64a3f9e7813e823cf724ea188c3928a911578286
max
  Thu Jun 4 00:32:22 2026 -0700
varFreqs: replace All Databases Combined with two phenotype-split tracks

Replace the single varFreqsAll combined track (and drop the varFreqsDisease
track) with two matched tracks for visual case-vs-background comparison:
varFreqsAffected   - variants seen in the affected/case arms of disease
cohorts (SFARI SPARK WES/WGS ASD probands, SCHEMA cases,
GREGoR affected, GA4K); ~130,000 individuals
varFreqsBackground - population reference cohorts + the unaffected/control
arms of disease cohorts ("all other variants");
~1.5 million individuals
A variant seen in both groups appears in both tracks. Genotyping-array cohorts
stay out of both (varFreqsArray unchanged).

vcfToBigBed.py gains --split-affected to emit both tracks in one pass; it reads
phenotype tags (affected/unaffected/unknown) from populations.tsv and
is_disease/disease_role from databases.tsv, and derives the length-filter
ranges from the observed data. TOPMed reclassified as a population cohort.
SPARK WGS display name changed to SFARI SPARK WGS for consistency with the
standalone subtracks. Fixed the trackDb mouseOver $-substitution prefix
collision by wrapping fields in ${}. New description pages for both tracks.

refs #36642

diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra
index a2c2053d2e8..1585bd1c296 100644
--- src/hg/makeDb/trackDb/human/varFreqs.ra
+++ src/hg/makeDb/trackDb/human/varFreqs.ra
@@ -1,440 +1,691 @@
 track varFreqs
 shortLabel SNV Frequencies
 longLabel SNV Frequencies from various cohorts or national projects
 group varRep
 type bed 12
 visibility hide
 superTrack on
 
-        track varFreqsAll
-        shortLabel All Databases Combined
-        longLabel SNV Frequencies: All Databases Combined with Consequence Annotations
+        track varFreqsAffected
+        shortLabel Affected/Case Individuals
+        longLabel SNV Frequencies: variants in ~130,000 affected or case individuals (autism, schizophrenia, rare disease cohorts)
         type bigBed 9 +
         parent varFreqs on
-        bigDataUrl /gbdb/$D/varFreqs/_all/varFreqsAll.bb
+        bigDataUrl /gbdb/$D/varFreqs/_affected/varFreqsAffected.bb
         visibility pack
         itemRgb on
         maxWindowToDraw 5000000
         priority 0.1
-        mouseOver <b>Var:</b> $name<br><b>AA change:</b> $aaChange<br><b>Var type:</b> $varType<br><b>Conseq:</b> $consequence<br><b>Max AF:</b> $maxAF<br><b>Total AC:</b> $totalAC<br><b>Sources:</b> $sources
-        # Source database filter
-        filterValues.sources AllOfUs|AllOfUs,SPARK|SPARK WES,SFARI_WGS|SFARI WGS,GenomeAsia|GenomeAsia SNVs,GenomeAsiaIndel|GenomeAsia Indels,NPM|NPM Singapore,KOVA|KOVA Korea,ToMMo|ToMMo Japan,FinnGen|FinnGen Finland,Saudi|Saudi,SweGen|SweGen Sweden,TOPMed|TOPMed,ABraOM|ABraOM Brazil,ALFA|ALFA,MGRB|MGRB Australia,HRC|HRC,SGDP|SGDP,HGDP1kG|gnomAD HGDP+1kG,GREGoR|GREGoR,SCHEMA|SCHEMA,GA4K|GA4K PacBio LR,CoLoRSdb|CoLoRSdb PacBio LR,SVatalog|SVatalog 101 10XG SR,Tishkoff180|Tishkoff 180 African WGS,WBBC|WBBC China,ChinaMAP|China ChinaMAP,GenomeIndia|GenomeIndia 9.7k WGS,GoNL|GoNL Netherlands ~13x SR
-        filterType.sources multipleListOr
-        filterLabel.sources Source Database
+        mouseOver <b>Var:</b> ${name}<br><b>AA change:</b> ${aaChange}<br><b>Var type:</b> ${varType}<br><b>Conseq:</b> ${consequence}<br><b>Affected AF:</b> ${affectedAF}<br><b>Affected AC:</b> ${affectedAC}<br><b>Affected cohorts:</b> ${affectedCohorts}<br><b>Background AF:</b> ${backgroundAF}
+        filterValues.affectedCohorts SPARK|SFARI SPARK WES,SFARI_WGS|SFARI SPARK WGS,GREGoR|GREGoR,SCHEMA|SCHEMA,GA4K|GA4K PacBio LR
+        filterType.affectedCohorts multipleListOr
+        filterLabel.affectedCohorts Affected/case cohort
+        filterValues.backgroundSources AllOfUs|AllOfUs,SPARK|SFARI SPARK WES,SFARI_WGS|SFARI SPARK WGS,GenomeAsia|GenomeAsia SNVs,GenomeAsiaIndel|GenomeAsia Indels,NPM|NPM Singapore,KOVA|KOVA Korea,ToMMo|ToMMo Japan,FinnGen|FinnGen Finland,Saudi|Saudi,SweGen|SweGen Sweden,TOPMed|TOPMed,ABraOM|ABraOM Brazil,ALFA|ALFA,MGRB|MGRB Australia,HRC|HRC,SGDP|SGDP,HGDP1kG|gnomAD HGDP+1kG,GREGoR|GREGoR,SCHEMA|SCHEMA,CoLoRSdb|CoLoRSdb PacBio LR,SVatalog|SVatalog 101 10XG SR,Tishkoff180|Tishkoff 180 African WGS,WBBC|WBBC China,ChinaMAP|China ChinaMAP,GenomeIndia|GenomeIndia 9.7k WGS,GoNL|GoNL Netherlands ~13x SR
+        filterType.backgroundSources multipleListOr
+        filterLabel.backgroundSources Background source (population or unaffected)
         # Variant type and consequence filters
         filterValues.varType SNV|SNV,INS|Insertion,DEL|Deletion,MNV|MNV
         filterLabel.varType Variant Type
         filterValues.consequence missense|Missense,synonymous|Synonymous,stop_gained|Stop Gained,frameshift|Frameshift,splice_donor|Splice Donor,splice_acceptor|Splice Acceptor,intron|Intron,3_prime_utr|3' UTR,5_prime_utr|5' UTR,non_coding|Non-coding,.|Intergenic,others|Other
         filterType.consequence multipleListOr
         filterLabel.consequence Consequence
         # Length filters
         filterByRange.refLen on
         filterLabel.refLen Reference Length
+        filter.refLen 1:28037
+        filterLimits.refLen 1:28037
         filterByRange.altLen on
         filterLabel.altLen Alternate Length
+        filter.altLen 1:6294
+        filterLimits.altLen 1:6294
         filterByRange.varLen on
         filterLabel.varLen Length Change
-        # Max AF filter
-        filterByRange.maxAF on
-        filterLabel.maxAF Max Allele Frequency
-        filterLimits.maxAF 0:1
-        # Total AC filter
-        filterByRange.totalAC on
-        filterLabel.totalAC Total Allele Count (all databases)
+        filter.varLen -28036:6293
+        filterLimits.varLen -28036:6293
+        # Affected/case frequency summary
+        filterByRange.affectedAF on
+        filterLabel.affectedAF Affected/case AF
+        filterLimits.affectedAF 0:1
+        filterByRange.affectedAC on
