Off-target records

A guide’s _offset is the uncompressed byte position of its line in crisprDetails.tab, resolved through the .gzi index. Each line is two columns:

_mismatchCounts   _crisprOfftargets
0,2,0,0,2         chr2;182255206-;466;117|chr15;101948968-;344;94|chr19;83578+;344;94|chr10;98762096+;172;21

  • _mismatchCounts off-target counts by mismatch bucket [0,1,2,3,4] over the 23-nt guide; the on-target site is not counted. Raw absolute totals, unaffected by chunking.

  • _crisprOfftargets |-separated. Each entry is chrom;pos±;enCas12a_cfd;asCas12a_cfd, the two CFD scores x1000. An off-target is listed only if its CFD clears --ucscgb_cfd_threshold; the list is capped at --ucscgb_list_cap. (So counts can exceed the number listed.)

Coordinate geometry

pos is the 0-based leftmost base of the 27-nt window (PAM + spacer); ± is the strand the guide binds. The browser fetches [pos, pos+27), reverse-complements it on -, then reads the first 4 nt as the PAM and the next 23 as the match, the same layout as the on-target row.

_offset = 0 and uniqueness

_offset = 0 means no off-target line is stored and the browser shows “No off-targets found.” Two distinct cases produce it:

Case

unique_TTTV

Why no list

Non-unique guide

False

an identical protospacer exists elsewhere; off-target analysis is skipped

Unique, perfectly specific

True

specificity 1.0, nothing cleared the CFD floor

So uniqueness is read from the unique_TTTV / unique_TTTN flags, not from _offset. Example non-unique row: TTTATTTTTTTTTTGTAGAGATG, unique_TTTV = False, _offset = 0.