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Revision as of 02:48, 19 December 2009
, 02:48, 19 December 2009no edit summary
Then, the mapping quality is defined as:
Then, the mapping quality is defined as:
<math>
MAPPING\_QUALITY = log_{10} \left ({1.0 - \frac {10^{-SUM\_BASE\_Q(best)}} {\sum_i 10^{-SUM\_BASE\_Q(i)}}} \right )
</math>
The quantity <math>10^{-SUM\_BASE\_Q(i)}</math> tries to approximate the probability of generating a particular read when alignment ''i'' is used as template. For example, if there is a single mismatch with base quality 20, we approximate the probability of sampling the read as ~0.01; with two mismatches with base quality 20, the approximation becomes ~0.0001. Note that because this quantity will be effectively zero for most possible alignments, only a small subset of all possible alignments (those that result in small numbers of mismatches) must be considered in evaluating the denominator.
For paired end reads, we calculate SUM_BASE_Q as the sum of base quality scores at mismatched bases for both reads.
For paired end reads, we calculate SUM_BASE_Q as the sum of base quality scores at mismatched bases for both reads.
