442e433a90b25deb87f10e6cf1b7b608bb0a6d67
max
  Sat Sep 26 21:56:06 2026 -0700
sfariSparkWgs45kAsd: flag 25M insertions of non-human (oral bacteria) sequence as FILTER NonHumanIns and hide them by default; add SFARI SPARK 45k WGS to the combined tracks without those insertions and relabel the 12k pilot as SFARI SPARK iWGS v1.1 Pilot, refs #38424

diff --git src/hg/makeDb/trackDb/human/varFreqsBackground.html src/hg/makeDb/trackDb/human/varFreqsBackground.html
index 56fdfc599b7..6ab74cc94ac 100644
--- src/hg/makeDb/trackDb/human/varFreqsBackground.html
+++ src/hg/makeDb/trackDb/human/varFreqsBackground.html
@@ -2,32 +2,35 @@
 <p>
 This track shows small variants (SNVs and short indels) seen in <b>population reference
 cohorts and in unaffected or control individuals</b> of disease-study cohorts, annotated
 with their predicted protein consequence and colored by severity. It is the background half
 of a matched pair: the companion
 <a href="hgTrackUi?g=varFreqsAffected">Disease cohorts</a> track shows the same
 kind of variants seen in affected or case individuals. Displaying the two together lets you
 see how common a variant is in the general/unaffected population compared with affected
 individuals. For the full list of contributing projects, see the
 <a href="hgTrackUi?g=varFreqs">SNV Frequencies</a> collection page.
 </p>
 <p>
 The background combines two kinds of data: the population/biobank reference cohorts (such as
 gnomAD HGDP+1kG, TOPMed, ALFA, HRC and the many national WGS projects), and the
 unaffected/control or unknown-phenotype arms of the disease-study cohorts (non-ASD family
-members in SFARI SPARK WES/WGS, SCHEMA controls, and GREGoR unaffected/unknown
-participants). Genotyping-array cohorts are not included. A variant that also appears in
+members in SFARI SPARK WES, iWGS v1.1 Pilot and 45k WGS, SCHEMA controls, and GREGoR
+unaffected/unknown participants). Genotyping-array cohorts are not included. From SFARI
+SPARK 45k WGS, the 25 million insertions flagged as non-human sequence (FILTER NonHumanIns,
+mostly oral bacteria DNA from the saliva samples, see the
+<a href="hgTrackUi?g=sfariSparkWgs45kAsd">subtrack's description</a>) were left out. A variant that also appears in
 affected individuals is shown in both this track and the
 <a href="hgTrackUi?g=varFreqsAffected">Disease cohorts</a> track.
 </p>
 
 <h2>Display Conventions</h2>
 <h3>Color by Consequence</h3>
 <p>Variants are colored by their most severe predicted consequence:</p>
 <table class="stdTbl">
 <tr><th>Color</th><th>Consequence class</th><th>Examples</th></tr>
 <tr><th style="background-color:#FF0000;width:2em">&nbsp;</th>
     <td>Protein-truncating / loss-of-function</td>
     <td>stop_gained, frameshift, splice_donor, splice_acceptor, stop_lost, start_lost</td></tr>
 <tr><th style="background-color:#1F77B4;width:2em">&nbsp;</th>
     <td>Missense / in-frame</td>
     <td>missense, inframe_insertion, inframe_deletion, protein_altering</td></tr>