Interpreting BCR rearragnements

[alexsteemers]

Hi! I have used MIXCR to look at the BCR clonality in my single cell WGS data. I have a single cell that has the following BCR annotation: IGHV3-21,IGHV3-7_IGHD6-19_IGHJ5. I am not sure how to interpret the "IGHV3-21,IGHV3-7" part. Any help will be much appreciated.

[mizraelson]

Hi,

Could you please share the command you used along with the output that is causing concern? If I understand your question correctly, you are asking why a certain clone is listed with two V genes in the table. This could be due to insufficient sequencing information to distinguish between the two genes.

Sincerely,
Mark

[alexsteemers]

Hi Mark,

I used the allVHitsWithScore output, and according to previous discussions it seems that using BestVHits is better.

[mizraelson]

Well, the difference is that 'allVHitsWithScore' shows all possible V genes along with their alignment scores, while 'bestVHits' shows only the V gene with the highest alignment score.