Figure 3
From: Improved base calling for the Illumina Genome Analyzer using machine learning strategies
Fraction of mapped reads and corresponding number of mismatches for the three tested lanes. (a) The result for one lane of human shot gun sequence analyzed on a 26 cycle Genome Analyzer I run (A1); (b) the PhiX control lane of the very same 26 cycle Genome Analyzer I run (A2); (c) the PhiX control lane of a 51 cycle Genome Analyzer II (B). The raw sequences of all three lanes were mapped to the corresponding reference genome (hg18/NCBI Build 36.1 and PhiX 174 RF1) with up to five mismatches but no gaps using SOAP v1.11. For A1, further analyses were restricted to sequences mapping with at most two mismatches to reduce the number false positive placements expected when mapping short reads to a large genome sequence.