68c5b3b5dfc4053ff78a6b1d236bd1ac90251cfa lrnassar Mon Jun 1 14:40:45 2026 -0700 varFreqs: description pages for the three combined tracks and "SNV" rename sweep. Add varFreqsDisease.html and varFreqsArray.html so the two new combined tracks have full Description/Display/Methods/Data Access/References. Add a Caveats section on varFreqsArray about chip-data quality vs sequencing. Update varFreqsAll.html and the supertrack varFreqs.html to reflect the three-combined-track family (cross-links between siblings, new "Combined Tracks" section, new table rows, and updated source/variant counts). Add a GoNL row to the supertrack table. Sweep 37 subtrack longLabels and four cross-referencing description pages (colorsDbSnv.html, mei.html, meiSwegen.html, phasedVars.html) from "Variant Frequencies:" to "SNV Frequencies:" to match the supertrack shortLabel. refs #36642 diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra index 03108bfab9b..a2c2053d2e8 100644 --- src/hg/makeDb/trackDb/human/varFreqs.ra +++ src/hg/makeDb/trackDb/human/varFreqs.ra @@ -1,825 +1,825 @@ 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 Variant Frequencies: All Databases Combined with Consequence Annotations + longLabel SNV Frequencies: All Databases Combined with Consequence Annotations type bigBed 9 + parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_all/varFreqsAll.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 # 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 filterByRange.altLen on filterLabel.altLen Alternate Length 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) # Per-database AF filters filterByRange.AllOfUsAF on filterLabel.AllOfUsAF AllOfUs AF filterByRange.SPARKAF on filterLabel.SPARKAF SPARK WES AF filterByRange.SFARI_WGSAF on filterLabel.SFARI_WGSAF SFARI WGS AF filterByRange.GenomeAsiaAF on filterLabel.GenomeAsiaAF GenomeAsia SNVs AF filterByRange.GenomeAsiaIndelAF on filterLabel.GenomeAsiaIndelAF GenomeAsia Indels 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) 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 filterByRange.SFARI_WGSAC on filterLabel.SFARI_WGSAC SFARI WGS AC filterByRange.GenomeAsiaAC on filterLabel.GenomeAsiaAC GenomeAsia SNVs AC filterByRange.GenomeAsiaIndelAC on filterLabel.GenomeAsiaIndelAC GenomeAsia Indels 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) 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. filterByRange.AllOfUsAF_AFR on filterLabel.AllOfUsAF_AFR AllOfUs African AF (local ancestry) filterByRange.AllOfUsAF_AMR on filterLabel.AllOfUsAF_AMR AllOfUs Indigenous American AF (local ancestry) filterByRange.AllOfUsAF_EAS on filterLabel.AllOfUsAF_EAS AllOfUs East Asian AF (local ancestry) filterByRange.AllOfUsAF_EUR on filterLabel.AllOfUsAF_EUR AllOfUs European AF (local ancestry) filterByRange.AllOfUsAF_OCE on filterLabel.AllOfUsAF_OCE AllOfUs Oceanian AF (local ancestry) filterByRange.AllOfUsAF_SAS on filterLabel.AllOfUsAF_SAS AllOfUs South Asian AF (local ancestry) filterByRange.AllOfUsAC_AFR on filterLabel.AllOfUsAC_AFR AllOfUs African AC (local ancestry) filterByRange.AllOfUsAC_AMR on filterLabel.AllOfUsAC_AMR AllOfUs Indigenous American AC (local ancestry) filterByRange.AllOfUsAC_EAS on filterLabel.AllOfUsAC_EAS AllOfUs East Asian AC (local ancestry) filterByRange.AllOfUsAC_EUR on filterLabel.AllOfUsAC_EUR AllOfUs European AC (local ancestry) filterByRange.AllOfUsAC_OCE on