e0612ace61b503bafc54cfa95b9177008a20ed5b max Mon Mar 8 06:41:52 2021 -0800 another tiny change to cadd docs page, refs #18492 diff --git src/hg/makeDb/trackDb/human/caddSuper.html src/hg/makeDb/trackDb/human/caddSuper.html index 2b30b03..8bf46fb 100644 --- src/hg/makeDb/trackDb/human/caddSuper.html +++ src/hg/makeDb/trackDb/human/caddSuper.html @@ -18,31 +18,39 @@ <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> <h2>Display Conventions and Configuration</h2> <p> There are six subtracks of this track: four for every possible single nucleotide mutation, one for insertions and one for deletions. All subtracks show the CADD Phred -score on mouseover.<p> +score on mouseover.</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 +score in the top 1%, regardless of the details of the annotation set, model +parameters, etc. +</p> <p> <b>Single nucleotide variants (SNV):</b> For SNVs, at every genome position, there are three values per position, one for every possible nucleotide mutation. The fourth value, "no mutation", e.g. A to A, is always set to zero.<br> When using this track, please zoom in until you can see every basepair at the top of the display. Otherwise, there are several nucleotides under your mouse cursor per pixel and instead of an actual score, the tooltip text can only show the average score of all nucleotides under the cursor, which is indicated by the prefix "~" in the mouseover and averages of scores are not useful for any application of CADD. </p> <p><b>Insertions and deletions:</b> Scores are also shown on mouseover for a