Table 6

Number of errors for simulated data
Space Probe Percentage Percentage mapped with 0 – 5 errors
generator mapped 0 1 2 3 4 5
Color None 77.1 38.4 16.7 10.5 6.2 3.6 1.8
1β0β0 78.4 48.6 10.2 9.7 5.0 3.2 1.7
10β00 78.3 48.4 10.3 9.7 5.0 3.2 1.7
1β010 78.3 49.8 9.1 9.7 4.9 3.2 1.7
Base None 47.2 38.4 2.3 1.6 1.8 1.8 1.2
1β0β0 64.3 49.6 4.7 2.1 3.1 2.6 2.1
10β00 65.5 49.4 6.2 3.0 2.3 2.4 2.2
1β010 64.9 50.8 5.0 2.2 2.4 2.4 2.2

Percentage of reads mapped (five edits or fewer), and mapped with a given number of errors, for one million simulated reads using the codes with probe generators as specified. For comparison, figures are also given using only the two-base-encoding probe set (probe generator ‘None’). Since color-space reads have their first position trimmed before mapping to produce reads 49 colors long, the percentages of mapped reads and reads with a given number of errors are slightly inflated compared to those given for base-space reads.

Massingham and Goldman

Massingham and Goldman BMC Bioinformatics 2012 13:145   doi:10.1186/1471-2105-13-145

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