base quality in the result of mpileup

Question

[897598644]

Excuse me:

When I analyzed the reads of variants, I used command of samtools mpileup and it printed out six colums. In the last column, I showed many letters or marks like BHIGDGIJ>?FF. I wanted to know what these marks mean.

Any help would be much appreciated. Links or documents would be better.

Best!

Answer 1

[Devon Ryan]

They're 33 plus the phred score. The resulting number is representable as a character in the ascii alphabet. Google for "ascii table" for a convenient table of the character to 33+Phred conversions.

[897598644]

Many thanks for your hints.

And, why did they use number of 33 as a baseline number? Is there any paper or link to prove that?

Best！

[Devon Ryan]

Nothing below 33 prints a character to the screen (they're control characters and things like tab and space). You'll find that 33 is a common offset for converting numbers that can start at 0 to printable characters.