d4951d6de0335238ce124b3fb9703d82d329b1ab max Sat Jun 13 06:35:27 2026 -0700 html updates to varFreqs, refs #36642 diff --git src/hg/makeDb/trackDb/relatedTracks.ra src/hg/makeDb/trackDb/relatedTracks.ra index da1696c7c3f..978403558ec 100644 --- src/hg/makeDb/trackDb/relatedTracks.ra +++ src/hg/makeDb/trackDb/relatedTracks.ra @@ -5,30 +5,36 @@ hg38 knownGene knownGeneArchive View previous versions of GENCODE Genes hg38 knownGeneArchive knownGene View the latest GENCODE Genes version hg38 miRnaAtlas nonCodingRNAs View associated precursor miRnas hg38 nonCodingRNAs miRnaAtlas View expression of cleaved miRnas hg38 caddSuper gnomad View associated variants hg38 gnomad caddSuper View CADD scores for this variant and region hg38 constraintSuper gnomadPLI Predicted constraint metrics from gnomAD hg38 gnomadPLI constraintSuper Container track of various constraint scores hg38 gnomadStr strVar A collection of population-level STR variation tracks across the genome hg38 strVar gnomadStr Population-level STR variation across disease-associated loci from gnomAD v3.1.3 +hg38 varFreqs gnomadVariants Harmonized allele frequencies from ~800,000 exomes and genomes (gnomAD) +hg38 gnomadVariants varFreqs Allele frequencies from population-scale projects worldwide, not reprocessed by gnomAD + +hg38 varFreqs strVar Population-level tandem repeat (STR) variation across disease-associated loci +hg38 strVar varFreqs SNV and indel allele frequencies from population-scale sequencing and array projects + hg38 revel liftHg38 Revel is based on hg19 and lifted to hg38. liftOver "chain" alignment from hg19 to hg38 hg38 liftHg38 revel Revel scores were lifted using UCSC liftOver chains from hg38 hg38 revel caddSuper CADD, a similar deleteriousness score, and not used as an input by REVEL hg38 caddSuper revel REVEL, a similar deleteriousness score hg38 liftHg19 grcIncidentDb GRC Incident database, to explore reasons why the assembly was changed hg38 grcIncidentDb liftHg19 LiftOver for hg38, explores how incident regions aligned between human assemblies hg38 ReMap liftHg19 NCBI ReMap, even though it has the same name, is a liftOver-like hg19/hg38 alignment, and unrelated to the ReMap database hg38 liftHg19 ReMap ReMap, even though it has the same name, is a database of transcription factor binding sites, unrelated to NCBI ReMap hg38 ReMap jaspar JASPAR is a database of predicted TF binding sites, based on short DNA matches. Unlike ReMap, the data is purely computational. hg38 jaspar ReMap ReMap is a database of TF binding sites inferred from ChIP-Seq Data. Unlike JASPAR predictions, these sites are supported by functional assay