Examples to illustrate base calling errors associated with homopolymers generated by PGM sequencing. A: An example of a homopolymer indel error illustrated with the PGM Ionogram. An ionogram is a graphical representation that demonstrates the conversion of PGM sequencing output to read sequences. The x-axis indicates the nucleotides along the read sequence. The y-axis indicates the number of consecutively identical nucleotide. One peak in the ionogram (arrowed) has a peak height of between three and four 'C' bases which suggests that the read sequence at this region could be ‘CCC’ or ‘CCCC’. During read alignment, if the reference sequence has four 'C' bases in this region, a deletion might be generated by reads with three 'C' bases. B: The top panel represents an IGV snapshot that indicates the read alignment of a DNA region with no indel generated by SOLiD sequencing. The bottom panel shows a “deletion” detected using PGM resequencing for the same region as the top panel.