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