+        filterLabel.affectedAC Affected/case AC
+        # Background (population + unaffected) frequency summary
+        filterByRange.backgroundAF on
+        filterLabel.backgroundAF Background AF (population + unaffected)
+        filterLimits.backgroundAF 0:1
+        filterByRange.backgroundAC on
+        filterLabel.backgroundAC Background AC (population + unaffected)
+        # Affected/case membership flag
+        filterByRange.inAffected on
+        filterLabel.inAffected Seen in an affected/case arm (1=yes, 0=no)
+        filter.inAffected 0:1
+        filterLimits.inAffected 0:1
         # Per-database AF filters
         filterByRange.AllOfUsAF on
         filterLabel.AllOfUsAF AllOfUs AF
         filterByRange.SPARKAF on
-        filterLabel.SPARKAF SPARK WES AF
+        filterLabel.SPARKAF SFARI SPARK WES AF
         filterByRange.SFARI_WGSAF on
-        filterLabel.SFARI_WGSAF SFARI WGS AF
+        filterLabel.SFARI_WGSAF SFARI SPARK WGS AF
         filterByRange.GenomeAsiaAF on
         filterLabel.GenomeAsiaAF GenomeAsia SNVs AF
         filterByRange.GenomeAsiaIndelAF on
         filterLabel.GenomeAsiaIndelAF GenomeAsia Indels AF
+        filterByRange.NPMAF on
+        filterLabel.NPMAF NPM Singapore AF
         filterByRange.KOVAAF on
         filterLabel.KOVAAF KOVA Korea AF
         filterByRange.ToMMoAF on
         filterLabel.ToMMoAF ToMMo Japan AF
         filterByRange.FinnGenAF on
         filterLabel.FinnGenAF FinnGen Finland AF
         filterByRange.SaudiAF on
         filterLabel.SaudiAF Saudi AF
         filterByRange.SweGenAF on
         filterLabel.SweGenAF SweGen Sweden AF
         filterByRange.TOPMedAF on
         filterLabel.TOPMedAF TOPMed AF
         filterByRange.ABraOMAF on
         filterLabel.ABraOMAF ABraOM Brazil AF
         filterByRange.ALFAAF on
         filterLabel.ALFAAF ALFA AF
         filterByRange.MGRBAF on
         filterLabel.MGRBAF MGRB Australia AF
         filterByRange.HRCAF on
         filterLabel.HRCAF HRC AF
         filterByRange.SGDPAF on
         filterLabel.SGDPAF SGDP AF
         filterByRange.HGDP1kGAF on
-        filterLabel.HGDP1kGAF gnomAD HGDP+1kG AF (4k cohort)
+        filterLabel.HGDP1kGAF gnomAD HGDP+1kG AF
         filterByRange.GREGoRAF on
         filterLabel.GREGoRAF GREGoR AF
         filterByRange.SCHEMAAF on
         filterLabel.SCHEMAAF SCHEMA AF
         filterByRange.GA4KAF on
         filterLabel.GA4KAF GA4K PacBio LR AF
         filterByRange.CoLoRSdbAF on
         filterLabel.CoLoRSdbAF CoLoRSdb PacBio LR AF
         filterByRange.SVatalogAF on
         filterLabel.SVatalogAF SVatalog 101 10XG SR AF
         filterByRange.Tishkoff180AF on
         filterLabel.Tishkoff180AF Tishkoff 180 African WGS AF
-        filterByRange.NPMAF on
-        filterLabel.NPMAF NPM Singapore AF
         filterByRange.WBBCAF on
         filterLabel.WBBCAF WBBC China AF
         filterByRange.ChinaMAPAF on
         filterLabel.ChinaMAPAF China ChinaMAP AF
         filterByRange.GenomeIndiaAF on
         filterLabel.GenomeIndiaAF GenomeIndia 9.7k WGS AF
         filterByRange.GoNLAF on
         filterLabel.GoNLAF GoNL Netherlands ~13x SR AF
         # Per-database AC filters
         filterByRange.AllOfUsAC on
         filterLabel.AllOfUsAC AllOfUs AC
         filterByRange.SPARKAC on
-        filterLabel.SPARKAC SPARK WES AC
+        filterLabel.SPARKAC SFARI SPARK WES AC
         filterByRange.SFARI_WGSAC on
-        filterLabel.SFARI_WGSAC SFARI WGS AC
+        filterLabel.SFARI_WGSAC SFARI SPARK WGS AC
         filterByRange.GenomeAsiaAC on
         filterLabel.GenomeAsiaAC GenomeAsia SNVs AC
         filterByRange.GenomeAsiaIndelAC on
         filterLabel.GenomeAsiaIndelAC GenomeAsia Indels AC
+        filterByRange.NPMAC on
+        filterLabel.NPMAC NPM Singapore AC
         filterByRange.KOVAAC on
         filterLabel.KOVAAC KOVA Korea AC
         filterByRange.ToMMoAC on
         filterLabel.ToMMoAC ToMMo Japan AC
         filterByRange.FinnGenAC on
         filterLabel.FinnGenAC FinnGen Finland AC
         filterByRange.SaudiAC on
         filterLabel.SaudiAC Saudi AC
         filterByRange.SweGenAC on
         filterLabel.SweGenAC SweGen Sweden AC
         filterByRange.TOPMedAC on
         filterLabel.TOPMedAC TOPMed AC
         filterByRange.ABraOMAC on
         filterLabel.ABraOMAC ABraOM Brazil AC
         filterByRange.ALFAAC on
         filterLabel.ALFAAC ALFA AC
         filterByRange.MGRBAC on
         filterLabel.MGRBAC MGRB Australia AC
         filterByRange.HRCAC on
         filterLabel.HRCAC HRC AC
         filterByRange.SGDPAC on
         filterLabel.SGDPAC SGDP AC
         filterByRange.HGDP1kGAC on
-        filterLabel.HGDP1kGAC gnomAD HGDP+1kG AC (4k cohort)
+        filterLabel.HGDP1kGAC gnomAD HGDP+1kG AC
         filterByRange.GREGoRAC on
         filterLabel.GREGoRAC GREGoR AC
         filterByRange.SCHEMAAC on
         filterLabel.SCHEMAAC SCHEMA AC
         filterByRange.GA4KAC on
         filterLabel.GA4KAC GA4K PacBio LR AC
         filterByRange.CoLoRSdbAC on
         filterLabel.CoLoRSdbAC CoLoRSdb PacBio LR AC
         filterByRange.SVatalogAC on
         filterLabel.SVatalogAC SVatalog 101 10XG SR AC
         filterByRange.Tishkoff180AC on
         filterLabel.Tishkoff180AC Tishkoff 180 African WGS AC
-        filterByRange.NPMAC on
-        filterLabel.NPMAC NPM Singapore AC
         filterByRange.WBBCAC on
         filterLabel.WBBCAC WBBC China AC
         filterByRange.ChinaMAPAC on
         filterLabel.ChinaMAPAC China ChinaMAP AC
         filterByRange.GenomeIndiaAC on
         filterLabel.GenomeIndiaAC GenomeIndia 9.7k WGS AC
         filterByRange.GoNLAC on
         filterLabel.GoNLAC GoNL Netherlands ~13x SR AC
         # Population-specific AF filters
-        # AllOfUs local-ancestry populations
-        # NB: these are local-ancestry-stratified frequencies (per-position, per-haplotype-class),
-        # NOT the AllOfUs paper's global Rye ancestry categories. See varFreqs.html for details.
