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Table 3 Base-calling probabilities example 3: 0-1 undercall

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

reference sequence: T

native 454: -

 

qs 0

qs 1

qs 2

qs 3

qs 4

Q S 454

-

-

-

-

-

HPCall: -

 

HPL 0

HPL 1

HPL 2

HPL 3

HPL 4

P Ì‚ { N nc = n bc }

0.75

0.25

2.9E-8

<1E-15

<1E-15

Q S HPCall

-6

1

0

0

0

  1. 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 Q SHPCall at HPL 0 of -6, indicating that an undercall is not unlikely.
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BMC Bioinformatics

ISSN: 1471-2105

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