Table 2.
Summaries of sgRNA sequence alignments across four CRISPR knockout libraries
| 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%) |
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
NTC non-targeting control, SM single-mismatch