naive question about phred score and ASCII endcoding and Bowtie

[andrewj]

I've been exploring some sequence data from SOLiD and have used Bowtie. When I was exploring the alignment, this was the ASCII-encoded read quality for one of the reads:

WYQPMQZ<8SF@NNDDLIIIINR@&9OOMA@8/BEF526+8HI<<+1J

When I convert this back to the qual score, it looks more like


54 56 48 47 44 48 57 27 23 50 37 31 45 45 35 35 43 40 40 40 40 45 49 31 5
24 46 46 44 32 31 23 14 33 36 37 20 17 21 10 23 39 40 27 27 10 16 41


However, in the .qual file, for that read, the quality score was

25 25 29 27 21 26 18 30 27 -1 23 27 10 21 24 21 14 21 22 18 22 18 22 23 26 5 -1 24 22 24 20 12 19 4 10 23 13 24 4 21 -1 10 13 26 14 13 14 4 20 21


Apologies if this question has been asked before, but why does it appear that the ASCII-encoded scores are much higher than what is in the .qual file. Does this have something to do with Bowtie?

[nilshomer]

WYQPMQZ<8SF@NNDDLIIIINR@&9OOMA@8/BEF526+8HI<<+1J

Is this quality from the CQ tag or from the QUAL field in the SAM file? The former should match the qual file, while the latter is the base qualities and may be different than the color qualities.

[andrewj]

Is this quality from the CQ tag or from the QUAL field in the SAM file? The former should match the qual file, while the latter is the base qualities and may be different than the color qualities.

Thanks. The output I showed is from the Bowtie output. I used the .qual file and .csfasta files for Bowtie and did it in color space, with the output in bases, not color space. Based on what you're saying, is it fair to say that the values are roughly the sum of the quality values from the color space?

[nilshomer]

Thanks. The output I showed is from the Bowtie output. I used the .qual file and .csfasta files for Bowtie and did it in color space, with the output in bases, not color space. Based on what you're saying, is it fair to say that the values are roughly the sum of the quality values from the color space?

I agree, it certainly looks like the color quality values observing the base are added to get the base quality.