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Old 10-28-2019, 12:27 PM   #2
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Location: USA

Join Date: Oct 2019
Posts: 4

Checking to see if folks have feedback on this. I read that "BWA actually follows the SAM spec and reports Phred scores as MAPQ values.* The calculation is based on the number of optimal (best) alignments found, as well as the number of sub-optimal alignments combined with the Phred scores of the bases which differ between the optimal and sub-optimal alignments."

Does that mean that the mapq score of a clipped read is a combination of the quality of the 'matched' alignment AND the quality of the alignment of the clipped bases? Perhaps this explains the strange finding I saw above.

If so, how does one extract the mapping quality of only the 'matched' portion of the read at this location (29446797)?
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