Illumina Quality Score 'B'
Posted 12:12 PM
When analyzing about 100 PhiX control lanes, by aligning to PhiX and calling any reference mismatch an "error", the quality score 'B' performs higher than 'C' on average. The 'B' score is approximately abot 3 phred-scores lower than the mean score for the whole run. I think the 'B' score represents the equivalent of "I don't know" on the Phred scale. For programs that rely on quality scores to indicate actual likelihoods of error, the 'B' score should be treated as a special case.
This is in addition to the known issue that reported phred scores have higher ovserved error rates overall, especially at the top end of the scale (Q-40's perform like Q-37's should, etc.)