SNP Tree Variants editor viewer

It is possible to inspect the actual difference in nucleotide counts at a given internal node. This can be done by selecting the internal node of interest (figure 11.12) and then switching from the Show Tree (Image tree) element view to the Show SNP Tree Variants (Image te_snp_tree_16_h_p) element view in the lower left corner of the visualization area.

Image snp_variants1
Figure 11.12: Visualization of SNP tree as a phylogram. An internal node is selected for further inspection of the nucleotide differences among the branching samples.

Once in the SNP Tree Variant element view, the table lists the actual SNP input positions used for creation of the SNP tree. The number of rows (in figure 11.13 this is 62,556) corresponds to the number of input positions stated in the filter status table of the SNP Tree report (see figure 11.7). Each row represents a given SNP position, and the distribution of observed nucleotide are counted for each of the subtrees. By filtering on the All agree column it is possible to count the fraction of positions that are identical or different, respectively.

Image snp_variants2
Figure 11.13: Counts of differences at a given position in the branches of the selected internal node.