This track represents intrahost variants for a subset of the 78 Sierra Leone EVD patients described in Gire et al., 2014. For a subset of these 78 patients, researchers took multiple blood samples from each patient at various time points, then isolated and sequenced the Ebola virus from each sample. This allowed them to to track the mutation and evolution of the virus within a single patient or host.
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 (A = red, C = blue, G = green, T = magenta, Indels = black). Hovering the pointer over any variant will prompt the display of the occurrences numbers for each allele in Gire et al., 2014. Clicking on any variant will result in full details of that variant being displayed.
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.
Each variant is a vertical bar with black representing the reference allele and white (invisible) 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.
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.