4b874bc40240615779138005711f6fbe52640933 jeltje.van.baren Tue Jan 21 12:21:39 2025 -0800 capitalizing track name to match paper diff --git src/hg/makeDb/trackDb/human/alphaMissense.html src/hg/makeDb/trackDb/human/alphaMissense.html index 91415751157..e1eb85d8839 100644 --- src/hg/makeDb/trackDb/human/alphaMissense.html +++ src/hg/makeDb/trackDb/human/alphaMissense.html @@ -1,36 +1,37 @@ <h2>Description</h2> <p> This track shows AlphaMissense predictions for all possible single amino acid substitutions in the human proteome. </p> <p> AlphaMissense is a deep learning method for predicting the pathogenicity of missense variants in human proteins. It classifies 32% of all missense variants as likely pathogenic and 57% as likely benign using a cutoff yielding 90% precision on the ClinVar dataset. </p> <h2>Display Conventions and Configuration</h2> <p>There are four lettered subtracks, one for every nucleotide, showing scores for mutation from the reference to that -nucleotide. All subtracks show the AlphaMissense ensemble score on mouseover. Across the exome, +nucleotide. All subtracks show the AlphaMissense score on mouseover. Across the exome, 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, "0.0". AlphaMissense 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". +amino acid change (synonymous) is not scored. These are shown in the tracks +with score "0.0". <p> 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><b>Track colors</b></p> <p> This track is colored according to the am_class column in the AlphaMissense_$db.tsv file. <table style="text-align: left;"> <thead> <tr> <th>Range</th>