Phred scores and Multiple/ Consensus reads

JimTurner2 jimturner2 at aol.com
Mon Mar 18 22:12:54 EST 2002


Laurence Hall writes:

>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 ??

Laurence,

I think that your interpretation is a reasonable one.  Since the forward and
reverse reads are done (relatively) independently, the phred quality score of
the base of interest should be about equal to the sum of the two confirming
opposite strand reads.  Each quality 20 read will be in error, on average, 1
time in 100.  For both strands to agree you can mulitply the probablilites
(since they are independent) and should expect only about 1 error in 10,000
situations where opposite strand reads agree.  Since phred scores are
logarithms, mulitplying the probabilites is equivalent to adding the phred
scores.

Jim Turner

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