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Old 08-25-2010, 02:27 AM   #1
Yushan Hsiao
Junior Member
Location: Taiwan

Join Date: Aug 2010
Posts: 6
Default Soap2: how to calculate the quality?

Hi, I just began to use Soap2 recently.
I have a problem with the output format after alignment.

For example,
"S-BD01.-4-3-23 AAAAAAAAAAAAAAAAAAAAAAA hhhhhhhhhhhhhhhhhhhhhhh 10000 a 23 + chr15 96346010 2 C->6A40 C->7A40 23M 6CC15"
I know "C->6A40" means the location 6 is C in the reference but A in my data, and the quality of it is 40.

My problem is: "How does this 40 be calculated?"
I couldn't find the explanation on the soap website.

I'm new to soap and bioinformatics too.
Hope someone could help!
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