19b8bfeadc8dc28380404a15e39ba662040dd279 gperez2 Thu Jul 30 09:27:03 2026 -0700 Adding v4.1.1 to gnomad.html's Constraint Metrics bullet, and updating gnomadPLI.html's general LOEUF threshold recommendation from <0.35 to <0.45. refs #37351 diff --git src/hg/makeDb/trackDb/human/hg38/gnomad.html src/hg/makeDb/trackDb/human/hg38/gnomad.html index 88aa93d0db9..094cd2e55f5 100644 --- src/hg/makeDb/trackDb/human/hg38/gnomad.html +++ src/hg/makeDb/trackDb/human/hg38/gnomad.html @@ -27,31 +27,31 @@ v3.1.1</strong></a> — Shows variants from 76,156 whole genomes (and no exomes), all mapped to GRCh38/hg38.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadGenomesVariantsV3_1#TRACK_HTML"><strong>Deprecated: gnomAD v3.1</strong></a> — Same underlying data as v3.1.1 with older annotations. Do not use; will be removed soon.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadGenomesVariantsV3#TRACK_HTML"><strong>gnomAD v3</strong></a> — Shows variants from 71,702 whole genomes from the v3.0 release.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadVariantsV2#TRACK_HTML"><strong>gnomAD v2</strong></a> — Shows variants from 125,748 exomes and 15,708 whole genomes, lifted from GRCh37/hg19 to GRCh38/hg38.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadConstraint#TRACK_HTML"><strong>gnomAD Mut Constraint</strong></a> — Shows the reduced variation caused by purifying natural selection for 1kbp windows across the genome (based on v3.1.2).</li> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadPLI#TRACK_HTML"><strong>gnomAD Constraint Metrics</strong></a> — Contains per-gene and per-transcript metrics of pathogenicity -(LOEUF, pLI, and Z-scores) for v2.1.1, v4, and v4.1.</li> +(LOEUF, pLI, and Z-scores) for v2.1.1, v4, v4.1, and v4.1.1.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomad3Coverage#TRACK_HTML"><strong>gnomAD v3 Genome Coverage</strong></a> — Shows various read depth metrics for genome samples from v3.0.1.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomad4ExomeCoverage#TRACK_HTML"><strong>gnomAD v4 Exome Coverage</strong></a> — Shows various read depth metrics for exome samples from v4.0.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadStructuralVariants#TRACK_HTML"><strong>gnomAD Structural Variants</strong></a> — Shows structural variant calls (variants >=50 nucleotides) from gnomAD v4.1.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadCopyNumberVariants#TRACK_HTML"><strong>gnomAD Rare CNV Variants</strong></a> — Shows rare copy number variants (<1% overall site frequency) from gnomAD v4.1.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadStr#TRACK_HTML"><strong>gnomAD STR</strong></a> — Shows short tandem repeat genotypes at disease-associated loci from gnomAD v3.1.3.</li>