+        # AllOfUs populations
         filterByRange.AllOfUsAF_AFR on
-        filterLabel.AllOfUsAF_AFR AllOfUs African AF (local ancestry)
+        filterLabel.AllOfUsAF_AFR AllOfUs African AF
         filterByRange.AllOfUsAF_AMR on
-        filterLabel.AllOfUsAF_AMR AllOfUs Indigenous American AF (local ancestry)
+        filterLabel.AllOfUsAF_AMR AllOfUs Indigenous American AF
         filterByRange.AllOfUsAF_EAS on
-        filterLabel.AllOfUsAF_EAS AllOfUs East Asian AF (local ancestry)
+        filterLabel.AllOfUsAF_EAS AllOfUs East Asian AF
         filterByRange.AllOfUsAF_EUR on
-        filterLabel.AllOfUsAF_EUR AllOfUs European AF (local ancestry)
+        filterLabel.AllOfUsAF_EUR AllOfUs European AF
         filterByRange.AllOfUsAF_OCE on
-        filterLabel.AllOfUsAF_OCE AllOfUs Oceanian AF (local ancestry)
+        filterLabel.AllOfUsAF_OCE AllOfUs Oceanian AF
         filterByRange.AllOfUsAF_SAS on
-        filterLabel.AllOfUsAF_SAS AllOfUs South Asian AF (local ancestry)
+        filterLabel.AllOfUsAF_SAS AllOfUs South Asian AF
         filterByRange.AllOfUsAC_AFR on
-        filterLabel.AllOfUsAC_AFR AllOfUs African AC (local ancestry)
+        filterLabel.AllOfUsAC_AFR AllOfUs African AC
         filterByRange.AllOfUsAC_AMR on
-        filterLabel.AllOfUsAC_AMR AllOfUs Indigenous American AC (local ancestry)
+        filterLabel.AllOfUsAC_AMR AllOfUs Indigenous American AC
         filterByRange.AllOfUsAC_EAS on
-        filterLabel.AllOfUsAC_EAS AllOfUs East Asian AC (local ancestry)
+        filterLabel.AllOfUsAC_EAS AllOfUs East Asian AC
         filterByRange.AllOfUsAC_EUR on
-        filterLabel.AllOfUsAC_EUR AllOfUs European AC (local ancestry)
+        filterLabel.AllOfUsAC_EUR AllOfUs European AC
         filterByRange.AllOfUsAC_OCE on
-        filterLabel.AllOfUsAC_OCE AllOfUs Oceanian AC (local ancestry)
+        filterLabel.AllOfUsAC_OCE AllOfUs Oceanian AC
         filterByRange.AllOfUsAC_SAS on
-        filterLabel.AllOfUsAC_SAS AllOfUs South Asian AC (local ancestry)
-        # GenomeAsia SNVs populations (7 groups in source VCF)
+        filterLabel.AllOfUsAC_SAS AllOfUs South Asian AC
+        # SFARI SPARK WES populations
+        filterByRange.SPARKAF_AUT on
+        filterLabel.SPARKAF_AUT SFARI SPARK WES ASD proband AF
+        filterByRange.SPARKAF_NON_AUT on
+        filterLabel.SPARKAF_NON_AUT SFARI SPARK WES Non-ASD family AF
+        filterByRange.SPARKAC_AUT on
+        filterLabel.SPARKAC_AUT SFARI SPARK WES ASD proband AC
+        filterByRange.SPARKAC_NON_AUT on
+        filterLabel.SPARKAC_NON_AUT SFARI SPARK WES Non-ASD family AC
+        # SFARI SPARK WGS populations
+        filterByRange.SFARI_WGSAF_AUT on
+        filterLabel.SFARI_WGSAF_AUT SFARI SPARK WGS ASD proband AF
+        filterByRange.SFARI_WGSAF_NON_AUT on
+        filterLabel.SFARI_WGSAF_NON_AUT SFARI SPARK WGS Non-ASD family AF
+        filterByRange.SFARI_WGSAC_AUT on
+        filterLabel.SFARI_WGSAC_AUT SFARI SPARK WGS ASD proband AC
+        filterByRange.SFARI_WGSAC_NON_AUT on
+        filterLabel.SFARI_WGSAC_NON_AUT SFARI SPARK WGS Non-ASD family AC
+        # GenomeAsia SNVs populations
         filterByRange.GenomeAsiaAF_NEA on
         filterLabel.GenomeAsiaAF_NEA GenomeAsia SNVs Northeast Asian AF
         filterByRange.GenomeAsiaAF_SEA on
         filterLabel.GenomeAsiaAF_SEA GenomeAsia SNVs Southeast Asian AF
         filterByRange.GenomeAsiaAF_SAS on
         filterLabel.GenomeAsiaAF_SAS GenomeAsia SNVs South Asian AF
         filterByRange.GenomeAsiaAF_OCE on
         filterLabel.GenomeAsiaAF_OCE GenomeAsia SNVs Oceanian AF
         filterByRange.GenomeAsiaAF_AMR on
         filterLabel.GenomeAsiaAF_AMR GenomeAsia SNVs American AF
         filterByRange.GenomeAsiaAF_AFR on
         filterLabel.GenomeAsiaAF_AFR GenomeAsia SNVs African AF
         filterByRange.GenomeAsiaAF_WER on
         filterLabel.GenomeAsiaAF_WER GenomeAsia SNVs Western European Ref AF
         filterByRange.GenomeAsiaAC_NEA on
         filterLabel.GenomeAsiaAC_NEA GenomeAsia SNVs Northeast Asian AC
         filterByRange.GenomeAsiaAC_SEA on
         filterLabel.GenomeAsiaAC_SEA GenomeAsia SNVs Southeast Asian AC
         filterByRange.GenomeAsiaAC_SAS on
         filterLabel.GenomeAsiaAC_SAS GenomeAsia SNVs South Asian AC
         filterByRange.GenomeAsiaAC_OCE on
         filterLabel.GenomeAsiaAC_OCE GenomeAsia SNVs Oceanian AC
         filterByRange.GenomeAsiaAC_AMR on
         filterLabel.GenomeAsiaAC_AMR GenomeAsia SNVs American AC
         filterByRange.GenomeAsiaAC_AFR on
         filterLabel.GenomeAsiaAC_AFR GenomeAsia SNVs African AC
         filterByRange.GenomeAsiaAC_WER on
         filterLabel.GenomeAsiaAC_WER GenomeAsia SNVs Western European Ref AC
-        # gnomAD HGDP+1kG: per-population AF/AC values are from the FULL gnomAD v3.1.2
-        # release (~76k genomes), not the 4,094-genome HGDP+1kG cohort. Only the
-        # cohort-level HGDP1kGAF / HGDP1kGAC fields above reflect the 4k-cohort.
