ef70dfff0e8710e8aa4bc369a939f838c75947fb lrnassar Fri Jun 5 14:59:06 2026 -0700 varFreqs: Phase-7 audit cleanup on the supertrack and combined-track description pages. Supertrack varFreqs.html: - Restore the consequence-filter "Other" bucket explanation that was lost when varFreqsAll.html was replaced by the Affected+Background pair (now documented once on the supertrack page, since all three combined tracks share the filter). - Add 6 primary citations that were already in standalone subtrack pages but not carried up: Bycroft (UK Biobank), Cao (ChinaMAP), Cong (WBBC), Genome of the Netherlands Consortium (GoNL), Malomane (Saudi), Yang (TPMI). - Reorder Ameur, Singh into correct alphabetical position. - Lowercase Description

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 (361k unrelated white British, imputed from the Neale Lab Round 2 release).

-The array track is kept separate from the -All Databases Combined WGS/WES summary so that +The array track is kept separate from the sequencing-based combined tracks +(Affected/Case Individuals and +Population + Unaffected) 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.

Display Conventions

Color by Consequence

Variants are colored by their most severe predicted consequence:

- - - - - - - - - - - - + + + + + + + - - - - - - - + + + +

Color	Consequence class	Examples
Red	Protein-truncating / Loss-of-function	stop_gained, frameshift, splice_donor, splice_acceptor, stop_lost, start_lost
Blue	Missense / In-frame	missense, inframe_insertion, inframe_deletion, protein_altering
Green
	Protein-truncating / loss-of-function	stop_gained, frameshift, splice_donor, splice_acceptor, stop_lost, start_lost
	Missense / in-frame	missense, inframe_insertion, inframe_deletion, protein_altering
	Synonymous	synonymous, stop_retained
Grey	Non-coding / Intergenic	intron, non_coding, intergenic, UTR
synonymous, stop_retained
	Non-coding / intergenic	intron, non_coding, intergenic, UTR

Amino Acid Change Notation

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).

Caveats

Allele frequencies from genotyping arrays are not directly comparable to those from whole-genome or whole-exome sequencing. Two limitations to keep in mind:

Probe coverage is sparse and curated. Array variants are only those the manufacturer designed probes for. Absence from this track does not mean a variant is absent in that population, only that it was not on the chip.
Per-variant call confidence varies and is sometimes unreported. TPMI publishes a per-probe 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. For both arrays, high-AF rare-disease candidates should be cross-checked against the - sequencing-based All Databases Combined track - before drawing conclusions.

Population + Unaffected

Filters

This track supports filtering via the track settings page. Click the track title or use the "Configure" button to access filters.

Variant Type and Consequence

Variant Type: SNV, Insertion, Deletion, or MNV.
Consequence: Missense, Synonymous, Stop Gained, Frameshift, Splice Donor, Splice Acceptor, Intron, 3' UTR, 5' UTR, Non-coding, Intergenic, or Other. The filter uses OR logic across the comma-separated consequence tokens on each variant. See the - All Databases Combined description page for a - complete description of the "Other" bucket.

SNV Frequencies

Frequency and Count Filters

Max Allele Frequency: Filter by the maximum AF observed across the three array sources.
Total Allele Count: Filter by the sum of allele counts across all three databases.
Per-database AF and AC: Filter by allele frequency or count in any specific source (TPMI Taiwan, Mexico Biobank, UK Biobank imputed).

Source Database

The Source Database filter restricts the display to variants present in specific databases. It uses OR logic.

Length Filters

Reference/Alternate Length: Filter by the length of the reference or alternate allele.
Length Change: Filter by the size difference between alternate and reference (positive = insertion, negative = deletion, zero = SNV or MNV).

Methods

-The same merge-and-annotate pipeline used for the -All Databases Combined track was run on the +The same merge-and-annotate pipeline used for the sequencing-based combined tracks +(Affected/Case Individuals and +Population + Unaffected) was run on the array-cohort subset of source VCFs. Each VCF was stripped of its INFO fields, normalized with bcftools norm (splitting multi-allelic sites), and merged with bcftools merge. The merged VCF was then annotated with predicted protein consequences using bcftools csq with the Ensembl GRCh38 release 115 gene annotation (GFF3).

The track's makeDoc file documents how each source VCF was converted. Scripts are available from Github.