Difference between revisions of "Mapping Quality Scores"
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Revision as of 18:34, 17 December 2009
Mapping Quality Scores quantify the probability that a read is misplaced. They were introduced by Heng Li and Richard Durbin in their paper describing MAQ and are usually reported on a Phred scale.
Calculating a Mapping Quality Score
For a particular short sequence read, consider its best alignment in the genome. For this alignment, calculate the sum of base quality scores at mismatched bases and define a quantity SUM_BASE_Q(best). Also, consider all other possible alignments for the read. For the alignment i, define SUM_BASE_Q(i) as the sum of base quality scores at mismatched bases for that alignment.
Then, the mapping quality is defined as:
MapQuality = SumBaseQual(best) / (Sigma_i (SumBaseQual(i))
