f08ed4da0b23337a71fab0aa53d5be03ad668d26 lrnassar Wed Oct 15 13:40:06 2025 -0700 Bolding the interpretation of CADD scores, refs #36519 diff --git src/hg/makeDb/trackDb/human/caddSuper.html src/hg/makeDb/trackDb/human/caddSuper.html index 5a2a8561ad5..8b82e81f1ae 100644 --- src/hg/makeDb/trackDb/human/caddSuper.html +++ src/hg/makeDb/trackDb/human/caddSuper.html @@ -16,38 +16,38 @@ </p> <p> CADD scores strongly correlate with allelic diversity, pathogenicity of both coding and non-coding variants, experimentally measured regulatory effects, and also rank causal variants within individual genome sequences with a higher value than non-causal variants. Finally, CADD scores of complex trait-associated variants from genome-wide association studies (GWAS) are significantly higher than matched controls and correlate with study sample size, likely reflecting the increased accuracy of larger GWAS. </p> <p> A CADD score represents a ranking not a prediction, and no threshold is defined -for a specific purpose. Higher scores are more likely to be deleterious: +for a specific purpose. <b>Higher scores are more likely to be deleterious</b>: Scores are <pre> 10 * -log of the rank</pre> -so that variants with scores above 20 are +so that <b>variants with scores above 20 are predicted to be among the 1.0% most deleterious possible substitutions in -the human genome. We recommend thinking carefully about what threshold is +the human genome.</b> We recommend thinking carefully about what threshold is appropriate for your application. </p> <h2>Display Conventions and Configuration</h2> <p> There are six subtracks of this track: four for single-nucleotide mutations, one for each base, showing all possible substitutions, one for insertions and one for deletions. All subtracks show the CADD Phred score on mouseover. Zooming in shows the exact score on mouseover, same basepair = score 0.0.</p> <p> PHRED-scaled scores are normalized to all potential ~9 billion SNVs, and thereby provide an externally comparable unit for analysis. For example, a scaled score of 10 or greater indicates a raw score in the top 10% of all possible reference genome SNVs, and a score of 20 or greater indicates a raw