2a8638e662e67cd99d49f8bad466ef471696c109 angie Wed Apr 22 11:15:18 2020 -0700 David H just noticed that the descriptions of white and black were swapped in VCF track descriptions! Oops. diff --git src/hg/makeDb/trackDb/ebola/gire2014Missense.html src/hg/makeDb/trackDb/ebola/gire2014Missense.html index ece05ad..9772b6a 100644 --- src/hg/makeDb/trackDb/ebola/gire2014Missense.html +++ src/hg/makeDb/trackDb/ebola/gire2014Missense.html @@ -8,32 +8,32 @@ In "dense" mode, a vertical line is drawn at the position of each variant. In "full" mode, in addition to the vertical line, a label to the left shows the reference allele first and variant alleles below (<span style='color:red;'>A = red</span>, <span style='color:blue;'>C = blue</span>, <span style='color:green;'>G = green</span>, <span style='color:magenta;'>T = magenta</span>, Indels = black). Hovering the pointer over any variant will prompt the display of the occurrences numbers for each allele in Gire <em>et al</em>., 2014. Clicking on any variant will result in full details of that variant being displayed.</p> <p> By default, in "pack" mode, the display shows a clustering of haplotypes in the viewed range, sorted by similarity of alleles weighted by proximity to a central variant. The clustering view can highlight local patterns of linkage.</p> <p> -Each variant is a vertical bar with black representing the reference allele -and white (invisible) representing the non-reference allele(s). +Each variant is a vertical bar with white (invisible) representing the reference allele +and black representing the non-reference allele(s). Tick marks are drawn at the top and bottom of each variant's vertical bar to make the bar more visible when most alleles are reference alleles. The vertical bar for the central variant used in clustering is outlined in purple. In order to avoid long compute times, the range of alleles used in clustering may be limited; alleles used in clustering have purple tick marks at the top and bottom.</p> <p> The clustering tree is displayed to the left of the main image. It does not represent relatedness of individuals; it simply shows the arrangement of local haplotypes by similarity. When a rightmost branch is purple, it means that all haplotypes in that branch are identical, at least within the range of variants used in clustering. </p> <!--#insert file="gireMethods.html"-->