0656b0a9ad98986ef3944b6ceaf305ab08ca4e39
max
  Fri Jul 24 01:10:13 2026 -0700
noyvertSv: swap UK Biobank r2 filter for leave-one-out metrics, revise description

Per author (Boris Noyvert) request, replace the r2Ukb (UK Biobank imputation
r2) filter with r2Loo and concordanceLoo, the primary SV imputation quality
measures for the multi-ancestry reference panel (r2Ukb mainly reflects
European-ancestry performance). Both fields already exist in noyvert.bb, so
this is a trackDb-only change. Also update the description page with the
author's revised text, including a comparison with the 1KG ONT Vienna dataset. refs #37888

diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra
index bb3b13296a6..fd6aa80a4d2 100644
--- src/hg/makeDb/trackDb/human/lrSv.ra
+++ src/hg/makeDb/trackDb/human/lrSv.ra
@@ -153,34 +153,38 @@
     filter.afEas 0:1
     filterByRange.afEas on
     filterLimits.afEas 0:1
     filterLabel.afEas AF East Asian
     filter.afEur 0:1
     filterByRange.afEur on
     filterLimits.afEur 0:1
     filterLabel.afEur AF European
     filter.afSas 0:1
     filterByRange.afSas on
     filterLimits.afSas 0:1
     filterLabel.afSas AF South Asian
     filter.nGwas 0:11
     filterByRange.nGwas on
     filterLabel.nGwas UK Biobank GWAS Hit Count
-    filter.r2Ukb 0:1
-    filterByRange.r2Ukb on
-    filterLimits.r2Ukb 0:1
-    filterLabel.r2Ukb Imputation r2 (UK Biobank)
+    filter.r2Loo 0:1
+    filterByRange.r2Loo on
+    filterLimits.r2Loo 0:1
+    filterLabel.r2Loo Imputation r2 (leave-one-out)
+    filter.concordanceLoo 0:1
+    filterByRange.concordanceLoo on
+    filterLimits.concordanceLoo 0:1
+    filterLabel.concordanceLoo Minor Allele Concordance (leave-one-out)
     skipEmptyFields on
 
     track lrSv1kLin
     parent longReadVariants
     release alpha
     bigDataUrl /gbdb/$D/lrSv/lin1218.bb
     shortLabel 1KG Merged 1218 SVs
     longLabel Structural Variants from 1000 Genomes merged - 1218 individuals (HiFi, ONT & assembly)
     type bigBed 9 +
     itemRgb on
     visibility hide
     mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>AC</b>: $AC/$AN<br><b>AF</b>: $AF<br><b>AF (African)</b>: $afAfr<br><b>AF (European)</b>: $afEur<br><b>Samples</b>: $NS
     filterValues.svType DEL,INS
     filterType.svType multipleListOr
     filterLabel.svType SV Type