The Life of Trees
(or: Still Another Phylogeny Program)

SAPP

The CSV-Analysis tool produces several tables to start:



Table of Kits and STRs and/or SNPs processed

This table summarizes the CSV files read in. You can use it to verify that the input read into the program includes all the STR and SNP data you expected to provide.



Subclade SNP Table

This table lists all the SNPs which may define branches within the group (i.e., which may indentify subclades of the group). SNPs are reported which are positive in two or more kits, AND negative in at least one kit. SOME SNP READS ARE REPORTED UNRELIABLY IN THE CSV FILES SO YOU MAY HAVE TO DOUBLECHECK THESE. To the right of the table, the SNP's position reference is checked against four "quality region" definitions for the Y chromosome - the CombBed (Yfull), Iain McDonald's regions, the full Poznik region (a larger definition from the Poznik et al. study) and the widest definition of quality is any position outside of the "bad" regions identified on YSeq's "Wish a SNP" page. Note if the "Report Only SNPs in Quality Regions" option is checked, SNPs which do not fall into Poznik, CombBed, or McDonald regions are not included in any of these tables.



Potential Subclade SNP Table

This is an optional table produced ONLY if the "Report Only SNPs Found In All Tests" option is unchecked. This table lists SNPs which MAY be Subclade SNPs, but which were "no-calls" (either not covered or not reliably read) in some kits in the group so their status as Subclade SNPs cannot be confirmed.



Private SNP Table

This table lists SNPs which are ONLY found in one kit - i.e. SNPs which are positive in one kit AND negative in all other kits.



Potential Private SNP Table

Again an optional table produced only if the "Report Only SNPs Found In All Tests" option is unchecked, this table lists SNPs which were only confirmed in one kit but which cannot be confirmed as Private SNPs because they were no-calls in some kits among the group.



The Generated SAPP Input TXT File

The last item produced by the tool is a TXT file containing all the STRs read in from the CSV files, and all the SNPs reported in the tables above, formatted into /STRDATA and /SNPDATA sections for input into the SAPP Program. This file can be downloaded by pressing the button at the end of the tool report and can be run in the SAPP tool to produce a tree report that draws the group and includes the STR mutation history and SNP branching as given by the tables above. Note that the automated TXT file includes ONLY the /STRDATA and /SNPDATA sections, you will need to add other optional sections manually.

Output (CSV Analysis)