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Table 1 Base-calling probabilities example 1: undercall

From: Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model

reference sequence: AAAAA

native 454: AAAA

 

qs 2

qs 3

qs 4

qs 5

qs 6

Q S 454

28

22

22

-

-

HPCall: AAAA

 

HPL 2

HPL 3

HPL 4

HPL 5

HPL 6

P Ì‚ { N nc = n bc }

<1E-15

7.4E-9

0.83

0.17

6.3E-11

Q S HPCall

0

0

-8

1

0

  1. The estimated probability for HPL 5 (0.17) and the associated Q SHPCall (-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.