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Old 04-18-2013, 06:09 PM   #1
Location: Bay Area

Join Date: May 2011
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Default quality scores discrepancy on wikipedia

I am modifying code that automatically guesses the scoring method used in a fastq file. I am using the wikipedia entry for guidance (

But the example they show has some discrepancies. In the top part of the image illumina-1.5+ scores start at position 66. But at the bottom of the image it starts at they start at 67.

The bigger problem I am having is that some fastqs that I am looking at have quality scores of 'i' which is not consistent with any of the scoring methods listed on wikipedia.

Can anyone clear this up for me? Is there a better source than wikipedia for this information?


Last edited by dphansti; 04-18-2013 at 06:12 PM.
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Old 04-18-2013, 07:09 PM   #2
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Read the note in the wiki. B doesn't really mean 2, it means crappier than 2, or it means the end of the read is poor.

Starting in Illumina 1.5 and before Illumina 1.8, the Phred scores 0 to 2 have a slightly different meaning. The values 0 and 1 are no longer used and the value 2, encoded by ASCII 66 "B", is used also at the end of reads as a Read Segment Quality Control Indicator.[6] The Illumina manual[7] (page 30) states the following: If a read ends with a segment of mostly low quality (Q15 or below), then all of the quality values in the segment are replaced with a value of 2 (encoded as the letter B in Illumina's text-based encoding of quality scores)... This Q2 indicator does not predict a specific error rate, but rather indicates that a specific final portion of the read should not be used in further analyses. Also, the quality score encoded as "B" letter may occur internally within reads at least as late as pipeline version 1.6
So C, or 3, is the lowest true quality value you can get in that encoding system.

If you have an "i", maybe you have a new read generated with new improved chemistry, which some quality scores of 41, that have for some reason been converted to the old quality scoring.
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Old 04-22-2013, 01:17 AM   #3
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In fact, Solexa and Illumina scores cover the whole of the printable ASCII alphabet (0-93) like Phred. However, mostly the scores are from 0-40, but with the new instruments you will often find scores above 40. If you read the wiki entry carefully it actually says so. Guessing correct encoding is a pest.
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