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
$\widehat{P}\{N_{\mathit{\text{nc}}}=n_{\mathit{\text{bc}}}\}$	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 QS_HPCall 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.