Mapping Quality Scores

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))