+        # NPM Singapore populations
+        filterByRange.NPMAF_Chinese on
+        filterLabel.NPMAF_Chinese NPM Singapore Singapore Chinese AF
+        filterByRange.NPMAF_Malay on
+        filterLabel.NPMAF_Malay NPM Singapore Singapore Malay AF
+        filterByRange.NPMAF_Indian on
+        filterLabel.NPMAF_Indian NPM Singapore Singapore Indian AF
+        filterByRange.NPMAC_Chinese on
+        filterLabel.NPMAC_Chinese NPM Singapore Singapore Chinese AC
+        filterByRange.NPMAC_Malay on
+        filterLabel.NPMAC_Malay NPM Singapore Singapore Malay AC
+        filterByRange.NPMAC_Indian on
+        filterLabel.NPMAC_Indian NPM Singapore Singapore Indian AC
+        # gnomAD HGDP+1kG populations
         filterByRange.HGDP1kGAF_afr on
-        filterLabel.HGDP1kGAF_afr gnomAD v3.1.2 African AF (full release)
+        filterLabel.HGDP1kGAF_afr gnomAD HGDP+1kG African AF
         filterByRange.HGDP1kGAF_ami on
-        filterLabel.HGDP1kGAF_ami gnomAD v3.1.2 Amish AF (full release)
+        filterLabel.HGDP1kGAF_ami gnomAD HGDP+1kG Amish AF
         filterByRange.HGDP1kGAF_amr on
-        filterLabel.HGDP1kGAF_amr gnomAD v3.1.2 Latino AF (full release)
+        filterLabel.HGDP1kGAF_amr gnomAD HGDP+1kG Latino AF
         filterByRange.HGDP1kGAF_asj on
-        filterLabel.HGDP1kGAF_asj gnomAD v3.1.2 Ashkenazi Jewish AF (full release)
+        filterLabel.HGDP1kGAF_asj gnomAD HGDP+1kG Ashkenazi Jewish AF
         filterByRange.HGDP1kGAF_eas on
-        filterLabel.HGDP1kGAF_eas gnomAD v3.1.2 East Asian AF (full release)
+        filterLabel.HGDP1kGAF_eas gnomAD HGDP+1kG East Asian AF
         filterByRange.HGDP1kGAF_fin on
-        filterLabel.HGDP1kGAF_fin gnomAD v3.1.2 Finnish AF (full release)
+        filterLabel.HGDP1kGAF_fin gnomAD HGDP+1kG Finnish AF
         filterByRange.HGDP1kGAF_mid on
-        filterLabel.HGDP1kGAF_mid gnomAD v3.1.2 Middle Eastern AF (full release)
+        filterLabel.HGDP1kGAF_mid gnomAD HGDP+1kG Middle Eastern AF
         filterByRange.HGDP1kGAF_nfe on
-        filterLabel.HGDP1kGAF_nfe gnomAD v3.1.2 Non-Finnish European AF (full release)
+        filterLabel.HGDP1kGAF_nfe gnomAD HGDP+1kG Non-Finnish European AF
         filterByRange.HGDP1kGAF_oth on
-        filterLabel.HGDP1kGAF_oth gnomAD v3.1.2 Other AF (full release)
+        filterLabel.HGDP1kGAF_oth gnomAD HGDP+1kG Other AF
         filterByRange.HGDP1kGAF_sas on
-        filterLabel.HGDP1kGAF_sas gnomAD v3.1.2 South Asian AF (full release)
+        filterLabel.HGDP1kGAF_sas gnomAD HGDP+1kG South Asian AF
         filterByRange.HGDP1kGAC_afr on
-        filterLabel.HGDP1kGAC_afr gnomAD v3.1.2 African AC (full release)
+        filterLabel.HGDP1kGAC_afr gnomAD HGDP+1kG African AC
         filterByRange.HGDP1kGAC_ami on
-        filterLabel.HGDP1kGAC_ami gnomAD v3.1.2 Amish AC (full release)
+        filterLabel.HGDP1kGAC_ami gnomAD HGDP+1kG Amish AC
         filterByRange.HGDP1kGAC_amr on
-        filterLabel.HGDP1kGAC_amr gnomAD v3.1.2 Latino AC (full release)
+        filterLabel.HGDP1kGAC_amr gnomAD HGDP+1kG Latino AC
         filterByRange.HGDP1kGAC_asj on
-        filterLabel.HGDP1kGAC_asj gnomAD v3.1.2 Ashkenazi Jewish AC (full release)
+        filterLabel.HGDP1kGAC_asj gnomAD HGDP+1kG Ashkenazi Jewish AC
         filterByRange.HGDP1kGAC_eas on
-        filterLabel.HGDP1kGAC_eas gnomAD v3.1.2 East Asian AC (full release)
+        filterLabel.HGDP1kGAC_eas gnomAD HGDP+1kG East Asian AC
         filterByRange.HGDP1kGAC_fin on
-        filterLabel.HGDP1kGAC_fin gnomAD v3.1.2 Finnish AC (full release)
+        filterLabel.HGDP1kGAC_fin gnomAD HGDP+1kG Finnish AC
         filterByRange.HGDP1kGAC_mid on
-        filterLabel.HGDP1kGAC_mid gnomAD v3.1.2 Middle Eastern AC (full release)
+        filterLabel.HGDP1kGAC_mid gnomAD HGDP+1kG Middle Eastern AC
         filterByRange.HGDP1kGAC_nfe on
-        filterLabel.HGDP1kGAC_nfe gnomAD v3.1.2 Non-Finnish European AC (full release)
+        filterLabel.HGDP1kGAC_nfe gnomAD HGDP+1kG Non-Finnish European AC
         filterByRange.HGDP1kGAC_oth on
-        filterLabel.HGDP1kGAC_oth gnomAD v3.1.2 Other AC (full release)
+        filterLabel.HGDP1kGAC_oth gnomAD HGDP+1kG Other AC
         filterByRange.HGDP1kGAC_sas on
-        filterLabel.HGDP1kGAC_sas gnomAD v3.1.2 South Asian AC (full release)
+        filterLabel.HGDP1kGAC_sas gnomAD HGDP+1kG South Asian AC
         # GREGoR populations
         filterByRange.GREGoRAF_AFF on
         filterLabel.GREGoRAF_AFF GREGoR Affected AF
         filterByRange.GREGoRAF_UNA on
         filterLabel.GREGoRAF_UNA GREGoR Unaffected AF
         filterByRange.GREGoRAF_UNK on
         filterLabel.GREGoRAF_UNK GREGoR Unknown AF
         filterByRange.GREGoRAC_AFF on
         filterLabel.GREGoRAC_AFF GREGoR Affected AC
         filterByRange.GREGoRAC_UNA on
         filterLabel.GREGoRAC_UNA GREGoR Unaffected AC
         filterByRange.GREGoRAC_UNK on
         filterLabel.GREGoRAC_UNK GREGoR Unknown AC
-        # NPM Singapore ancestry groups
-        filterByRange.NPMAF_Chinese on
-        filterLabel.NPMAF_Chinese NPM Singapore Chinese AF
-        filterByRange.NPMAF_Malay on
-        filterLabel.NPMAF_Malay NPM Singapore Malay AF
-        filterByRange.NPMAF_Indian on
-        filterLabel.NPMAF_Indian NPM Singapore Indian AF
-        filterByRange.NPMAC_Chinese on
-        filterLabel.NPMAC_Chinese NPM Singapore Chinese AC
-        filterByRange.NPMAC_Malay on
-        filterLabel.NPMAC_Malay NPM Singapore Malay AC
-        filterByRange.NPMAC_Indian on
-        filterLabel.NPMAC_Indian NPM Singapore Indian AC
+        # SCHEMA populations
+        filterByRange.SCHEMAAF_CASE on
+        filterLabel.SCHEMAAF_CASE SCHEMA Schizophrenia case AF
