets 1126 (71.5%) 1014 (70.9%) 1098 (71.4%) 281 (70.4%)
Number (%) of clean guides (up to 1 mm) 66,757 (91.7%) 106,538 (95.4%) 71,614 (93.7%) 67,886 (95.7%)
  1. For the Avana library, we report summary statistics for the Avana library version used in the Achilles project screens (4 sgRNAs per gene and processing as described in the “Material and methods” section). For the GeCKOv2 library alignment summaries, we excluded 6835 guides targeting miRNAs. A clean guide refers to a guide with only one-target alignment and no single-mismatch alignments
  2. NTC non-targeting control, SM single-mismatch