Intro
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PhyResSE is not a black box!
Genotype and Resistance are based on well-characterized SNPs collected in
one
list ("Resi-List-<version>.txt"). You can
As it will change over time, it is important to record its version at the time of analysis. Export (see below) records the current version of the SNP list in the header (along with other critical metadata such as the current version of the program as well as the one of the reference genome). However, the header will comprise only the SNP list version, but not its content. Please download the SNP list along with your results to document exactly which SNPs your analysis has been based on. |  |
Handling
The table lists found variants that are typical for a particular genotype (bacterial strain). The + icon of the quality column reveals whether or not considerably strict quality criteria are met. The first (position) column displays the nucleotide distribution at each position by mouse-over.It also links to a simple viewer detailing all contributing reads, color-coded according to base (top panel) and mapping (bottom) quality. Links by other columns provide further detail about genes and publications involved. More columns can be added by means of the "Skipped columns" + icon (likewise columns can be skipped by clicking the according x icons).
Export Table data can be taken home as described. While both tables have an export button located nearby, each button exports the content of both tables at the same time into one spreatsheet. (Please simply remove what you do not need, it is faster than combining two tables.)
Computational Steps
(Warning: Nerdy bioinformatics stuff. If you believe a p-value may be the probability that your data are not true, just skip this.)- no other programs invoked -