filterLabel.AllOfUsAC_OCE AllOfUs Oceanian AC (local ancestry) filterByRange.AllOfUsAC_SAS on filterLabel.AllOfUsAC_SAS AllOfUs South Asian AC (local ancestry) # GenomeAsia SNVs populations (7 groups in source VCF) 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. filterByRange.HGDP1kGAF_afr on filterLabel.HGDP1kGAF_afr gnomAD v3.1.2 African AF (full release) filterByRange.HGDP1kGAF_ami on filterLabel.HGDP1kGAF_ami gnomAD v3.1.2 Amish AF (full release) filterByRange.HGDP1kGAF_amr on filterLabel.HGDP1kGAF_amr gnomAD v3.1.2 Latino AF (full release) filterByRange.HGDP1kGAF_asj on filterLabel.HGDP1kGAF_asj gnomAD v3.1.2 Ashkenazi Jewish AF (full release) filterByRange.HGDP1kGAF_eas on filterLabel.HGDP1kGAF_eas gnomAD v3.1.2 East Asian AF (full release) filterByRange.HGDP1kGAF_fin on filterLabel.HGDP1kGAF_fin gnomAD v3.1.2 Finnish AF (full release) filterByRange.HGDP1kGAF_mid on filterLabel.HGDP1kGAF_mid gnomAD v3.1.2 Middle Eastern AF (full release) filterByRange.HGDP1kGAF_nfe on filterLabel.HGDP1kGAF_nfe gnomAD v3.1.2 Non-Finnish European AF (full release) filterByRange.HGDP1kGAF_oth on filterLabel.HGDP1kGAF_oth gnomAD v3.1.2 Other AF (full release) filterByRange.HGDP1kGAF_sas on filterLabel.HGDP1kGAF_sas gnomAD v3.1.2 South Asian AF (full release) filterByRange.HGDP1kGAC_afr on filterLabel.HGDP1kGAC_afr gnomAD v3.1.2 African AC (full release) filterByRange.HGDP1kGAC_ami on filterLabel.HGDP1kGAC_ami gnomAD v3.1.2 Amish AC (full release) filterByRange.HGDP1kGAC_amr on filterLabel.HGDP1kGAC_amr gnomAD v3.1.2 Latino AC (full release) filterByRange.HGDP1kGAC_asj on filterLabel.HGDP1kGAC_asj gnomAD v3.1.2 Ashkenazi Jewish AC (full release) filterByRange.HGDP1kGAC_eas on filterLabel.HGDP1kGAC_eas gnomAD v3.1.2 East Asian AC (full release) filterByRange.HGDP1kGAC_fin on filterLabel.HGDP1kGAC_fin gnomAD v3.1.2 Finnish AC (full release) filterByRange.HGDP1kGAC_mid on filterLabel.HGDP1kGAC_mid gnomAD v3.1.2 Middle Eastern AC (full release) filterByRange.HGDP1kGAC_nfe on filterLabel.HGDP1kGAC_nfe gnomAD v3.1.2 Non-Finnish European AC (full release) filterByRange.HGDP1kGAC_oth on filterLabel.HGDP1kGAC_oth gnomAD v3.1.2 Other AC (full release) filterByRange.HGDP1kGAC_sas on filterLabel.HGDP1kGAC_sas gnomAD v3.1.2 South Asian AC (full release) # 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 # WBBC China populations filterByRange.WBBCAF_North on filterLabel.WBBCAF_North WBBC North Han AF filterByRange.WBBCAF_Central on filterLabel.WBBCAF_Central WBBC Central Han AF filterByRange.WBBCAF_South on filterLabel.WBBCAF_South WBBC South Han AF filterByRange.WBBCAF_Lingnan on filterLabel.WBBCAF_Lingnan WBBC Lingnan Han AF filterByRange.WBBCAC_North on filterLabel.WBBCAC_North WBBC North Han AC filterByRange.WBBCAC_Central on filterLabel.WBBCAC_Central WBBC Central Han AC filterByRange.WBBCAC_South on filterLabel.WBBCAC_South WBBC 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 skipEmptyFields on track varFreqsDisease shortLabel Disease-related Databases Combined - longLabel Variant Frequencies: Disease-related cohorts combined (autism, schizophrenia, rare disease, NHLBI heart/lung/blood) + longLabel SNV Frequencies: Disease-related cohorts combined (autism, schizophrenia, rare disease, NHLBI heart/lung/blood) type bigBed 9 + parent varFreqs off bigDataUrl /gbdb/$D/varFreqs/_disease/varFreqsDisease.bb visibility hide 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 