4ea3d549b2d0aa682aa22e6b31e844fee78d2cfc gperez2 Tue Oct 21 13:55:33 2025 -0700 Code review edit, refs #36551 diff --git src/hg/makeDb/trackDb/human/spliceImpactSuper.html src/hg/makeDb/trackDb/human/spliceImpactSuper.html index c2f3d795d29..0b0748f94bc 100644 --- src/hg/makeDb/trackDb/human/spliceImpactSuper.html +++ src/hg/makeDb/trackDb/human/spliceImpactSuper.html @@ -101,31 +101,31 @@ </ul> </p> Mouseover on items shows the variant, gene name, type of change (donor gain/loss, acceptor gain/loss), location of affected cryptic splice, and spliceAI score. Clicking on any item brings up a table with this information. </p> <p> The scores range from 0 to 1 and can be interpreted as the probability of the variant being splice-altering. In the paper, a detailed characterization is provided for 0.2 (high recall), 0.5 (recommended), and 0.8 (high precision) cutoffs.</p> <h3>SpliceAI Wildtype</h3> <p> These tracks are in bigWig format. The signal height represents the SpliceAI probability score. This track may be configured in a variety of ways to highlight different aspects of the displayed -information. Click the "Graph configuration help" link for an explanation of configuration +information. Click the "Graph configuration help" link for an explanation of configuration options.</p> <h3>SpliceVarDB</h3> <p>According to the strength of their supporting evidence, variants were classified as "splice-altering" (~25%), "not splice-altering" (~25%), and "low-frequency splice-altering" (~50%), which correspond to weak or indeterminate evidence of spliceogenicity. 55% of the splice-altering variants in SpliceVarDB are outside the canonical splice sites (5.6% are deep intronic). The data is shown as lollipop plots that can be clicked, the details page then shows a link to SpliceVarDB with full details. </p> <p>The classification thresholds primarily follow those established by the original study. However, most studies only defined criteria for splice-altering variants and did not define criteria for variants that resulted in normal splicing. The authors implemented stringent