+        filterByRange.SCHEMAAF_CTRL on
+        filterLabel.SCHEMAAF_CTRL SCHEMA Control AF
+        filterByRange.SCHEMAAC_CASE on
+        filterLabel.SCHEMAAC_CASE SCHEMA Schizophrenia case AC
+        filterByRange.SCHEMAAC_CTRL on
+        filterLabel.SCHEMAAC_CTRL SCHEMA Control AC
         # WBBC China populations
         filterByRange.WBBCAF_North on
-        filterLabel.WBBCAF_North WBBC North Han AF
+        filterLabel.WBBCAF_North WBBC China North Han AF
         filterByRange.WBBCAF_Central on
-        filterLabel.WBBCAF_Central WBBC Central Han AF
+        filterLabel.WBBCAF_Central WBBC China Central Han AF
         filterByRange.WBBCAF_South on
-        filterLabel.WBBCAF_South WBBC South Han AF
+        filterLabel.WBBCAF_South WBBC China South Han AF
         filterByRange.WBBCAF_Lingnan on
-        filterLabel.WBBCAF_Lingnan WBBC Lingnan Han AF
+        filterLabel.WBBCAF_Lingnan WBBC China Lingnan Han AF
         filterByRange.WBBCAC_North on
-        filterLabel.WBBCAC_North WBBC North Han AC
+        filterLabel.WBBCAC_North WBBC China North Han AC
         filterByRange.WBBCAC_Central on
-        filterLabel.WBBCAC_Central WBBC Central Han AC
+        filterLabel.WBBCAC_Central WBBC China Central Han AC
         filterByRange.WBBCAC_South on
-        filterLabel.WBBCAC_South WBBC South Han AC
+        filterLabel.WBBCAC_South WBBC China South Han AC
         filterByRange.WBBCAC_Lingnan on
-        filterLabel.WBBCAC_Lingnan WBBC Lingnan Han AC
-        # SFARI SPARK WES autism phenotype split (asd column of individuals_registration)
-        filterByRange.SPARKAF_AUT on
-        filterLabel.SPARKAF_AUT SPARK WES ASD proband AF
-        filterByRange.SPARKAF_NON_AUT on
-        filterLabel.SPARKAF_NON_AUT SPARK WES Non-ASD family AF
-        filterByRange.SPARKAC_AUT on
-        filterLabel.SPARKAC_AUT SPARK WES ASD proband AC
-        filterByRange.SPARKAC_NON_AUT on
-        filterLabel.SPARKAC_NON_AUT SPARK WES Non-ASD family AC
-        # SFARI SPARK WGS autism phenotype split
-        filterByRange.SFARI_WGSAF_AUT on
-        filterLabel.SFARI_WGSAF_AUT SFARI WGS ASD proband AF
-        filterByRange.SFARI_WGSAF_NON_AUT on
-        filterLabel.SFARI_WGSAF_NON_AUT SFARI WGS Non-ASD family AF
-        filterByRange.SFARI_WGSAC_AUT on
-        filterLabel.SFARI_WGSAC_AUT SFARI WGS ASD proband AC
-        filterByRange.SFARI_WGSAC_NON_AUT on
-        filterLabel.SFARI_WGSAC_NON_AUT SFARI WGS Non-ASD family AC
-        # SCHEMA schizophrenia case/control (summed across analysis groups)
-        filterByRange.SCHEMAAF_CASE on
-        filterLabel.SCHEMAAF_CASE SCHEMA Schizophrenia case AF
-        filterByRange.SCHEMAAF_CTRL on
-        filterLabel.SCHEMAAF_CTRL SCHEMA Control AF
-        filterByRange.SCHEMAAC_CASE on
-        filterLabel.SCHEMAAC_CASE SCHEMA Schizophrenia case AC
-        filterByRange.SCHEMAAC_CTRL on
-        filterLabel.SCHEMAAC_CTRL SCHEMA Control AC
+        filterLabel.WBBCAC_Lingnan WBBC China Lingnan Han AC
         skipEmptyFields on
 
-        track varFreqsDisease
-        shortLabel Disease-related Databases Combined
-        longLabel SNV Frequencies: Disease-related cohorts combined (autism, schizophrenia, rare disease, NHLBI heart/lung/blood)
+        track varFreqsBackground
+        shortLabel Population + Unaffected
+        longLabel SNV Frequencies: variants in ~1.5 million individuals from population cohorts and unaffected or control arms
         type bigBed 9 +
-        parent varFreqs off
-        bigDataUrl /gbdb/$D/varFreqs/_disease/varFreqsDisease.bb
-        visibility hide
+        parent varFreqs on
+        bigDataUrl /gbdb/$D/varFreqs/_background/varFreqsBackground.bb
+        visibility pack
         itemRgb on
         maxWindowToDraw 5000000
-        priority 0.15
-        mouseOver <b>Var:</b> $name<br><b>AA change:</b> $aaChange<br><b>Var type:</b> $varType<br><b>Conseq:</b> $consequence<br><b>Max AF:</b> $maxAF<br><b>Total AC:</b> $totalAC<br><b>Sources:</b> $sources
-        filterValues.sources SPARK|SPARK WES,SFARI_WGS|SFARI WGS,TOPMed|TOPMed,SCHEMA|SCHEMA,GREGoR|GREGoR,GA4K|GA4K PacBio LR
-        filterType.sources multipleListOr
-        filterLabel.sources Source Database
+        priority 0.11
+        mouseOver <b>Var:</b> ${name}<br><b>AA change:</b> ${aaChange}<br><b>Var type:</b> ${varType}<br><b>Conseq:</b> ${consequence}<br><b>Background AF:</b> ${backgroundAF}<br><b>Background AC:</b> ${backgroundAC}<br><b>Sources:</b> ${backgroundSources}<br><b>Affected AF:</b> ${affectedAF}
+        filterValues.affectedCohorts SPARK|SFARI SPARK WES,SFARI_WGS|SFARI SPARK WGS,GREGoR|GREGoR,SCHEMA|SCHEMA,GA4K|GA4K PacBio LR
+        filterType.affectedCohorts multipleListOr
+        filterLabel.affectedCohorts Affected/case cohort
+        filterValues.backgroundSources AllOfUs|AllOfUs,SPARK|SFARI SPARK WES,SFARI_WGS|SFARI SPARK WGS,GenomeAsia|GenomeAsia SNVs,GenomeAsiaIndel|GenomeAsia Indels,NPM|NPM Singapore,KOVA|KOVA Korea,ToMMo|ToMMo Japan,FinnGen|FinnGen Finland,Saudi|Saudi,SweGen|SweGen Sweden,TOPMed|TOPMed,ABraOM|ABraOM Brazil,ALFA|ALFA,MGRB|MGRB Australia,HRC|HRC,SGDP|SGDP,HGDP1kG|gnomAD HGDP+1kG,GREGoR|GREGoR,SCHEMA|SCHEMA,CoLoRSdb|CoLoRSdb PacBio LR,SVatalog|SVatalog 101 10XG SR,Tishkoff180|Tishkoff 180 African WGS,WBBC|WBBC China,ChinaMAP|China ChinaMAP,GenomeIndia|GenomeIndia 9.7k WGS,GoNL|GoNL Netherlands ~13x SR
+        filterType.backgroundSources multipleListOr
+        filterLabel.backgroundSources Background source (population or unaffected)
+        # Variant type and consequence filters
         filterValues.varType SNV|SNV,INS|Insertion,DEL|Deletion,MNV|MNV
         filterLabel.varType Variant Type
