SNP tree

The SNP tree can be vizualized in Tree view (Image tree), Table view (Image table_16_n_p), and SNP Tree Variants view (Image te_snp_tree_variant_16_n_p).

Tree view (Image tree)

The SNP tree layout, node and label settings is adjusted from the Tree Settings Side Panel found in the left side of the view area. For details about the settings, see

If a Result Metadata Table was provided as input, it is possible to decorate the SNP tree with one or more metadata layers from the Side Panel section Metadata, see This enables visual identification of potential correlation between samples, metadata layers, and tree typology (figure 9.8).

Image snp_tree_meta
Figure 9.8: Visualization of SNP tree including selected metadata and analysis result metadata.

SNP Tree Variants view (Image te_snp_tree_variant_16_n_p)

With the SNP Tree Variants view it is possible to inspect the variants relating to a given internal node in the SNP tree. To populate the table with the SNPs of interest, first select the internal node of interest in the Tree view and then go to the SNP Tree Variants (Image te_snp_tree_variant_16_n_p) view (figure 9.9).

Image snp_variants2
Figure 9.9: Counts of differences at a given position in the branches of the selected internal node. Top: SNP information As summary. Bottom: SNP information By sample.

The table lists the following columns:

With the Side Panel section SNP information you can choose to have SNP information presented As summary or By sample: