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  • Question about the values of quality

    Hi everybody:

    This is my first post here and it will be not the last one .

    After checking some quality values for reads (Solid system) , i saw that most the values are between 2 and 34 and sometime (-1) which corresponds to the dot.
    Anyone have an idea about these values range.

    Thanks in advance.

  • #2

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    • #3
      Your data doesn't sound very high quality. 80% of the quality values should be greater than 30 (max of 40 with the 3Plus)

      http://seqanswers.com/forums/showthread.php?t=1089

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      • #4
        The probability of a base being wrong p is given by p = 1/10 ^ QV/10

        (The ^ means 10 to the QV/10 exponential ). Thus a QV of 20 means 1 in 100 chance of being wrong, 30 is 1 in 1000 etc.


        http://www.plosone.org/article/info:...0004108-Ewing1

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        • #5
          Also, ABI claims that 80% of the QV should be greater than 30. I haven't checked this personally. They do funny things with their statistics like counting only mapped reads. Since only ~70% of the tags typically will map to a reference genome this seems a bit suspicious.

          Illumina does something similar though in that it first filters out poor tags before creating the text data files.

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          • #6
            Got it , thanks a lot for your answers

            Best regards

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