ASCII offset

[Bakhtiyar Taghizada]

Sanger format FASTQ reads have offset 33. What does it mean, how can I define offset?

[Brian Bushnell]

That means the quality characters are equal to their quality plus 33. For example, a base with quality 0 gets a '!' symbol, because ! is ASCII character 33.

[dpryan]

Suppose the phred score for a base call is 30. We add 33 to that, resulting in 63. In ASCII, 63 is the character '?'. The reason for the offset of 33 is because the first 33 ASCII characters aren't normal characters, but control characters or things such as tab or a space. The general idea is to convert from numeric value to a convenient character representation, since the file is text and including the phred scores as is would vastly increase the file size and computation time (in C, characters are integers, so doing computations on them is simple).

Edit. I should have refreshed, I see Brian beat me to it!

[Bakhtiyar Taghizada]

Thank you, two answers made it more clear for me to understand!

[Brian Bushnell]

Edit. I should have refreshed, I see Brian beat me to it!

That's OK, your answer was more thorough