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) # Per-database AF filters filterByRange.SPARKAF on filterLabel.SPARKAF SPARK WES AF filterByRange.SFARI_WGSAF on filterLabel.SFARI_WGSAF SFARI WGS AF filterByRange.TOPMedAF on filterLabel.TOPMedAF TOPMed AF filterByRange.SCHEMAAF on filterLabel.SCHEMAAF SCHEMA AF filterByRange.GREGoRAF on filterLabel.GREGoRAF GREGoR AF filterByRange.GA4KAF on filterLabel.GA4KAF GA4K PacBio LR AF # Per-database AC filters filterByRange.SPARKAC on filterLabel.SPARKAC SPARK WES AC filterByRange.SFARI_WGSAC on filterLabel.SFARI_WGSAC SFARI WGS AC filterByRange.TOPMedAC on filterLabel.TOPMedAC TOPMed AC filterByRange.SCHEMAAC on filterLabel.SCHEMAAC SCHEMA AC filterByRange.GREGoRAC on filterLabel.GREGoRAC GREGoR AC filterByRange.GA4KAC on filterLabel.GA4KAC GA4K PacBio LR AC # SPARK WES autism phenotype split 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 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 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 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 skipEmptyFields on track varFreqsArray shortLabel Genotyping Array Databases Combined - longLabel Variant Frequencies: Genotyping-array cohorts combined (TPMI, Mexico Biobank, UK Biobank imputed) + 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> $sources filterValues.sources TPMI|TPMI Taiwan,MexBB|Mexico Biobank,UKBB|UK Biobank imputed filterType.sources multipleListOr filterLabel.sources Source Database filterValues.varType SNV|SNV,INS|Insertion,DEL|Deletion,MNV|MNV filterLabel.varType Variant Type filterValues.consequence missense|Missense,synonymous|Synonymous,stop_gained|Stop Gained,frameshift|Frameshift,splice_donor|Splice Donor,splice_acceptor|Splice Acceptor,intron|Intron,3_prime_utr|3' UTR,5_prime_utr|5' UTR,non_coding|Non-coding,.|Intergenic,others|Other filterType.consequence multipleListOr filterLabel.consequence Consequence filterByRange.refLen on filterLabel.refLen Reference Length filterByRange.altLen on filterLabel.altLen Alternate Length filterByRange.varLen on filterLabel.varLen Length Change filterByRange.maxAF on filterLabel.maxAF Max Allele Frequency filterLimits.maxAF 0:1 filterByRange.totalAC on filterLabel.totalAC Total Allele Count (all databases) filterByRange.TPMIAF on filterLabel.TPMIAF TPMI Taiwan AF filterByRange.MexBBAF on filterLabel.MexBBAF Mexico Biobank AF filterByRange.UKBBAF on filterLabel.UKBBAF UK Biobank imputed AF filterByRange.TPMIAC on filterLabel.TPMIAC TPMI Taiwan AC filterByRange.MexBBAC on filterLabel.MexBBAC Mexico Biobank AC filterByRange.UKBBAC on filterLabel.UKBBAC UK Biobank imputed AC skipEmptyFields on track allofus shortLabel AllOfUs v7 245k WGS - longLabel Variant Frequencies: AllOfUs v7 - 245k WGS, local-ancestry-stratified, AC>=20 + longLabel SNV Frequencies: AllOfUs v7 - 245k WGS, local-ancestry-stratified, AC>=20 type vcfTabix parent varFreqs on bigDataUrl /gbdb/$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 Variant Frequencies: Regeneron One Million Exomes (ME) Project - 983k WGS + #longLabel SNV Frequencies: Regeneron One Million Exomes (ME) Project - 983k WGS #parent varFreqs on #bigDataUrl /gbdb/$D/varFreqs/me/me.freq.vcf.gz #visibility pack #type vcfTabix #hapClusterEnabled true #dataVersion 10/04/2023, v1.1.3 #tableBrowser off #priority 1 track topmed shortLabel NHLBI TOPMed 10 151k WGS - longLabel Variant Frequencies: NHLBI TOPMed - 151k WGS + longLabel SNV Frequencies: NHLBI TOPMed - 151k WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_topmed/topmed10.vcf.gz dataVersion Freeze 10 tableBrowser off visibility hide priority 2 track sfariSparkExomes shortLabel SFARI SPARK 140k WES - longLabel Variant Frequencies: SFARI SPARK - 140k WES + longLabel SNV Frequencies: SFARI SPARK - 140k WES type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_sfari/SPARK.iWES_v3.2024_08.deepvariant.norm.vcf.gz dataVersion iWES v3 2024_08 tableBrowser off visibility hide priority 2.5 track sfariSparkWgs shortLabel SFARI SPARK 12k WGS - longLabel Variant Frequencies: SFARI SPARK - 12,519 WGS + longLabel SNV Frequencies: SFARI SPARK - 12,519 WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$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 Variant Frequencies: Mexico City Prospective Study (MCPS) + #longLabel SNV Frequencies: Mexico City Prospective Study (MCPS) #tableBrowser off #parent varFreqs on #bigDataUrl /gbdb/$D/varFreqs/mcps/mcps.freq.vcf.gz #visibility pack #type vcfTabix #dataVersion May 2023 (v1.2.0) #priority 3 track tommo60kjpn shortLabel Japan ToMMo 61k WGS - longLabel Variant Frequencies: Japan 61k - ToMMo SNV+Indels + longLabel SNV Frequencies: Japan 61k - ToMMo SNV+Indels type vcfTabix parent varFreqs on bigDataUrl /gbdb/$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 Variant Frequencies: Westlake BioBank for Chinese - 4,480 WGS, 4 regional Han groups + longLabel SNV Frequencies: Westlake BioBank for Chinese - 4,480 WGS, 4 regional Han groups type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/wbbc/wbbc.vcf.gz visibility hide dataVersion Phase I v20210103 priority 5.5 track chinamap shortLabel China ChinaMAP 10.5k WGS - longLabel Variant Frequencies: ChinaMAP phase 1 - 10,588 WGS at ~40x, Chinese natural population + longLabel SNV Frequencies: ChinaMAP phase 1 - 10,588 WGS at ~40x, Chinese natural population type vcfTabix parent varFreqs on bigDataUrl /gbdb/$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 Variant Frequencies: Taiwan Precision Medicine Initiative - Axiom TPM1 chip, Han Chinese + longLabel SNV Frequencies: Taiwan Precision Medicine Initiative - Axiom TPM1 chip, Han Chinese type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_tpmi/tpmi.vcf.gz visibility hide dataVersion Axiom TPM1 2022-06 priority 5.6 tableBrowser off track alfaVcf shortLabel NCBI ALFA 408k mixed - longLabel Variant Frequencies: NCBI ALFA (dbGaP data) - 408k mixed WGS/WES/array, 163M variants + longLabel SNV Frequencies: NCBI ALFA (dbGaP data) - 408k mixed WGS/WES/array, 163M variants type vcfTabix parent varFreqs on bigDataUrl /gbdb/$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 Variant Frequencies: Finland FinnGen - 500k samples, arrays, imputation used 8.5k WGS + longLabel SNV Frequencies: Finland FinnGen - 500k samples, arrays, imputation used 8.5k WGS priority 4.5 bigDataUrl /gbdb/$D/varFreqs/_finngen/finnge_R12_annotated_variants_v1.vcf.gz dataVersion R12 tableBrowser off track ukbb parent varFreqs on visibility hide type vcfTabix shortLabel UK Biobank 361k imputed - longLabel Variant Frequencies: UK Biobank Genotypes - 361k White British, Neale Lab Round 2 imputed + longLabel SNV Frequencies: UK Biobank Genotypes - 361k White British, Neale Lab Round 2 imputed priority 4.6 bigDataUrl /gbdb/$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 Variant Frequencies: Sweden SweGen - 1k WGS + longLabel SNV Frequencies: Sweden SweGen - 1k WGS priority 4.7 bigDataUrl /gbdb/$D/varFreqs/_swefreq/swegen_frequencies_fixploidy_GRCh38_20190204.vcf.gz dataVersion 20251201 tableBrowser off track gonl parent varFreqs on visibility hide type vcfTabix shortLabel Netherlands GoNL 498 WGS - longLabel Variant Frequencies: Genome of the Netherlands - 250 Dutch trios + longLabel SNV Frequencies: Genome of the Netherlands - 250 Dutch trios priority 4.75 bigDataUrl /gbdb/$D/varFreqs/gonl/gonl.vcf.gz dataVersion GRCh38 1.0 track mgrb shortLabel Australia MGRB 4k WGS - longLabel Variant Frequencies: Australia Medical Genome Reference Bank - 4,011 WGS + longLabel SNV Frequencies: Australia Medical Genome Reference Bank - 4,011 WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_mgrb/MGRB.phase3.GRCh38.norm.vcf.gz dataVersion Phase 3 visibility hide # no downloads as per Matt Hobbs email Jan 28 2026 tableBrowser off track gasp shortLabel GenomeAsia 1.7k SNVs - longLabel Variant Frequencies: GenomeAsia Pilot - Substitutions + longLabel SNV Frequencies: GenomeAsia Pilot - Substitutions type vcfTabix parent varFreqs on bigDataUrl /gbdb/$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 Variant Frequencies: GenomeAsia Pilot - Indels + longLabel SNV Frequencies: GenomeAsia Pilot - Indels type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga100k/ga100k.indels.vcf.gz visibility hide dataVersion Pilot 2019 (lifted to hg38, May 2026) html gasp track abraom shortLabel Brazil ABraOM 1k WGS - longLabel Variant Frequencies: ABraOM Brazil - 1,171 unrelated individuals + longLabel SNV Frequencies: ABraOM Brazil - 1,171 unrelated individuals type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/abraom/abraom.vcf.gz visibility hide dataVersion SABE-WGS-1171 Sep 2020 track indigenomes shortLabel India IndiGenomes 1k WGS - longLabel Variant Frequencies: IndiGenomes India - 1,029 samples + longLabel SNV Frequencies: IndiGenomes India - 1,029 samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/indigenomes/IndiGenomes_Variants.vcf.gz visibility hide dataVersion IndiGen pilot (Jain 2021) track genomeindia shortLabel India GenomeIndia 9.7k WGS - longLabel Variant Frequencies: GenomeIndia - 9,768 WGS, 83 populations (Bhattacharyya 2025) + longLabel SNV Frequencies: GenomeIndia - 9,768 WGS, 83 populations (Bhattacharyya 2025) type vcfTabix parent varFreqs on bigDataUrl /gbdb/$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 Variant Frequencies: KOVA Korea - 5305 samples, 1.9k WGS+3.4k WES + longLabel SNV Frequencies: KOVA Korea - 5305 samples, 1.9k WGS+3.4k WES type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_kova/kova.v7.vcf.gz visibility hide tableBrowser off dataVersion V7 track npm shortLabel Singapore NPM 9.7k WGS - longLabel Variant Frequencies: NPM Singapore - 9,770 WGS samples + longLabel SNV Frequencies: NPM Singapore - 9,770 WGS samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$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 Variant Frequencies: Haplotype Reference Consortium - 30k WGS (excl. 1000 Genomes) + longLabel SNV Frequencies: Haplotype Reference Consortium - 30k WGS (excl. 1000 Genomes) type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/hrc/hrc.vcf.gz visibility hide dataVersion r1.1 track saudi shortLabel Saudi