The output provides common information for all the alleles:
Which method was chosen to get the predictions
What was the input format (FASTA or PEPTIDE)
Thresholds used to identify strong and weak binders
For each allele the allele name is given and if NetMHCcons method was chosen, it is specified which method or combination of methods was used to get predictions for that allele.
The prediction output for each allele consists of 8 columns:
Prediction score (called 1-log50K(aff))
Affinity as IC50 value in nM (only for white-listed alleles)
%Rank - % Rank of prediction score to a set of 200.000 random natural 9mer peptides
Binding level (SB: strong binder, WB: weak binder). The peptide will be identified as a strong binder if the % Rank OR binding affinity (IC50) is below the specified threshold for the strong binders. The peptide will be identified as a weak binder if the % Rank OR binding affinity (IC50) is above the threshold of the strong binders but below the specified threshold for the weak binders.
Fianlly, at the end of predictions for each allele, the numbers of total strong and weak binders are given.