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  • Newbie needs help on a simple calculation

    Hi all.
    I have been reading up on Phred quality calculations.

    Phred quality = -10log(p) and p is the probability the base is NOT correct.

    My mentor wants to know how p was calculated and wants a working example. I searched high and low and I cant find a working example.

    If someone can show me an example of how to calculate p, it would be greatly appreciated.
    Thanks in advance
    Last edited by kwatts59; 04-15-2011, 06:24 PM. Reason: typo

  • #2
    http://en.wikipedia.org/wiki/Phred_quality_score,
    maybe, you can get the answer.

    Comment


    • #3
      For the original Phred scores you can see how p is calculated from the papers describing the method:
      The availability of massive amounts of DNA sequence information has begun to revolutionize the practice of biology. As a result, current large-scale sequencing output, while impressive, is not adequate to keep pace with growing demand and, in particular, is far short of what will be required to obta …

      Elimination of the data processing bottleneck in high-throughput sequencing will require both improved accuracy of data processing software and reliable measures of that accuracy. We have developed and implemented in our base-calling program phred the ability to estimate a probability of error for e …

      However this is for Sanger reads which I doubt you are talking about if you are posting on this forum. It is far less transparent how p is calculated for base qualities from Illumina, ABI SOLiD, etc. It will be dependent on the technology. Of course Phred scores are also being adapted in many other applications, e.g., NGS read mapping programs to measure the quality of an alignment. For such programs the details behind the calculation of p will be program-dependent.

      Comment


      • #4
        It appears that people are not understanding my question.
        I know how to calculate Q, the Phred quality.
        The question is how to calculate "p".

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        Let's say for sake of argument that the intensity of T is 1, the intensity of A is 0.5, and the intensity of G and C is 0.25.
        What is the value of "p" that is used to calculate the Phred quality Q?

        Q = -10log(p)
        Last edited by kwatts59; 04-16-2011, 08:40 PM. Reason: premature posting

        Comment


        • #5
          My response above is answering your question. The answer is that how p is calculated will be program-dependent.

          If you have Sanger reads that you are analyzing with Phred the second linked ref in my response above describes how error probabilities are calculated.

          Comment

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