9a56fd00c6ee9cba19d36d6fe4ae0222523cdcd8 lrnassar Thu Jul 23 14:10:55 2026 -0700 Update popEVE color-legend anchors to the dense-rebuild values. refs #37791 The description page's color table still showed the sparse build's saturation anchors (-5.74 / -2.29); the dense rebuild recomputed them to -6.04 / -2.41. Caught in visual QA. diff --git src/hg/makeDb/trackDb/human/popEve.html src/hg/makeDb/trackDb/human/popEve.html index 9bd05a3f109..7b648d708fd 100644 --- src/hg/makeDb/trackDb/human/popEve.html +++ src/hg/makeDb/trackDb/human/popEve.html @@ -25,43 +25,43 @@ single-nucleotide change (roughly 6 of 19 per position) and therefore appear sparser. </p> <p> Unlike per-gene scores, popEVE is calibrated across the whole proteome, so cells are colored on a single global gradient keyed to the raw popEVE score (lower, more negative scores are more deleterious). The color is interpolated between the five anchors below: the published severe and moderate thresholds are fixed anchors, and the extremes saturate at the 0.5th and 99.5th percentiles of the proteome-wide score distribution. </p> <table style="border-collapse: collapse; border: 1px solid #ccc;"> <tr><th style="border:1px solid #ccc;padding:6px 12px;background:#f2f2f2;">Color</th> <th style="border:1px solid #ccc;padding:6px 12px;background:#f2f2f2;">popEVE score</th> <th style="border:1px solid #ccc;padding:6px 12px;background:#f2f2f2;">Interpretation</th></tr> <tr><td style="border:1px solid #ccc;background:#b2182b;width:50px;"> </td> - <td style="border:1px solid #ccc;padding:4px 10px;">≤ −5.74</td> + <td style="border:1px solid #ccc;padding:4px 10px;">≤ −6.04</td> <td style="border:1px solid #ccc;padding:4px 10px;">Most deleterious (color saturates here)</td></tr> <tr><td style="border:1px solid #ccc;background:#d6604d;width:50px;"> </td> <td style="border:1px solid #ccc;padding:4px 10px;">≈ −5.056</td> <td style="border:1px solid #ccc;padding:4px 10px;">Severe threshold: high-confidence deleterious (99.99% likelihood of falling in the more deleterious distribution)</td></tr> <tr><td style="border:1px solid #ccc;background:#f4a582;width:50px;"> </td> <td style="border:1px solid #ccc;padding:4px 10px;">≈ −4.617</td> <td style="border:1px solid #ccc;padding:4px 10px;">Moderate threshold</td></tr> <tr><td style="border:1px solid #ccc;background:#f7f7f7;width:50px;"> </td> <td style="border:1px solid #ccc;padding:4px 10px;">≈ −3.5</td> <td style="border:1px solid #ccc;padding:4px 10px;">Near the proteome-wide median</td></tr> <tr><td style="border:1px solid #ccc;background:#2166ac;width:50px;"> </td> - <td style="border:1px solid #ccc;padding:4px 10px;">≥ −2.29</td> + <td style="border:1px solid #ccc;padding:4px 10px;">≥ −2.41</td> <td style="border:1px solid #ccc;padding:4px 10px;">Most tolerated (color saturates here)</td></tr> </table> <p> <b>Note:</b> popEVE ranks deleteriousness to organismal fitness, weighted toward severe, often early-onset phenotypes, rather than classic clinical pathogenicity. Some well-known disease genes whose variants act mainly through loss of function or cause adult-onset conditions (for example BRCA1) may therefore show few or no cells in the severe range. </p> <p> Hovering over a cell shows a summary of that substitution and the scores behind it, for example: </p> <p style="border:1px solid #ccc; padding:6px 12px; display:inline-block;"> G1042→A<br>