pgen value of 0

[ALGW71]

CAVEGYNTDKLIL 0.000000e+00
CAVERSTGGFKTIF 0.000000e+00
CAVRPLTSGSRLTF 0.000000e+00

The above seqeucnes have given me zero values from pgen humanTRA.

Does this suggest that my sequencing information is wrong?

How do we interpret zero probabilities if we find these in nature (assuming the output of MiXCR is correct)?

[giulioisac]

Hello,

pgen of zero means that the sequences are not compatible with any recombination scenario. This could arise from multiple reasons, but the most probable is that there is some sequencing error.

Bests,
Giulio

[ddcham]

We are currently looking at pgens of human TCR and BCR sequences and while TCR sequences appear to have few pgens of 0 in our BCR sequences ~62% of sequences show a pgen of 0.
This large number zeros suggests to me something other than pure sequencing error.
What could be other reasons contributing to this large fraction of pgen = 0?

Thanks

[iskandr]

pgen of zero means that the sequences are not compatible with any recombination scenario.

This seems very implausible in the general sense but maybe you mean it's not compatible with any scenario OLGA considers? If so, that seems like a significant limitation...