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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