Table 3
Base-calling probabilities example 3: 0-1 undercall
reference sequence: T
native 454: -
qs 0 qs 1 qs 2 qs 3 qs 4
QS454 - - - - -
HPCall: -
HPL 0 HPL 1 HPL 2 HPL 3 HPL 4
<a onClick="popup('http://www.biomedcentral.com/1471-2105/13/303/mathml/M15','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/303/mathml/M15">View MathML</a> 0.75 0.25 2.9E-8 <1E-15 <1E-15
QSHPCall -6 1 0 0 0

Because there is no base called by the native 454 base-caller, also no quality score is provided. HPCall on the other hand generates probabilities for HPL 0 (0.75) and HPL 1 (0.25) and an associated QSHPCall at HPL 0 of -6, indicating that an undercall is not unlikely.

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

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