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?
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Ben,
So, does Bowtie give its own mapping quality values somewhere or it does not report any mapping quality values at all? As the manual said, --best option can report best-worst order alignments, how can I measure the level between a better alignment to a worse alignment without mapping quality? Thanks.Comment
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Hi,Originally posted by dawe View Post
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,Comment
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Well, many facts manifest that the higher the value, the better the alignment with 255 of its maximum. So, I guess "mapping quality is not available" means the value 255 is meaningless for such a perfect alignment, right?Originally posted by Hunny View PostComment
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Would like to revisit this. Is it clear now that 255 means a top score alignment?Comment
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Found this elsewhere on the web>
Tophat/bowtie don’t report mapping quality values that are as meaningful as BWA, but there is some information in the mapping quality values tophat reports. Tophat yields 4 distinct values for its mapping quality values (you can do a “unique” count on the mapping quality field of any SAM file from tophat to verify this):
255 = unique mapping
3 = maps to 2 locations in the target
2 = maps to 3 locations
1 = maps to 4-9 locations
0 = maps to 10 or more locations.
Except for the 255 case, the simple rule that was encoded by the authors is the usual phred quality scale:
MapQ = -10 log10(P)
Where P = probability that this mapping is NOT the correct one. The authors ignore the number of mismatches in this calculation and simply assume that if it maps to 2 locations then P = 0.5, 3 locations implies P = 2/3, 4 locations => P = 3/4 etc.
As you can clearly see, then MapQ = -10 log10(0.5) = 3; -10 log10(2/3) = 1.76 (rounds to 2);
-10 log10(3/4) = 1.25 (rounds to 1), etc.Comment
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Thanks carmeyeii. That is very helpful!Comment
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BWA or bowtie2 report actual mapping qualities, which can be very useful, especially if you are analyzing ChIP-Seq or do SNP calling. Bowtie does not.Comment
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