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 ${}. New description pages for both tracks. refs #36642 diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra index a2c2053d2e8..1585bd1c296 100644 --- src/hg/makeDb/trackDb/human/varFreqs.ra +++ src/hg/makeDb/trackDb/human/varFreqs.ra @@ -1,825 +1,1076 @@ track varFreqs shortLabel SNV Frequencies longLabel SNV Frequencies from various cohorts or national projects group varRep type bed 12 visibility hide superTrack on - track varFreqsAll - shortLabel All Databases Combined - longLabel SNV Frequencies: All Databases Combined with Consequence Annotations + track varFreqsAffected + shortLabel Affected/Case Individuals + longLabel SNV Frequencies: variants in ~130,000 affected or case individuals (autism, schizophrenia, rare disease cohorts) type bigBed 9 + parent varFreqs on - bigDataUrl /gbdb/$D/varFreqs/_all/varFreqsAll.bb + bigDataUrl /gbdb/$D/varFreqs/_affected/varFreqsAffected.bb visibility pack itemRgb on maxWindowToDraw 5000000 priority 0.1 - mouseOver Var: $name
AA change: $aaChange
Var type: $varType
Conseq: $consequence
Max AF: $maxAF
Total AC: $totalAC
Sources: $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 Var: ${name}
AA change: ${aaChange}
Var type: ${varType}
Conseq: ${consequence}
Affected AF: ${affectedAF}
Affected AC: ${affectedAC}
Affected cohorts: ${affectedCohorts}
Background AF: ${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 Var: $name
AA change: $aaChange
Var type: $varType
Conseq: $consequence
Max AF: $maxAF
Total AC: $totalAC
Sources: $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 Var: ${name}
AA change: ${aaChange}
Var type: ${varType}
Conseq: ${consequence}
Background AF: ${backgroundAF}
Background AC: ${backgroundAC}
Sources: ${backgroundSources}
Affected AF: ${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 Var: $name
AA change: $aaChange
Var type: $varType
Conseq: $consequence
Max AF: $maxAF
Total AC: $totalAC
Sources: $sources filterValues.sources TPMI|TPMI Taiwan,MexBB|Mexico Biobank,UKBB|UK Biobank imputed filterType.sources multipleListOr filterLabel.sources Source Database filterValues.varType SNV|SNV,INS|Insertion,DEL|Deletion,MNV|MNV filterLabel.varType Variant Type filterValues.consequence missense|Missense,synonymous|Synonymous,stop_gained|Stop Gained,frameshift|Frameshift,splice_donor|Splice Donor,splice_acceptor|Splice Acceptor,intron|Intron,3_prime_utr|3' UTR,5_prime_utr|5' UTR,non_coding|Non-coding,.|Intergenic,others|Other filterType.consequence multipleListOr filterLabel.consequence Consequence filterByRange.refLen on filterLabel.refLen Reference Length filterByRange.altLen on filterLabel.altLen Alternate Length filterByRange.varLen on filterLabel.varLen Length Change filterByRange.maxAF on filterLabel.maxAF Max Allele Frequency filterLimits.maxAF 0:1 filterByRange.totalAC on filterLabel.totalAC Total Allele Count (all databases) filterByRange.TPMIAF on filterLabel.TPMIAF TPMI Taiwan AF filterByRange.MexBBAF on filterLabel.MexBBAF Mexico Biobank AF filterByRange.UKBBAF on filterLabel.UKBBAF UK Biobank imputed AF filterByRange.TPMIAC on filterLabel.TPMIAC TPMI Taiwan AC filterByRange.MexBBAC on filterLabel.MexBBAC Mexico Biobank AC filterByRange.UKBBAC on filterLabel.UKBBAC UK Biobank imputed AC skipEmptyFields on track allofus shortLabel AllOfUs v7 245k WGS longLabel SNV Frequencies: AllOfUs v7 - 245k WGS, local-ancestry-stratified, AC>=20 type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_allofus/allOfUs.locAncFreq.vcf.gz dataVersion V7 visibility hide tableBrowser off priority 0.5 #track me #shortLabel Regeneron Million Exomes 983k WES #longLabel SNV Frequencies: Regeneron One Million Exomes (ME) Project - 983k WGS #parent varFreqs on #bigDataUrl /gbdb/$D/varFreqs/me/me.freq.vcf.gz #visibility pack #type vcfTabix #hapClusterEnabled true #dataVersion 10/04/2023, v1.1.3 #tableBrowser off #priority 1 track topmed shortLabel NHLBI TOPMed 10 151k WGS longLabel SNV Frequencies: NHLBI TOPMed - 151k WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_topmed/topmed10.vcf.gz dataVersion Freeze 10 tableBrowser off visibility hide priority 2 track sfariSparkExomes shortLabel SFARI SPARK 140k WES longLabel SNV Frequencies: SFARI SPARK - 140k WES