Table 1

Base-calling probabilities example 1: undercall
reference sequence: AAAAA
native 454: AAAA
qs 2 qs 3 qs 4 qs 5 qs 6
QS454 28 22 22 - -
HPCall: AAAA
HPL 2 HPL 3 HPL 4 HPL 5 HPL 6
<a onClick="popup('http://www.biomedcentral.com/1471-2105/13/303/mathml/M13','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/303/mathml/M13">View MathML</a> <1E-15 7.4E-9 0.83 0.17 6.3E-11
QSHPCall 0 0 -8 1 0

The estimated probability for HPL 5 (0.17) and the associated QSHPCall (-8) provided by HPCall clearly indicate the possibility of having an undercall with respect to the reference sequence, whereas this information is lacking in the quality scores of the native 454 base-caller.

Beuf et al.

Beuf et al. BMC Bioinformatics 2012 13:303   doi:10.1186/1471-2105-13-303

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