Extended Data Table 3. Numbers of closely matched sites in the mouse genome with canonical NGG, alternate NAG, and other alternate non-NGG/non-NAG PAMs for gP, gM, and gMH.
Top panel shows the total numbers of these sites identified by Cas-OFFinder and CIRCLE-seq. In the bottom panel, the sites with alternate NAG PAMs identified by Cas-OFFinder are shown by the number of mismatches present in the spacer region for each gRNA.
| Guide RNA | Method for finding off-target sites | Canonical NGG PAM | NAG PAM | Non-canonical Non-NAG | Total sites |
|---|---|---|---|---|---|
| gp | Found in mouse genome by Cas-OFFinder | 120773 | 64538 | 78925 | 264236 |
| gp | Found by CIRCLE-seg | 472 | 2668 | 263 | 3403 |
| gM | Found in mouse genome by Cas-OFFinder | 64274 | 10285 | 37421 | 111980 |
| gM | Found by CIRCLE-seg | 130 | 25 | 28 | 183 |
| gMH | Found in mouse genome by Cas-OFFinder | 68160 | 16404 | 79049 | 163613 |
| aMH | Found by CIRCLE-seg | 448 | 52 | 30 | 530 |
| Sites with NAG PAM | |||
|---|---|---|---|
| Number of mismatches | gP sites | gMH sites | gM sites |
| 1 | 0 | 0 | 0 |
| 2 | 14 | 0 | 0 |
| 3 | 331 | 4 | 0 |
| 4 | 11349 | 26 | 8 |
| 5 | 7817 | 220 | 122 |
| 6 | 12416 | 1858 | 1676 |
| 7 | 32611 | 14296 | 8479 |