Fig. S1.

The first page a user sees in the web tool homepage. This page provides an overview of the number of affected genes per strain in all 3 classes using the cutoffs set at the top of the page. The 3 cutoff fields can be set by the user, and on submitting the changes, the table will be updated with the new cutoffs. The default cutoffs for SG and SL are 1, which means not to use any minimal deletion or extension size. The PROVEAN cutoff is set at −2.5, as suggested by the authors of the PROVEAN software as a good tradeoff between specificity and sensitivity. Lower values are more specific, but at the cost of finding less true positives; higher scores are more sensitive, but with the disadvantage of picking up more false-positives.