d0f769fd1aadc0641c34e742791c2ad9e27f5f7b
lrnassar
Wed Jul 6 10:02:33 2022 -0700
Fixing up the track desc in response by author, refs #23883
diff --git src/hg/makeDb/trackDb/human/constraintSuper.html src/hg/makeDb/trackDb/human/constraintSuper.html
index 20c5b5a..59cb427 100644
--- src/hg/makeDb/trackDb/human/constraintSuper.html
+++ src/hg/makeDb/trackDb/human/constraintSuper.html
@@ -33,31 +33,32 @@
HMC - Homologous Missense Constraint:
Homologous Missense Constraint (HMC) is a amino acid level measure
of genetic intolerance of missense variants within human populations.
For all assessable amino-acid positions in Pfam domains, the number of
missense substitutions directly observed in gnomAD (Observed) was counted
and compared to the expected value under a neutral evolution
model (Expected). The upper limit of a 95% confidence interval for the
Observed/Expected ratio is defined as the HMC score. Missense variants
disrupting the amino-acid positions with HMC<0.8 are predicted to be
likely deleterious.
MetaDome - Tolerance Landscape Score (hg19 only):
MetaDome Tolerance Landscape scores are computed as a missense over synonymous
- variant count ratio, which is calculated in a sliding window manner to provide
+ variant count ratio, which is calculated in a sliding window (with a size of 21
+ codons/residues) manner to provide
a per-position indication of regional tolerance to missense variation. The
variants are based on gnomAD and corrected for codon composition. Scores
<0.7 are considered intolerant.
MTR - Missense Tolerance Ratio (hg19 only):
Missense Tolerance Ratio (MTR) scores aim to quantify the amount of purifying
selection acting specifically on missense variants in a given window of
protein-coding sequence. It is estimated across sliding windows of 31 codons
(default) and uses observed standing variation data from the WES component of
gnomAD / the Exome Aggregation Consortium Database (ExAC), version 2.0. Scores
were computed using Ensembl v95 release.
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