Mutational Outcomes

Targeting efficiency

For each sample the fraction of non wild-type reads are shown.

Mutation types

for each sample the mutation types are shown in this interactive plot. Both relative and absolute fractions can be shown.

Homology plot - Deletions and Tandem duplications only

the homology that was used for repair. NOTE: only deletions and tandem duplications can be included in this plot.

Size Plot

a representation of the sizes of all events. Deletion size or Insertion size can be specified in a heatmap or violin plot representation.

Single-nucleotide variations (SNVs)

The frequency of SNVs at each position is shown. SNVs can be combined in one plot to compare rates at each position. NOTE: the SNV fraction is based on the mutation type(s) selected.

Target Alteration plot

For each location relative to the target site the fraction of alteration is shown. Note: Insertions and TDs are not included in the plot.

Sample Information plots

This page contains a number of plots to help you assess which samples should be included in the analysis. Samples with low number of reads can be excluded using the slider on the left. A second plot is shown with the fraction of correct reads from the total of merged reads. This gives an indication of how many merged reads pass various filter (e.g. primers included, minimum quality). A third plot shows for all the samples analyzed the number of merged reads from the total reads.

Tornado Plot - Templated Insertions

A newly designed interactive plot to show the origin of templated flank insertions. The plot can be customized by altering the settings on the left. NOTE: only deletions with templated inserts are shown

Outcomes

The outcomes plot is specifically designed to view all your data simultaneously. Especially when you have many samples this is a powerful method to look at differences between samples. It currently supports: UMAP, PCA, XY scatter, heatmap and Top X alleles.

HeatmapEnds

Not sure yet what will be put here

1bp insertion

display the contribution of the 1bp insertions

Note: to download all data, please select Show 'All' entries (slow on large sets)

About SIQPlotteR

The SIQPlotteR web app is a dedicated tool for exploring data that has been generated by SIQ. Users can explore their data by generating different kind of plots. Every plot can be adjusted in terms of filtering of type of events, changing sort order, altering colors. There is also the possibility to explore data from the SIQ paper.

You can find more information on SIQ and SIQPlotter, including a detailed user guide and video tutorials here

SIQPlotteR Version - 1.0 created by Robin van Schendel