Mapping Quality Scores - Revision history

Zhanxw: /* Calculating a Mapping Quality Score */

2010-02-18T07:21:27Z

Calculating a Mapping Quality Score

← Older revision		Revision as of 03:21, 18 February 2010
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	<math>		<math>
	MAPPING\_QUALITY = log_{10} \left ({1.0 - \frac {10^{-SUM\_BASE\_Q(best)}} {\sum_i 10^{-SUM\_BASE\_Q(i)}}} \right )		MAPPING\_QUALITY = - log_{10} \left ({1.0 - \frac {10^{-SUM\_BASE\_Q(best)}} {\sum_i 10^{-SUM\_BASE\_Q(i)}}} \right )
	</math>		</math>

Goncalo at 06:48, 19 December 2009

2009-12-19T06:48:42Z

← Older revision		Revision as of 02:48, 19 December 2009
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	Then, the mapping quality is defined as:		Then, the mapping quality is defined as:

	~~MapQuality~~ = ~~SumBaseQual~~(best) ~~/ (Sigma_i (SumBaseQual~~(i))		<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.

Zhanxw at 17:35, 18 December 2009

2009-12-18T17:35:01Z

← Older revision		Revision as of 13:35, 18 December 2009
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	MapQuality = SumBaseQual(best) / (Sigma_i (SumBaseQual(i))		MapQuality = SumBaseQual(best) / (Sigma_i (SumBaseQual(i))


			For paired end reads, we calculate SUM_BASE_Q as the sum of base quality scores at mismatched bases for both reads.

	== Reference ==		== Reference ==

	Li H, Ruan J, Durbin R. (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. ''Genome Research'' '''18''':1851-8.		Li H, Ruan J, Durbin R. (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. ''Genome Research'' '''18''':1851-8.

Goncalo at 22:38, 17 December 2009

2009-12-17T22:38:41Z

← Older revision		Revision as of 18:38, 17 December 2009
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	MapQuality = SumBaseQual(best) / (Sigma_i (SumBaseQual(i))		MapQuality = SumBaseQual(best) / (Sigma_i (SumBaseQual(i))

			== Reference ==

			Li H, Ruan J, Durbin R. (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. ''Genome Research'' '''18''':1851-8.

Goncalo: Created page with ''''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 r…'

2009-12-17T22:34:22Z

Created page with ''''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 r…'

New page

'''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))