9711cb56111546aeed1be4b2c0ba1738080c848c lrnassar Tue Jul 28 17:31:52 2026 -0700 Fix "basepair" wording and Methods punctuation on the Deleteriousness Predictions description pages per QA feedback. refs #37510 Changes "basepair" to "base" in the shared zoom-in instructions on clinPred, revel, alphaMissense, caddSuper, and caddSuper1_7, and normalizes predictionScoresSuper from "base pair" to "base" so the container is consistent. Removes an awkward comma in the source-repository sentence on clinPred and revel. Switches the hgdownload links on the clinPred page to https to match the other links on that page. diff --git src/hg/makeDb/trackDb/human/caddSuper1_7.html src/hg/makeDb/trackDb/human/caddSuper1_7.html index a43eb4b32d4..23b4b13bfbf 100644 --- src/hg/makeDb/trackDb/human/caddSuper1_7.html +++ src/hg/makeDb/trackDb/human/caddSuper1_7.html @@ -33,55 +33,55 @@ <pre> 10 * -log of the rank</pre> so that variants with <b>scores above 20 are predicted to be among the 1.0% most deleterious possible substitutions in 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> +base = 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 score in the top 1%, regardless of the details of the annotation set, model parameters, etc. </p> <p> The four single-nucleotide mutation tracks have a default viewing range of score 10 to 50. As explained in the paragraph above, that results in slightly less than 10% of the data displayed. The deletion and insertion tracks have a default filter of 10-100, because they display discrete items and not graphical data. </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", representing the reference allele, e.g., A to A, is always set to zero. </p> <p> -When using this track, zoom in until you can see every basepair at the +When using this track, zoom in until you can see every base at the top of the display. Otherwise, there are several nucleotides per pixel under your mouse cursor and instead of an actual score, the tooltip text will show the average score of all nucleotides under the cursor. This is indicated by the prefix "~" in the mouseover. 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 set of insertions and deletions. On hg38, the set has been obtained from gnomAD3. On hg19, the set of indels has been obtained from various sources (gnomAD2, ExAC, 1000 Genomes, ESP). If your insertion or deleletion of interest is not in the track, you will need to use CADD's <a target="_blank" href="https://cadd.gs.washington.edu/score">online scoring tool</a> to obtain them.</p>