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How to calculate my own phred quality score

I am planning to calculate my own phred quality score. I need to share some idea how to calculate my own Q Score. I have sequences like below:

AAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAA
                    ....
TAAAAAAAAAAAAAAAAAAAAA

So in the above case, There is A: 100 and T: 1 on the first base. So that position has 99% accuracy. And from 99% accuracy how I can get Q = 20?

What if there is A: 151 and 1 T on the first position? Anyone knows how to calculate that score from the percentage?

Thank you

phred-quality-score fastq qscore
• 12,953 views • link
updated by Ram Ram • written by clear.choi • clear.choi

1 answer

From Wikipedia page:

Q=-10\ \log _{10}P

Keep in mind that the original Phred score is intrinsic to the sequencing machine, which determines the score based on peak shape and resolution at every base. Assuming you still want to represent your percentages as Phred scores, you have to use the probability of the wrong base in the above equation. For example, if a base is 99% of the times 'A', then the probability of the base not being 'A' is 0.01. And Q score can then be derived as

Q = -10 * log10(0.01) = 20

Cheers

• 0 views • link
updated by Ram Ram • written by Tej Sowpati Tej Sowpati

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