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Have I understood the ASCII-FastQ Offset 33 concept properly?

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  • Have I understood the ASCII-FastQ Offset 33 concept properly?

    Hello,

    I have read that FASTQ reads have an ASCII offset of 33.

    However, I am not sure whether I have understood the concept properly:

    Is it saying that for example, lets say that an ASCII code of 'h' gave a phred quality score of 40, then that would mean that 'a' would represent a phred quality score of 33

    because:

    If 'h' is Phred qual score 40
    That means that 'h' ASCII value is 73
    Because 73 - 33(offset) = 40

    so would that mean that 'a' would yield a phred quality score of 33?

  • #2
    almost.
    First of all, you need to distinguish between lowercase "a" and uppercase "A". I think you actually mean uppercase "A" here, because the lowercase "a" does not turn up until position 97 in the ascii table and is therefore not part of the typical phred33 quality encoding range (which usually only goes to around 40).

    And actually the phred scores start at "0" (even though that value actually practically can't be assigned in any real world case). So "!" corresponds to a score of 0 and "A" would correspond to a score of 32.

    "I" would correspond to a score value of 40 and "H" would corespond to a score of 39

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