type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_sfari/SPARK.iWES_v3.2024_08.deepvariant.norm.vcf.gz dataVersion iWES v3 2024_08 tableBrowser off visibility hide priority 2.5 track sfariSparkWgs shortLabel SFARI SPARK 12k WGS longLabel SNV Frequencies: SFARI SPARK - 12,519 WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_sfari/wgs_12519_genome.deepvariant.norm.vcf.gz dataVersion iWGS v1.1 visibility hide priority 2.5 html sfariSparkExomes tableBrowser off #track mcps #shortLabel Mexico City Prospective Study 10k WGS+141k WES #longLabel SNV Frequencies: Mexico City Prospective Study (MCPS) #tableBrowser off #parent varFreqs on #bigDataUrl /gbdb/$D/varFreqs/mcps/mcps.freq.vcf.gz #visibility pack #type vcfTabix #dataVersion May 2023 (v1.2.0) #priority 3 track tommo60kjpn shortLabel Japan ToMMo 61k WGS longLabel SNV Frequencies: Japan 61k - ToMMo SNV+Indels type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/tommo61kjpn/tommo-61kjpn-20250616-GRCh38-snvindel-af-autosome.vcf.gz visibility hide dataVersion 2025-06-16 priority 5 track wbbc shortLabel China WBBC 4.5k WGS longLabel SNV Frequencies: Westlake BioBank for Chinese - 4,480 WGS, 4 regional Han groups type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/wbbc/wbbc.vcf.gz visibility hide dataVersion Phase I v20210103 priority 5.5 track chinamap shortLabel China ChinaMAP 10.5k WGS longLabel SNV Frequencies: ChinaMAP phase 1 - 10,588 WGS at ~40x, Chinese natural population type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_chinamap/chinamap.vcf.gz visibility hide dataVersion Phase 1 (v2020-03.beta) priority 5.55 tableBrowser off track tpmi shortLabel Taiwan TPMI Axiom array longLabel SNV Frequencies: Taiwan Precision Medicine Initiative - Axiom TPM1 chip, Han Chinese type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_tpmi/tpmi.vcf.gz visibility hide dataVersion Axiom TPM1 2022-06 priority 5.6 tableBrowser off track alfaVcf shortLabel NCBI ALFA 408k mixed longLabel SNV Frequencies: NCBI ALFA (dbGaP data) - 408k mixed WGS/WES/array, 163M variants type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA.vcf.gz visibility hide dataVersion R4 priority 4.1 url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab urlLabel NCBI Variation Page track finngen parent varFreqs on visibility hide type vcfTabix shortLabel FinnGen R12 500k imputed longLabel SNV Frequencies: Finland FinnGen - 500k samples, arrays, imputation used 8.5k WGS priority 4.5 bigDataUrl /gbdb/$D/varFreqs/_finngen/finnge_R12_annotated_variants_v1.vcf.gz dataVersion R12 tableBrowser off track ukbb parent varFreqs on visibility hide type vcfTabix shortLabel UK Biobank 361k imputed longLabel SNV Frequencies: UK Biobank Genotypes - 361k White British, Neale Lab Round 2 imputed priority 4.6 bigDataUrl /gbdb/$D/varFreqs/ukbb/ukbb.vcf.gz dataVersion Neale Lab R2 08-2018 track swefreq parent varFreqs on visibility hide type vcfTabix shortLabel Sweden SweGen 1k WGS longLabel SNV Frequencies: Sweden SweGen - 1k WGS priority 4.7 bigDataUrl /gbdb/$D/varFreqs/_swefreq/swegen_frequencies_fixploidy_GRCh38_20190204.vcf.gz dataVersion 20251201 tableBrowser off track gonl parent varFreqs on visibility hide type vcfTabix shortLabel Netherlands GoNL 498 WGS longLabel SNV Frequencies: Genome of the Netherlands - 250 Dutch trios priority 4.75 bigDataUrl /gbdb/$D/varFreqs/gonl/gonl.vcf.gz dataVersion GRCh38 1.0 track mgrb shortLabel Australia MGRB 4k WGS longLabel SNV Frequencies: Australia Medical Genome Reference Bank - 4,011 WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_mgrb/MGRB.phase3.GRCh38.norm.vcf.gz dataVersion Phase 3 visibility hide # no downloads as per Matt Hobbs email Jan 28 2026 tableBrowser off track gasp shortLabel GenomeAsia 1.7k SNVs longLabel SNV Frequencies: GenomeAsia Pilot - Substitutions type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga100k/ga100k.subst.vcf.gz visibility hide dataVersion Pilot 2019 (lifted to hg38, May 2026) track gaspIndel shortLabel GenomeAsia 1.7k Indels longLabel SNV Frequencies: GenomeAsia Pilot - Indels type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga100k/ga100k.indels.vcf.gz visibility hide dataVersion Pilot 2019 (lifted to hg38, May 2026) html gasp track abraom shortLabel Brazil ABraOM 1k WGS longLabel