1259dcfba3a263d92d2602665fd866dc44b47996 lrnassar Sun Jun 21 11:17:10 2026 -0700 Clarify varFreqs description page wording per code review feedback. refs #37733 Reword the default_an sentence in the Pooled allele frequency sections of varFreqsAffected.html and varFreqsBackground.html to explain that cohorts publishing only AF are pooled via an assigned default_an, with per-arm AC derived as round(AF * default_an). Change "tokens" to "terms" in the Consequence filter section of varFreqs.html. diff --git src/hg/makeDb/trackDb/human/varFreqs.html src/hg/makeDb/trackDb/human/varFreqs.html index 44840eb1a7c..fb6fc359c6c 100644 --- src/hg/makeDb/trackDb/human/varFreqs.html +++ src/hg/makeDb/trackDb/human/varFreqs.html @@ -52,31 +52,31 @@ </ul> <p> On the Disease and Population reference tracks, <b>Affected AF</b> and <b>Background AF</b> are pooled across contributing cohort arms (sum of allele counts divided by sum of allele numbers), not the maximum across arms, so the displayed frequency matches the carrier-count scale and a small cohort with a high local frequency does not dominate the value. See the "Pooled allele frequency" section on each combined track's description page for which cohorts contribute to the pool numerator and denominator. </p> <h3>Consequence filter — the "Other" bucket</h3> <p> All three combined tracks share the same Consequence filter (Missense, Synonymous, Stop Gained, Frameshift, Splice Donor, Splice Acceptor, Intron, 3' UTR, 5' UTR, Non-coding, -Intergenic, Other). The filter uses OR logic across the comma-separated consequence tokens +Intergenic, Other). The filter uses OR logic across the comma-separated consequence terms on each variant: a variant tagged <code>stop_gained,frameshift</code> is selected by either the "Stop Gained" or the "Frameshift" filter. The "Other" bucket catches the less common <a href="http://www.sequenceontology.org/" target="_blank">Sequence Ontology</a> consequence that don't fit the named buckets above. Examples include <code>splice_region</code> (variant near a splice site but outside the canonical donor/acceptor), <code>start_lost</code> / <code>stop_lost</code> (variant disrupts the start codon or replaces the stop codon with a coding amino acid), <code>stop_retained</code> (variant changes the stop codon but keeps it a stop), <code>inframe_insertion</code> / <code>inframe_deletion</code> (in-frame indel that adds or removes whole codons), and <code>coding_sequence</code> (CDS variant where the precise impact is undetermined). If you include "Other" in the filter selection, no records will be hidden by the consequence filter. </p>