         filterValues.consequence missense|Missense,synonymous|Synonymous,stop_gained|Stop Gained,frameshift|Frameshift,splice_donor|Splice Donor,splice_acceptor|Splice Acceptor,intron|Intron,3_prime_utr|3' UTR,5_prime_utr|5' UTR,non_coding|Non-coding,.|Intergenic,others|Other
         filterType.consequence multipleListOr
         filterLabel.consequence Consequence
+        # Length filters
         filterByRange.refLen on
         filterLabel.refLen Reference Length
+        filter.refLen 1:28037
+        filterLimits.refLen 1:28037
         filterByRange.altLen on
         filterLabel.altLen Alternate Length
+        filter.altLen 1:6294
+        filterLimits.altLen 1:6294
         filterByRange.varLen on
         filterLabel.varLen Length Change
-        filterByRange.maxAF on
-        filterLabel.maxAF Max Allele Frequency
-        filterLimits.maxAF 0:1
-        filterByRange.totalAC on
-        filterLabel.totalAC Total Allele Count (all databases)
+        filter.varLen -28036:6293
+        filterLimits.varLen -28036:6293
+        # Affected/case frequency summary
+        filterByRange.affectedAF on
+        filterLabel.affectedAF Affected/case AF
+        filterLimits.affectedAF 0:1
+        filterByRange.affectedAC on
+        filterLabel.affectedAC Affected/case AC
+        # Background (population + unaffected) frequency summary
+        filterByRange.backgroundAF on
+        filterLabel.backgroundAF Background AF (population + unaffected)
+        filterLimits.backgroundAF 0:1
+        filterByRange.backgroundAC on
+        filterLabel.backgroundAC Background AC (population + unaffected)
+        # Affected/case membership flag
+        filterByRange.inAffected on
+        filterLabel.inAffected Seen in an affected/case arm (1=yes, 0=no)
+        filter.inAffected 0:1
+        filterLimits.inAffected 0:1
         # Per-database AF filters
+        filterByRange.AllOfUsAF on
+        filterLabel.AllOfUsAF AllOfUs AF
         filterByRange.SPARKAF on
-        filterLabel.SPARKAF SPARK WES AF
+        filterLabel.SPARKAF SFARI SPARK WES AF
         filterByRange.SFARI_WGSAF on
-        filterLabel.SFARI_WGSAF SFARI WGS AF
+        filterLabel.SFARI_WGSAF SFARI SPARK WGS AF
+        filterByRange.GenomeAsiaAF on
+        filterLabel.GenomeAsiaAF GenomeAsia SNVs AF
+        filterByRange.GenomeAsiaIndelAF on
+        filterLabel.GenomeAsiaIndelAF GenomeAsia Indels AF
+        filterByRange.NPMAF on
+        filterLabel.NPMAF NPM Singapore AF
+        filterByRange.KOVAAF on
+        filterLabel.KOVAAF KOVA Korea AF
+        filterByRange.ToMMoAF on
+        filterLabel.ToMMoAF ToMMo Japan AF
+        filterByRange.FinnGenAF on
+        filterLabel.FinnGenAF FinnGen Finland AF
+        filterByRange.SaudiAF on
+        filterLabel.SaudiAF Saudi AF
+        filterByRange.SweGenAF on
+        filterLabel.SweGenAF SweGen Sweden AF
         filterByRange.TOPMedAF on
         filterLabel.TOPMedAF TOPMed AF
-        filterByRange.SCHEMAAF on
-        filterLabel.SCHEMAAF SCHEMA AF
+        filterByRange.ABraOMAF on
+        filterLabel.ABraOMAF ABraOM Brazil AF
+        filterByRange.ALFAAF on
+        filterLabel.ALFAAF ALFA AF
+        filterByRange.MGRBAF on
+        filterLabel.MGRBAF MGRB Australia AF
+        filterByRange.HRCAF on
+        filterLabel.HRCAF HRC AF
+        filterByRange.SGDPAF on
+        filterLabel.SGDPAF SGDP AF
+        filterByRange.HGDP1kGAF on
+        filterLabel.HGDP1kGAF gnomAD HGDP+1kG AF
         filterByRange.GREGoRAF on
         filterLabel.GREGoRAF GREGoR AF
+        filterByRange.SCHEMAAF on
+        filterLabel.SCHEMAAF SCHEMA AF
         filterByRange.GA4KAF on
         filterLabel.GA4KAF GA4K PacBio LR AF
+        filterByRange.CoLoRSdbAF on
+        filterLabel.CoLoRSdbAF CoLoRSdb PacBio LR AF
+        filterByRange.SVatalogAF on
+        filterLabel.SVatalogAF SVatalog 101 10XG SR AF
+        filterByRange.Tishkoff180AF on
+        filterLabel.Tishkoff180AF Tishkoff 180 African WGS AF
+        filterByRange.WBBCAF on
+        filterLabel.WBBCAF WBBC China AF
+        filterByRange.ChinaMAPAF on
+        filterLabel.ChinaMAPAF China ChinaMAP AF
+        filterByRange.GenomeIndiaAF on
+        filterLabel.GenomeIndiaAF GenomeIndia 9.7k WGS AF
+        filterByRange.GoNLAF on
+        filterLabel.GoNLAF GoNL Netherlands ~13x SR AF
         # Per-database AC filters
+        filterByRange.AllOfUsAC on
+        filterLabel.AllOfUsAC AllOfUs AC
         filterByRange.SPARKAC on
-        filterLabel.SPARKAC SPARK WES AC
+        filterLabel.SPARKAC SFARI SPARK WES AC
         filterByRange.SFARI_WGSAC on
-        filterLabel.SFARI_WGSAC SFARI WGS AC
+        filterLabel.SFARI_WGSAC SFARI SPARK WGS AC
+        filterByRange.GenomeAsiaAC on
+        filterLabel.GenomeAsiaAC GenomeAsia SNVs AC
+        filterByRange.GenomeAsiaIndelAC on
+        filterLabel.GenomeAsiaIndelAC GenomeAsia Indels AC
+        filterByRange.NPMAC on
+        filterLabel.NPMAC NPM Singapore AC
+        filterByRange.KOVAAC on
+        filterLabel.KOVAAC KOVA Korea AC
+        filterByRange.ToMMoAC on
+        filterLabel.ToMMoAC ToMMo Japan AC
+        filterByRange.FinnGenAC on
+        filterLabel.FinnGenAC FinnGen Finland AC
+        filterByRange.SaudiAC on
+        filterLabel.SaudiAC Saudi AC
+        filterByRange.SweGenAC on
+        filterLabel.SweGenAC SweGen Sweden AC
         filterByRange.TOPMedAC on
         filterLabel.TOPMedAC TOPMed AC
-        filterByRange.SCHEMAAC on
-        filterLabel.SCHEMAAC SCHEMA AC
+        filterByRange.ABraOMAC on
+        filterLabel.ABraOMAC ABraOM Brazil AC
+        filterByRange.ALFAAC on
+        filterLabel.ALFAAC ALFA AC
+        filterByRange.MGRBAC on
+        filterLabel.MGRBAC MGRB Australia AC