Genome 302 WGS - longLabel Variant Frequencies: Saudi Genome Project - 302 WGS samples + longLabel SNV Frequencies: Saudi Genome Project - 302 WGS samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/saudi/saudi.vcf.gz visibility hide dataVersion SHGP (figshare 51297884, 2025) track schema shortLabel SCHEMA 121k WES Sz - longLabel Variant Frequencies: SCHEMA Schizophrenia Exome Meta-Analysis - WES 24k cases, 97k controls + longLabel SNV Frequencies: SCHEMA Schizophrenia Exome Meta-Analysis - WES 24k cases, 97k controls type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/schema/SCHEMA_variant_results_withAF.vcf.gz visibility hide dataVersion 2022 priority 4.9 url https://schema.broadinstitute.org/ urlLabel SCHEMA Browser track mxbFreq shortLabel Mexico Biobank 6k Array - longLabel Variant Frequencies: Mexico Biobank - 6,011 individuals, genotyping array + longLabel SNV Frequencies: Mexico Biobank - 6,011 individuals, genotyping array type vcfTabix parent varFreqs on bigDataUrl /gbdb/$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 Variant Frequencies: Simons Genome Diversity Project - 279 WGS, 142 populations + longLabel SNV Frequencies: Simons Genome Diversity Project - 279 WGS, 142 populations type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/sgdpFreq/sgdp.freq.vcf.gz visibility hide dataVersion 2016-12-07 (hg38 lift) priority 7 track gregor shortLabel GREGoR R4 3.6k WGS - longLabel Variant Frequencies: GREGoR Consortium - Release 4, 3,624 WGS samples, rare disease families + longLabel SNV Frequencies: GREGoR Consortium - Release 4, 3,624 WGS samples, rare disease families type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/gregor/gregor.vcf.gz visibility hide dataVersion R04 (Oct 2025) priority 8 track hgdp1kFreq shortLabel gnomAD HGDP+1kG 4k WGS - longLabel Variant Frequencies: gnomAD HGDP + 1000 Genomes - 4,094 WGS, 80 populations + longLabel SNV Frequencies: gnomAD HGDP + 1000 Genomes - 4,094 WGS, 80 populations type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/hgdp1kFreq/hgdp1k.freq.vcf.gz visibility hide dataVersion v3.1.2 priority 8 track ga4kSnv shortLabel GA4K 552 PacBio LR - longLabel Variant Frequencies: GA4K Children's Mercy - 552 PacBio HiFi WGS, pediatric RD + longLabel SNV Frequencies: GA4K Children's Mercy - 552 PacBio HiFi WGS, pediatric RD type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga4k/ga4kSnv.vcf.gz visibility hide dataVersion Cohen 2022 release priority 9 track colorsDbSnv shortLabel CoLoRSdb 1k LR SNV/Ind - longLabel Variant Frequencies: CoLoRSdb v1.2.0 - 1,027 PacBio HiFi WGS, SNV/indel callset + longLabel SNV Frequencies: CoLoRSdb v1.2.0 - 1,027 PacBio HiFi WGS, SNV/indel callset type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/colorsDb/colorsDbSnv.vcf.gz visibility hide dataVersion v1.2.0 priority 9.5 track svatalogSnv shortLabel SVatalog 101 WGS - longLabel Variant Frequencies: GWAS SVatalog - 101 samples, 10X Genomics linked-read SNPs + longLabel SNV Frequencies: GWAS SVatalog - 101 samples, 10X Genomics linked-read SNPs type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/svatalog/svatalog.vcf.gz visibility hide dataVersion Chirmade 2025 release priority 10 track tishkoff180 shortLabel 12 Afr Pops 180 WGS - longLabel Variant Frequencies: 180 WGS from 12 Indigenous African Populations (Fan 2023) + 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