between 96–97% of the total error. Substitution errors had the highest variation in frequency, with a standard deviation ranging from 26%–56% of the mean substitution rate. The standard deviation of indel errors was between 19%–34% of the mean indel rates. The raw indel error rates observed in our study (1.62%, 4.66% and 2.83% for each of the 100 bp One Touch, 200 bp Manual and 200 bp OneTouch kits) are substantially higher than reported for quality trimmed data (100 bp OneTouch – 1.1% [1] using simple flow-cycle, 1.5% [2] using Samba, 1.78% [3] for the 200 bp manual using Samba flow-cycle). We attribute these differences to two factors, (1) our indel tolerance in read mapping which allows more of the data to map to the reference, and (2) the effect of quality trimming (discussed below).