+        filterByRange.HRCAC on
+        filterLabel.HRCAC HRC AC
+        filterByRange.SGDPAC on
+        filterLabel.SGDPAC SGDP AC
+        filterByRange.HGDP1kGAC on
+        filterLabel.HGDP1kGAC gnomAD HGDP+1kG AC
         filterByRange.GREGoRAC on
         filterLabel.GREGoRAC GREGoR AC
+        filterByRange.SCHEMAAC on
+        filterLabel.SCHEMAAC SCHEMA AC
         filterByRange.GA4KAC on
         filterLabel.GA4KAC GA4K PacBio LR AC
-        # SPARK WES autism phenotype split
+        filterByRange.CoLoRSdbAC on
+        filterLabel.CoLoRSdbAC CoLoRSdb PacBio LR AC
+        filterByRange.SVatalogAC on
+        filterLabel.SVatalogAC SVatalog 101 10XG SR AC
+        filterByRange.Tishkoff180AC on
+        filterLabel.Tishkoff180AC Tishkoff 180 African WGS AC
+        filterByRange.WBBCAC on
+        filterLabel.WBBCAC WBBC China AC
+        filterByRange.ChinaMAPAC on
+        filterLabel.ChinaMAPAC China ChinaMAP AC
+        filterByRange.GenomeIndiaAC on
+        filterLabel.GenomeIndiaAC GenomeIndia 9.7k WGS AC
+        filterByRange.GoNLAC on
+        filterLabel.GoNLAC GoNL Netherlands ~13x SR AC
+        # Population-specific AF filters
+        # AllOfUs populations
+        filterByRange.AllOfUsAF_AFR on
+        filterLabel.AllOfUsAF_AFR AllOfUs African AF
+        filterByRange.AllOfUsAF_AMR on
+        filterLabel.AllOfUsAF_AMR AllOfUs Indigenous American AF
+        filterByRange.AllOfUsAF_EAS on
+        filterLabel.AllOfUsAF_EAS AllOfUs East Asian AF
+        filterByRange.AllOfUsAF_EUR on
+        filterLabel.AllOfUsAF_EUR AllOfUs European AF
+        filterByRange.AllOfUsAF_OCE on
+        filterLabel.AllOfUsAF_OCE AllOfUs Oceanian AF
+        filterByRange.AllOfUsAF_SAS on
+        filterLabel.AllOfUsAF_SAS AllOfUs South Asian AF
+        filterByRange.AllOfUsAC_AFR on
+        filterLabel.AllOfUsAC_AFR AllOfUs African AC
+        filterByRange.AllOfUsAC_AMR on
+        filterLabel.AllOfUsAC_AMR AllOfUs Indigenous American AC
+        filterByRange.AllOfUsAC_EAS on
+        filterLabel.AllOfUsAC_EAS AllOfUs East Asian AC
+        filterByRange.AllOfUsAC_EUR on
+        filterLabel.AllOfUsAC_EUR AllOfUs European AC
+        filterByRange.AllOfUsAC_OCE on
+        filterLabel.AllOfUsAC_OCE AllOfUs Oceanian AC
+        filterByRange.AllOfUsAC_SAS on
+        filterLabel.AllOfUsAC_SAS AllOfUs South Asian AC
+        # SFARI SPARK WES populations
         filterByRange.SPARKAF_AUT on
-        filterLabel.SPARKAF_AUT SPARK WES ASD proband AF
+        filterLabel.SPARKAF_AUT SFARI SPARK WES ASD proband AF
         filterByRange.SPARKAF_NON_AUT on
-        filterLabel.SPARKAF_NON_AUT SPARK WES Non-ASD family AF
+        filterLabel.SPARKAF_NON_AUT SFARI SPARK WES Non-ASD family AF
         filterByRange.SPARKAC_AUT on
-        filterLabel.SPARKAC_AUT SPARK WES ASD proband AC
+        filterLabel.SPARKAC_AUT SFARI SPARK WES ASD proband AC
         filterByRange.SPARKAC_NON_AUT on
-        filterLabel.SPARKAC_NON_AUT SPARK WES Non-ASD family AC
-        # SFARI WGS autism phenotype split
+        filterLabel.SPARKAC_NON_AUT SFARI SPARK WES Non-ASD family AC
+        # SFARI SPARK WGS populations
         filterByRange.SFARI_WGSAF_AUT on
-        filterLabel.SFARI_WGSAF_AUT SFARI WGS ASD proband AF
+        filterLabel.SFARI_WGSAF_AUT SFARI SPARK WGS ASD proband AF
         filterByRange.SFARI_WGSAF_NON_AUT on
-        filterLabel.SFARI_WGSAF_NON_AUT SFARI WGS Non-ASD family AF
+        filterLabel.SFARI_WGSAF_NON_AUT SFARI SPARK WGS Non-ASD family AF
         filterByRange.SFARI_WGSAC_AUT on
-        filterLabel.SFARI_WGSAC_AUT SFARI WGS ASD proband AC
+        filterLabel.SFARI_WGSAC_AUT SFARI SPARK WGS ASD proband AC
         filterByRange.SFARI_WGSAC_NON_AUT on
-        filterLabel.SFARI_WGSAC_NON_AUT SFARI WGS Non-ASD family AC
-        # SCHEMA schizophrenia case/control
-        filterByRange.SCHEMAAF_CASE on
-        filterLabel.SCHEMAAF_CASE SCHEMA Schizophrenia case AF
-        filterByRange.SCHEMAAF_CTRL on
-        filterLabel.SCHEMAAF_CTRL SCHEMA Control AF
-        filterByRange.SCHEMAAC_CASE on
-        filterLabel.SCHEMAAC_CASE SCHEMA Schizophrenia case AC
-        filterByRange.SCHEMAAC_CTRL on
-        filterLabel.SCHEMAAC_CTRL SCHEMA Control AC
-        # GREGoR affected/unaffected/unknown
+        filterLabel.SFARI_WGSAC_NON_AUT SFARI SPARK WGS Non-ASD family AC
+        # GenomeAsia SNVs populations
+        filterByRange.GenomeAsiaAF_NEA on
+        filterLabel.GenomeAsiaAF_NEA GenomeAsia SNVs Northeast Asian AF
+        filterByRange.GenomeAsiaAF_SEA on
+        filterLabel.GenomeAsiaAF_SEA GenomeAsia SNVs Southeast Asian AF
+        filterByRange.GenomeAsiaAF_SAS on
+        filterLabel.GenomeAsiaAF_SAS GenomeAsia SNVs South Asian AF
+        filterByRange.GenomeAsiaAF_OCE on
+        filterLabel.GenomeAsiaAF_OCE GenomeAsia SNVs Oceanian AF
+        filterByRange.GenomeAsiaAF_AMR on
+        filterLabel.GenomeAsiaAF_AMR GenomeAsia SNVs American AF
+        filterByRange.GenomeAsiaAF_AFR on
+        filterLabel.GenomeAsiaAF_AFR GenomeAsia SNVs African AF
+        filterByRange.GenomeAsiaAF_WER on
+        filterLabel.GenomeAsiaAF_WER GenomeAsia SNVs Western European Ref AF
+        filterByRange.GenomeAsiaAC_NEA on
+        filterLabel.GenomeAsiaAC_NEA GenomeAsia SNVs Northeast Asian AC
+        filterByRange.GenomeAsiaAC_SEA on
+        filterLabel.GenomeAsiaAC_SEA GenomeAsia SNVs Southeast Asian AC
+        filterByRange.GenomeAsiaAC_SAS on
+        filterLabel.GenomeAsiaAC_SAS GenomeAsia SNVs South Asian AC
+        filterByRange.GenomeAsiaAC_OCE on
+        filterLabel.GenomeAsiaAC_OCE GenomeAsia SNVs Oceanian AC
+        filterByRange.GenomeAsiaAC_AMR on
