4bf8cd5b339e46ed05d34677f0fed28eb2b03463
lrnassar
  Thu May 26 17:14:43 2022 -0700
Setting MTR track to QA ready. Choosing new .ra setting to highlight low values, updating the make script, and improving the desc page. Refs #29152

diff --git src/hg/makeDb/trackDb/human/constraintSuper.html src/hg/makeDb/trackDb/human/constraintSuper.html
index 7c40d0a..bfdb885 100644
--- src/hg/makeDb/trackDb/human/constraintSuper.html
+++ src/hg/makeDb/trackDb/human/constraintSuper.html
@@ -62,31 +62,33 @@
 HMC scores are displayed as a signal ("wiggle") track, with one score per genome position.
 Mousing over the bars displays the exact values. The highly-constrained cutoff
 of 0.8 is indicated with a line.</p>
 <p>
 The HMC scores were downloaded and converted to .bedGraph files with a
 custom Python script. The bedGraph files were then converted to bigWig files,
 as documented in our <a
 href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg19.txt"
 target=_blank>makeDoc</a> hg19 build log.</p>
 
 <h3>MTR</h3>
 <p>
 MTR data can be found on two tracks, <b>MTR All data</b> and <b>MTR Scores</b>. In the
 <b>MTR Scores</b> track the data has been converted into 4 separate signal tracks
 representing each base pair mutation, with the lowest possible score represented when
-multiple transcripts overlap. It is recommended that the data be explored using
+multiple transcripts overlap. A horizontal line is drawn on the 0.8 score line
+to roughly represent the 25th percentile, meaning the items below may be of particular
+interest. It is recommended that the data be explored using
 this version of the track, as it condenses the information substatially while
 retaining the magnitude of the data.</p>
 
 <p>Any specific point mutations of interest can then be researched in the <b>
 MTR All data</b> track. This track contains all of the information from
 <a href="http://biosig.unimelb.edu.au/mtr-viewer/downloads" target="_blank">
 MTRV2</a> including more than 3 possible scores per base when transcripts overlap.
 A mouse-over on this track shows the ref and alt allele, as well as the MTR score
 and the MTR score percentile. Filters are available for MTR score, False Discovery Rate
 (FDR), MTR percentile, and variant consequence. By default, only items in the bottom
 25 percentile are shown. Items in the track are colored according
 to their MTR percentile:</p>
 <ul>
 <li><b><font color=green>Green items</font></b> MTR percentiles over 75
 <li><b><font color=black>Black items</font></b> MTR percentiles between 25 and 75