SNV Frequencies: ABraOM Brazil - 1,171 unrelated individuals type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/abraom/abraom.vcf.gz visibility hide dataVersion SABE-WGS-1171 Sep 2020 track indigenomes shortLabel India IndiGenomes 1k WGS longLabel SNV Frequencies: IndiGenomes India - 1,029 samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/indigenomes/IndiGenomes_Variants.vcf.gz visibility hide dataVersion IndiGen pilot (Jain 2021) track genomeindia shortLabel India GenomeIndia 9.7k WGS longLabel SNV Frequencies: GenomeIndia - 9,768 WGS, 83 populations (Bhattacharyya 2025) type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_genomeindia/genomeindia.vcf.gz visibility hide dataVersion 9768GI_SummaryStats (Apr 2025) priority 4.8 track kova shortLabel Korea KOVA 5.3k mixed longLabel SNV Frequencies: KOVA Korea - 5305 samples, 1.9k WGS+3.4k WES type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_kova/kova.v7.vcf.gz visibility hide tableBrowser off dataVersion V7 track npm shortLabel Singapore NPM 9.7k WGS longLabel SNV Frequencies: NPM Singapore - 9,770 WGS samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_npm/SG10K_Health_r5.3.2.sites.vcf.bgz visibility hide tableBrowser off dataVersion r5.3.2 track hrc shortLabel HRC 30k WGS longLabel SNV Frequencies: Haplotype Reference Consortium - 30k WGS (excl. 1000 Genomes) type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/hrc/hrc.vcf.gz visibility hide dataVersion r1.1 track saudi shortLabel Saudi Genome 302 WGS longLabel SNV Frequencies: Saudi Genome Project - 302 WGS samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/saudi/saudi.vcf.gz visibility hide dataVersion SHGP (figshare 51297884, 2025) track schema shortLabel SCHEMA 121k WES Sz longLabel SNV Frequencies: SCHEMA Schizophrenia Exome Meta-Analysis - WES 24k cases, 97k controls type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/schema/SCHEMA_variant_results_withAF.vcf.gz visibility hide dataVersion 2022 priority 4.9 url https://schema.broadinstitute.org/ urlLabel SCHEMA Browser track mxbFreq shortLabel Mexico Biobank 6k Array longLabel SNV Frequencies: Mexico Biobank - 6,011 individuals, genotyping array type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_mxb/mxb.freq.vcf.gz visibility hide dataVersion Nov 2025 (hg38 lift) tableBrowser off priority 6 track sgdpFreq shortLabel SGDP 279 WGS longLabel SNV Frequencies: Simons Genome Diversity Project - 279 WGS, 142 populations type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/sgdpFreq/sgdp.freq.vcf.gz visibility hide dataVersion 2016-12-07 (hg38 lift) priority 7 track gregor shortLabel GREGoR R4 3.6k WGS longLabel SNV Frequencies: GREGoR Consortium - Release 4, 3,624 WGS samples, rare disease families type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/gregor/gregor.vcf.gz visibility hide dataVersion R04 (Oct 2025) priority 8 track hgdp1kFreq shortLabel gnomAD HGDP+1kG 4k WGS longLabel SNV Frequencies: gnomAD HGDP + 1000 Genomes - 4,094 WGS, 80 populations type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/hgdp1kFreq/hgdp1k.freq.vcf.gz visibility hide dataVersion v3.1.2 priority 8 track ga4kSnv shortLabel GA4K 552 PacBio LR longLabel SNV Frequencies: GA4K Children's Mercy - 552 PacBio HiFi WGS, pediatric RD type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga4k/ga4kSnv.vcf.gz visibility hide dataVersion Cohen 2022 release priority 9 track colorsDbSnv shortLabel CoLoRSdb 1k LR SNV/Ind longLabel SNV Frequencies: CoLoRSdb v1.2.0 - 1,027 PacBio HiFi WGS, SNV/indel callset type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/colorsDb/colorsDbSnv.vcf.gz visibility hide dataVersion v1.2.0 priority 9.5 track svatalogSnv shortLabel SVatalog 101 WGS longLabel SNV Frequencies: GWAS SVatalog - 101 samples, 10X Genomics linked-read SNPs type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/svatalog/svatalog.vcf.gz visibility hide dataVersion Chirmade 2025 release priority 10 track tishkoff180 shortLabel 12 Afr Pops 180 WGS longLabel SNV Frequencies: 180 WGS from 12 Indigenous African Populations (Fan 2023) type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_tishkoff/tishkoff180.vcf.gz visibility hide dataVersion Cell 2023 (hg19 lift) tableBrowser off priority 7.5