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Old 05-24-2011, 08:52 PM   #5
Location: Beijing, China

Join Date: Apr 2011
Posts: 23

Originally Posted by dawe View Post
Hi, how do you interpret the quality of the alignment in SAM files generated by bowtie? I only see values being 0 or 255 (for unmapped and mapped sequences), is this just me?


I have the same problem when aligning reads using Tophat.

The values in my sam file generated by tophat range from 0 to 255, which is different from your example.

I look up the field interpretation for the quality value by reading The SAM Format Speci cation, which tells me that in the attached snapshot.

The value ranges from 0 to +∞ with that the zero represents the highest probability of mapping wrong and +∞ is for the lowest probability of mapping wrong, according to the formula given in the document. The range 0~+∞ could be normalized into 0~255, right?

But why does the document tell that the value 255 indicates that the mapping quality is not available? I have an inverse answer to it.

I am wondering if I have made a mistake of understanding.

Hope someone could help me.

Thanks in advance,
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