f57e872b724de4bb82b14f07db837aeed4f5174a gperez2 Wed Jun 17 03:55:08 2026 -0700 Fix commas and update wording in varFreqs description pages. refs #37733 diff --git src/hg/makeDb/trackDb/human/varFreqsArray.html src/hg/makeDb/trackDb/human/varFreqsArray.html index b92b7fb5a94..0a8fed95a94 100644 --- src/hg/makeDb/trackDb/human/varFreqsArray.html +++ src/hg/makeDb/trackDb/human/varFreqsArray.html @@ -1,21 +1,21 @@
This track merges variants from three genotyping-array cohorts into a single bigBed file with predicted protein consequences and cross-database filtering. It contains 14.7 million variants from the Taiwan Precision Medicine Initiative (TPMI Axiom TPM1 chip, -~1 million Han Chinese), the Mexico Biobank (MexBB, 6,011 individuals), and UK Biobank +~1 million Han Chinese), the Mexico Biobank (MexBB, 6,011 individuals), and the UK Biobank (361k unrelated white British, imputed from the Neale Lab Round 2 release).
The array track is kept separate from the sequencing-based combined tracks (Disease cohorts and Population reference) so that sequencing-based and array-based frequencies can be inspected independently. For a summary of all available variant frequency databases, see the SNV Frequencies supertrack page.
The "AA change" field uses bcftools csq notation: 23I>23V means position 23 changed from Isoleucine (I) to Valine (V) (missense). 23I alone (no arrow) means position 23 is Isoleucine and unchanged (synonymous). A "*" indicates a stop codon (e.g. 45R>45* is a stop_gained).
Allele frequencies from genotyping arrays are not directly comparable to those from whole-genome or whole-exome sequencing. Two limitations to keep in mind:
NGS_concordance value (chip-vs-sequencing concordance from
its own validation) in the source VCF; high-AF claims with low concordance are
- common. MexBB ships only AN/AF/AC with no FILTER column and no per-site QC at all.
+ common. MexBB provides only AN/AF/AC with no FILTER column and no per-site QC.
For both arrays, high-AF rare-disease candidates should be cross-checked against the
sequencing-based
Population reference track before
drawing conclusions.This track supports filtering via the track settings page. Click the track title or use the "Configure" button to access filters.