This is a test version of Biostars. For the public version, visit https://www.biostars.org.
base quality in the result of mpileup

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!

next-gen-sequencing
• 2,228 views • link
updated by Ram Ram • written by 897598644 897598644

1 answer

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.

• 0 views • link
written by Devon Ryan Devon Ryan

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！

• 0 views • link
written by 897598644 897598644

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.

• 0 views • link
updated by Ram Ram • written by Devon Ryan Devon Ryan

Log in to answer this question.

More posts like this