J and V gene calling

[jmmontagne]

I used MiXCR-2.1.10​ with the parameters:
-OassemblingFeatures="[{CDR3Begin:FR4End}]" and
-OseparateByJ=true

I chose to include FR4 in our clonal sequence because we use a reverse primer in the C region of the TCRbeta chain during library preparation (and thus we should have accurate J region information in our data).
I initially thought these two parameters would be redundant, as including FR4 in the clonal sequence should account for any differences in J gene. However, in my output files, there are identical clonal sequences (encompassing CDR3-FR4) with different J genes called. How can this happen?

Additionally, I want to be sure I understand what is happening when multiple V or J hits are being called. Is this the result of alignment to these regions, with multiple alleles scoring above a pre-defined threshold, such that MiXCR cannot accurately assign a single V or J gene?