Base-error rates were calculated as the number of errors in the alignment, divided by the length of the alignment. This was to ensure that deletion errors, which are quite common on this platform, would be reflected by the error rate. Flow-error rates were calculated as the number of incorrect flow-calls divided by the total number of flow-calls. For specific break-downs (such as error rate for homopolymer of length X), it was the number of miscalled X-mer flows, divided by the total number of flows which were, or should have been, an X-mer, according to the reference genome.
