length. The variance of flow-values with respect to homopolymer length, cycle number, and position-within a cycle (PIC) will present challenges to studies, such as indel variant detection, which often assume a global base error rate. Consequently, higher read coverage and use of PGM flow-specific error rates will be required for applications to confidently distinguish PGM indel errors from genuine variants. However, the substitution error rate, which occurs at an order of magnitude lower than the indel error rate (0.04%–0.1%), suggests that Ion Torrent could be used to detect SNP variants that occur at frequencies greater than 0.1%.
