bc1b5ba86e1748595027762a35c8f9a05d769a08 lrnassar Tue Aug 17 11:41:33 2021 -0700 Changing default CADD scores and adding a note to the desc page refs #28010 diff --git src/hg/makeDb/trackDb/human/caddSuper.html src/hg/makeDb/trackDb/human/caddSuper.html index 977a825..4a89573 100644 --- src/hg/makeDb/trackDb/human/caddSuper.html +++ src/hg/makeDb/trackDb/human/caddSuper.html @@ -29,30 +29,37 @@ <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 score in the top 1%, regardless of the details of the annotation set, model parameters, etc. </p> +<p> +The four single-nucleotide mutations 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 which helps visualization. The +deletion and insertion tracks have a default filter of 10-100 since 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. <br> When using this track, zoom in until you can see every basepair 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>