+        filterLabel.GenomeAsiaAC_AMR GenomeAsia SNVs American AC
+        filterByRange.GenomeAsiaAC_AFR on
+        filterLabel.GenomeAsiaAC_AFR GenomeAsia SNVs African AC
+        filterByRange.GenomeAsiaAC_WER on
+        filterLabel.GenomeAsiaAC_WER GenomeAsia SNVs Western European Ref AC
+        # NPM Singapore populations
+        filterByRange.NPMAF_Chinese on
+        filterLabel.NPMAF_Chinese NPM Singapore Singapore Chinese AF
+        filterByRange.NPMAF_Malay on
+        filterLabel.NPMAF_Malay NPM Singapore Singapore Malay AF
+        filterByRange.NPMAF_Indian on
+        filterLabel.NPMAF_Indian NPM Singapore Singapore Indian AF
+        filterByRange.NPMAC_Chinese on
+        filterLabel.NPMAC_Chinese NPM Singapore Singapore Chinese AC
+        filterByRange.NPMAC_Malay on
+        filterLabel.NPMAC_Malay NPM Singapore Singapore Malay AC
+        filterByRange.NPMAC_Indian on
+        filterLabel.NPMAC_Indian NPM Singapore Singapore Indian AC
+        # gnomAD HGDP+1kG populations
+        filterByRange.HGDP1kGAF_afr on
+        filterLabel.HGDP1kGAF_afr gnomAD HGDP+1kG African AF
+        filterByRange.HGDP1kGAF_ami on
+        filterLabel.HGDP1kGAF_ami gnomAD HGDP+1kG Amish AF
+        filterByRange.HGDP1kGAF_amr on
+        filterLabel.HGDP1kGAF_amr gnomAD HGDP+1kG Latino AF
+        filterByRange.HGDP1kGAF_asj on
+        filterLabel.HGDP1kGAF_asj gnomAD HGDP+1kG Ashkenazi Jewish AF
+        filterByRange.HGDP1kGAF_eas on
+        filterLabel.HGDP1kGAF_eas gnomAD HGDP+1kG East Asian AF
+        filterByRange.HGDP1kGAF_fin on
+        filterLabel.HGDP1kGAF_fin gnomAD HGDP+1kG Finnish AF
+        filterByRange.HGDP1kGAF_mid on
+        filterLabel.HGDP1kGAF_mid gnomAD HGDP+1kG Middle Eastern AF
+        filterByRange.HGDP1kGAF_nfe on
+        filterLabel.HGDP1kGAF_nfe gnomAD HGDP+1kG Non-Finnish European AF
+        filterByRange.HGDP1kGAF_oth on
+        filterLabel.HGDP1kGAF_oth gnomAD HGDP+1kG Other AF
+        filterByRange.HGDP1kGAF_sas on
+        filterLabel.HGDP1kGAF_sas gnomAD HGDP+1kG South Asian AF
+        filterByRange.HGDP1kGAC_afr on
+        filterLabel.HGDP1kGAC_afr gnomAD HGDP+1kG African AC
+        filterByRange.HGDP1kGAC_ami on
+        filterLabel.HGDP1kGAC_ami gnomAD HGDP+1kG Amish AC
+        filterByRange.HGDP1kGAC_amr on
+        filterLabel.HGDP1kGAC_amr gnomAD HGDP+1kG Latino AC
+        filterByRange.HGDP1kGAC_asj on
+        filterLabel.HGDP1kGAC_asj gnomAD HGDP+1kG Ashkenazi Jewish AC
+        filterByRange.HGDP1kGAC_eas on
+        filterLabel.HGDP1kGAC_eas gnomAD HGDP+1kG East Asian AC
+        filterByRange.HGDP1kGAC_fin on
+        filterLabel.HGDP1kGAC_fin gnomAD HGDP+1kG Finnish AC
+        filterByRange.HGDP1kGAC_mid on
+        filterLabel.HGDP1kGAC_mid gnomAD HGDP+1kG Middle Eastern AC
+        filterByRange.HGDP1kGAC_nfe on
+        filterLabel.HGDP1kGAC_nfe gnomAD HGDP+1kG Non-Finnish European AC
+        filterByRange.HGDP1kGAC_oth on
+        filterLabel.HGDP1kGAC_oth gnomAD HGDP+1kG Other AC
+        filterByRange.HGDP1kGAC_sas on
+        filterLabel.HGDP1kGAC_sas gnomAD HGDP+1kG South Asian AC
+        # GREGoR populations
         filterByRange.GREGoRAF_AFF on
         filterLabel.GREGoRAF_AFF GREGoR Affected AF
         filterByRange.GREGoRAF_UNA on
         filterLabel.GREGoRAF_UNA GREGoR Unaffected AF
         filterByRange.GREGoRAF_UNK on
         filterLabel.GREGoRAF_UNK GREGoR Unknown AF
         filterByRange.GREGoRAC_AFF on
         filterLabel.GREGoRAC_AFF GREGoR Affected AC
         filterByRange.GREGoRAC_UNA on
         filterLabel.GREGoRAC_UNA GREGoR Unaffected AC
         filterByRange.GREGoRAC_UNK on
         filterLabel.GREGoRAC_UNK GREGoR Unknown AC
+        # SCHEMA populations
+        filterByRange.SCHEMAAF_CASE on
+        filterLabel.SCHEMAAF_CASE SCHEMA Schizophrenia case AF
+        filterByRange.SCHEMAAF_CTRL on
+        filterLabel.SCHEMAAF_CTRL SCHEMA Control AF
+        filterByRange.SCHEMAAC_CASE on
+        filterLabel.SCHEMAAC_CASE SCHEMA Schizophrenia case AC
+        filterByRange.SCHEMAAC_CTRL on
+        filterLabel.SCHEMAAC_CTRL SCHEMA Control AC
+        # WBBC China populations
+        filterByRange.WBBCAF_North on
+        filterLabel.WBBCAF_North WBBC China North Han AF
+        filterByRange.WBBCAF_Central on
+        filterLabel.WBBCAF_Central WBBC China Central Han AF
+        filterByRange.WBBCAF_South on
+        filterLabel.WBBCAF_South WBBC China South Han AF
+        filterByRange.WBBCAF_Lingnan on
+        filterLabel.WBBCAF_Lingnan WBBC China Lingnan Han AF
+        filterByRange.WBBCAC_North on
+        filterLabel.WBBCAC_North WBBC China North Han AC
+        filterByRange.WBBCAC_Central on
+        filterLabel.WBBCAC_Central WBBC China Central Han AC
+        filterByRange.WBBCAC_South on
+        filterLabel.WBBCAC_South WBBC China South Han AC
+        filterByRange.WBBCAC_Lingnan on
+        filterLabel.WBBCAC_Lingnan WBBC China Lingnan Han AC
         skipEmptyFields on
 
         track varFreqsArray
         shortLabel Genotyping Array Databases Combined
         longLabel SNV Frequencies: Genotyping-array cohorts combined (TPMI, Mexico Biobank, UK Biobank imputed)
         type bigBed 9 +
         parent varFreqs off
         bigDataUrl /gbdb/$D/varFreqs/_array/varFreqsArray.bb
         visibility hide
         itemRgb on
         maxWindowToDraw 5000000
         priority 0.2
         mouseOver <b>Var:</b> $name<br><b>AA change:</b> $aaChange<br><b>Var type:</b> $varType<br><b>Conseq:</b> $consequence<br><b>Max AF:</b> $maxAF<br><b>Total AC:</b> $totalAC<br><b>Sources:</b> $sources
         filterValues.sources TPMI|TPMI Taiwan,MexBB|Mexico Biobank,UKBB|UK Biobank imputed
         filterType.sources multipleListOr