To illustrate the other filtering performed, when multiplex strategies rather than generic were used for amplification Figure 5 also contains the raw and mask filtered results of this region for the A/Puerto Rico/8/34 sample. It was necessary to perform additional filtering to remove potential biasing caused by the specific primers as described in the methods. In the case shown in Figure 5 , a sequence of 18 bases present in the raw result are made N after filtering since they are in a location that interacts with the primers. If these base calls were included in the subsequences constructed, even though the HybSeq would still be split into the same number of SubSeq, the query for the ProSeq would favor an incorrect strain.