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One glance at the filter energy plot (also present for B1-1-2 in GRv15r46p1) shows a substantial chunk of events missing below 1 GeV for the all the tests, for example at lower energy for AllGamma (below left).
On the bright side, we are removing background events with a shocking efficiency.
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Tracy took a look at the discrepancy and found that this is a problem in the MC simulations handling caused exposed by the new and early processed "non-physics" filter bit. This is not a problem for data and did not appear in the test bed studies. The new filter version makes a cut on GEM bits, and these are not being set properly in the simulation. This will clearly need to be fixed in the simulations, but Tracy concludes it will not impact data processing.