2364a502e18417609bb987659315c61a2dfc1f8b max Mon Jun 7 06:17:27 2021 -0700 fixing track docs of revel track based on author feedback, refs #27142 diff --git src/hg/makeDb/trackDb/human/revel.html src/hg/makeDb/trackDb/human/revel.html index 688b467..aa025e7 100644 --- src/hg/makeDb/trackDb/human/revel.html +++ src/hg/makeDb/trackDb/human/revel.html @@ -17,31 +17,33 @@ </p> <h2>Display Conventions and Configuration</h2> <p> There are four subtracks for this track: one for every nucleotide showing a score for the mutation represented by a mutation from the reference to that nucleotide. All subtracks show the REVEL ensemble score on mouseover, representing each of the possible ~9 billion SNVs in the genome. The score is an aggregation of the outputs of the 13 tools. </p> <p> For single nucleotide variants (SNV), 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. +the reference allele, e.g. A to A, is always set to zero, "0.0". REVEL only +takes into account amino acid changes, so a nucleotide change that results in no +amino acid change (synonymous) also receives the score "0.0". <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 no score will be shown on the mouseover tooltip. </p> <p>For hg38, note that the data was converted from the hg19 data using the UCSC liftOver program, by the REVEL authors. This can lead to missing values or duplicated values. When a hg38 position is annotated with two scores due to the lifting, the authors removed all the scores for this position. They did the same when the reference allele has changed from hg19 to hg38. Also, on hg38, the track has the "lifted" icon to indicate this. You can double-check if a nucleotide position is possibly affected by the lifting procedure by activating the track "Hg19 Mapping" under "Mapping and Sequencing".