Phred scores and Multiple/ Consensus reads

[Laurence Hall]

Dear colleague,

I have a question regarding Phred. If you have a base from a sequencing
read that has a designated Phred score of 20 and the equivalent base
from the complementary strand also has a designated score of 20, what
would be the confidence value  in a concensus built from these two
strands ??

Given that each base has at Phred 20, by definition, a 1% chance of
being wrong is the error rate for the resulting concensus 1% of 1%, in
other words 1 in 10,000 that is q40 ?? If not how is the resulting Phred
score computed ??

Thanks for any assistance


Laurence Hall


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Laurence S Hall
Senior Research Associate
Rubicon Genomics
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EMail : hall at rubicongenomics.com

           lhall48108 at yahoo.com

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