data/sae/annotation-changes.json

{"what":"Every verified annotation change we could locate in the corpus, scored by whether the report's splice feature reads higher at the position the newer release places the site or at the position it superseded.","method":"Candidate sites come from diffing each species' two annotation builds per transcript. A site is kept only if the window's own annotation carries a site of the expected class at the expected base, the new position carries none, the new boundary is absent from every isoform of the old build (so a re-pick is not counted as a move), and both positions lie at least 200 bp from a window edge. Each position is scored as the feature's maximum within 2 bases of it. A site counts as decided when one position exceeds the other by more than 1.5x.","feature_used":{"moved_donor":4131,"moved_acceptor":586},"totals":{"sites":98,"windows":82,"decided_sites":70,"favour_revised_sites":61,"favour_superseded_sites":9,"no_separation_sites":28,"decided_windows":59,"favour_revised_windows":50,"favour_superseded_windows":9,"exactly_zero_at_superseded":41,"binomial_p_per_site":1.28e-10,"binomial_p_per_window":5.26e-08},"by_species":{"slycopersicum":{"newer_release":"ITAG3.2","same_assembly":true,"favour_revised_windows":29,"favour_superseded_windows":2},"osativa":{"newer_release":"RAP-DB 2026-02-05","same_assembly":true,"favour_revised_windows":16,"favour_superseded_windows":2},"athaliana":{"newer_release":"TAIR12_1Feb26","same_assembly":false,"favour_revised_windows":5,"favour_superseded_windows":5,"note":"TAIR12 is a new assembly, so each position had to be tied to the TAIR10 frame by anchoring on identical flanking sequence, and its revisions are often whole-model rather than a single moved site"}},"limits":["Sites were selected by annotation change alone, with no reference to how the feature behaves, so the comparison is not circular - but neither is it a controlled benchmark.","29% of sites show no separation and are excluded from the ratio.","One dictionary, one layer, three annotation updates, two of them on the same assembly as the windows.","A feature reading higher at a position is not evidence that the position is correct; it is evidence that the model's representation prefers it."],"sites":[{"uid":"B00005282","event":"moved_acceptor","old":2737,"new":2759,"gene":"ELP1","species":"athaliana","build_new":"TAIR12 1Feb26","shift":22,"old_val":1.319,"new_val":11.445,"verdict":"new"},{"uid":"B00000073","event":"moved_acceptor","old":2632,"new":2560,"gene":"AT4G21640","species":"athaliana","build_new":"TAIR12 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