9.7 Nomination Lists

A *_combined_nominations.tsv file is produced for each condition and contains the subset of break sites nominated as putatively induced by the editing mechanism.

Nomination rationales

Frequency-based

Break sites are sorted by absolute break count. The number of members in each recurrency class (sites with the same count) is counted. When the number of members in a recurrency class exceeds 10, that class and all lower-recurrency classes are removed, retaining only break sites with higher recurrency.

Homology-based

Break sites that overlap with expected cut sites of the nuclease mechanism used, within target locations that have sequence similarity to the guide as predicted in silico.

Default mismatch allowances:

• Up to 6 mismatches for break sites with > 2 recurrent breaks.
• Up to 4 mismatches for singleton break sites (1 break).

Exclusion rule

Any break site where, after normalisation based on total sample breaks, the number of breaks in the edited sample is less than 2-fold the number in the same region of the control is excluded.

Note

Where only a single break exists in the control sample, there is a reasonable likelihood it results from a stochastic endogenous process. In this case it is counted as if there were no breaks, and no exclusion occurs.

The nomination list contains the same columns as the Summary TSVs.