f57e872b724de4bb82b14f07db837aeed4f5174a gperez2 Wed Jun 17 03:55:08 2026 -0700 Fix commas and update wording in varFreqs description pages. refs #37733 diff --git src/hg/makeDb/trackDb/human/varFreqsBackground.html src/hg/makeDb/trackDb/human/varFreqsBackground.html index 4a7f3b9f2b2..2b7d13f8ecb 100644 --- src/hg/makeDb/trackDb/human/varFreqsBackground.html +++ src/hg/makeDb/trackDb/human/varFreqsBackground.html @@ -35,31 +35,31 @@ <td>Synonymous</td> <td>synonymous, stop_retained</td></tr> <tr><th style="background-color:#808080;width:2em"> </th> <td>Non-coding / intergenic</td> <td>intron, non_coding, intergenic, UTR</td></tr> </table> <p> The score (used for shading) is the pooled background allele frequency times 1000. </p> <h3>Pooled allele frequency</h3> <p> <b>Background AF</b> is the pooled rate across contributing population cohorts and unaffected/control arms: <code>backgroundAF = sum(AC) / sum(AN)</code>, where <b>backgroundAC</b> sums the allele counts and <b>backgroundAN</b> sums the allele -numbers across each cohort/arm that ships both AC and AF (the per-arm AN is derived as +numbers across each cohort/arm that provides both AC and AF (the per-arm AN is derived as <code>round(AC / AF)</code>). Two cohorts that publish only AF (ABraOM, ALFA) contribute via a configured <code>default_an</code> in the build configuration. Cohorts that publish only AC with no <code>default_an</code> set (currently MGRB and the GREGoR unaffected and unknown arms), and cohorts that contribute only through per-population AC/AF (currently AllOfUs), are listed in <b>backgroundSources</b> but do not contribute to the pool numerator or denominator; their data remain visible in the per-database and per-population AC/AF columns. The pooled rate is preferred over a max-across-cohorts statistic so a small cohort with a high local AF (for example AllOfUs Oceanian) cannot dominate the displayed frequency. </p> <h2>Filters</h2> <ul> <li><b>Variant Type</b> and <b>Consequence</b>: restrict to SNV/insertion/deletion/MNV and to predicted consequence classes (the Consequence filter uses OR logic over the