SNP tree output report

The Create SNP Tree tool can optionally output a report that summarizes the consequence of the applied filtering settings, as well as a summary of ignored positions attributed to the different read mappings.

The first section of the report, "Filter Status", contains the actual counts found during analysis. The different categories are described below:

The second section consists of a graphical and a tabular representation of the number of positions that was filtered because of the individual read mappings. The tabular view has three columns:

In the example below, we are creating a tree based on three read mappings, mapping 1, mapping 2 and mapping 3.

In this case

We will get a table like this:

Read mapping Filtered, total Filtered, only by this
Mapping 1 3 1
Mapping 2 4 1
Mapping 3 3 0

An example of report content shown in figures 13.4, 13.5, 13.6 and 13.7.

Image snp_rep_filter
Figure 13.4: Report on Filter Status for the created SNP tree.

Image snp_rep_ignore
Figure 13.5: Visualization of the filter effect across data used for generation of SNP tree.

Image snp_rep_filtde1
Figure 13.6: Listing filtering results of the first 10 rows of the 47 rows of the data sets. Each row show the number of ignored positions generally across all data set as well as number of ignored positions when filtering on the particular data set only.

Image snp_rep_filtde2
Figure 13.7: Listing filtering results of the last 14 rows of the 47 rows of the data sets. Each row show the number of ignored positions generally across all data set as well as number of ignored positions when filtering on the particular data set only. The tabular information indicates that sample acc no ERR277235_1 shows significantly lower quality than the other samples.

In the applied example, ERR277235_1 shows significantly higher number of positions ignored than the other samples (see figures 13.5 and 13.7), and one might consider rerunning the tree without this sample in an attempt to get a higher resolution in the tree.