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Figure 2 | Genome Biology

Figure 2

From: Improved base calling for the Illumina Genome Analyzer using machine learning strategies

Figure 2

Analysis of mismatches. Analysis of mismatches seen for (a) Bustard raw reads and (b) Ibis raw reads of a lane with 11,478,043 PhiX 174 RF1 raw reads sequenced with 51 cycles and mapped to the corresponding reference genome allowing up to 5 mismatches (including N characters). For Bustard 9,110,666 (79.4%) raw reads can be mapped, and for Ibis 9,695,354 (84.5%) raw reads. The sequencing error, measured as the mismatch rate, increases with cycle number. For Bustard, starting around cycle 25, guanine is mistaken as thymine. In later cycles adenosine and cytosine are also mistaken as thymine, due to increasing T accumulation. The error rate of the last base is especially high due to incomplete phasing correction. The patterns of specific base mismatches are not observed when Ibis is used.

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