Table 2

Base-calling probabilities example 2: overcall
reference sequence: AA
native 454: AAA
qs 1 qs 2 qs 3 qs 4 qs 5
QS454 22 22 23 - -
HPCall: AAA
HPL 1 HPL 2 HPL 3 HPL 4 HPL 5
<a onClick="popup('http://www.biomedcentral.com/1471-2105/13/303/mathml/M14','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/303/mathml/M14">View MathML</a> 1.7E-10 0.29 0.71 3E-9 <1E-15
QSHPCall 0 -1 5 0 0

Base-calling probabilities example 2: overcall. HPCall gives a probability for HPL 3 of 0.29 and an associated QSHPCall of 5. This indicates that it is not unlikely that the fourth called A is an overcall. This information can not be extracted from 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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