Bowtie mapping quality in SAM

[dawe]

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?

d

[Ben Langmead]

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?

d

Bowtie doesn't calculate Maq-like mapping quality values, so (per the SAM spec) it prints 255 there if the read aligns or 0 otherwise.

Ben

[xinwu]

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.

[dariober]

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.

I'm also interested in this question...

Dario

[Hunny]

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?

d

Hi,

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 Specication, 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,

[Hunny]

Hi,

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 Specication, 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,

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?

[carmeyeii]

Would like to revisit this. Is it clear now that 255 means a top score alignment?

[carmeyeii]

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.

[foxriverlin]

Thanks carmeyeii. That is very helpful!

[apredeus]

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.