Figure 1

Effect of base-calling improvements on error bias. This figure is based on figures from Bravo and Irizarry [15]. Choosing a site that was a false-positive variant as determined by MAQ [28], the authors examined the pattern of nucleotide calls according to the read cycle the different calls occurred at. (a) Results with the default base-calling software; (b) results after application of the base-calling method of Bravo and Irizarry. The x-axis shows read cycle and the colored points indicate the percentage of calls at each cycle that were made for a particular nucleotide. In (a), the letter T becomes much more frequent in reads that align to the SNP site only at later sequencing cycles, indicating a technical bias in base calls at this position, while the plot in (b) shows a strong reduction in this bias. In addition, the location is no longer determined as a variant by MAQ after the improved base calling.