Question: Calculate average mapping quality at a position
0
gravatar for hpapoli
10 weeks ago by
hpapoli70
Sweden
hpapoli70 wrote:

Hello,

I want to filter my non-variant positions for mapping quality. I used mpileup to output the mapping qualities across all sites. To do the filtering, can I take an arithmetic mean of the mapping qualities for each read that the base belong to?

For example:

NW_008793873.1 13 G 2 .^S. AB HS

Position 13 is covered by two reads with mapping qualities H and S. Would (39 + 50)/2 = 44.5 be correct?

I ask this because in connection to mapping qualities, usually root mean square is mentioned so I was wondering what would the correct approach be in this case?

Thank you!

mpileup mapping quality • 229 views
ADD COMMENTlink modified 10 weeks ago by Gabriel R.2.5k • written 10 weeks ago by hpapoli70

aren't you mixing up MAPQ mapping qualities and read qualities ?

ADD REPLYlink written 10 weeks ago by Pierre Lindenbaum113k
1

I think this is using "samtools mpileup -s" which outputs the base quality followed by the mapping qualities for the read that supports the base.

ADD REPLYlink written 10 weeks ago by Gabriel R.2.5k

got it , thanks

ADD REPLYlink written 10 weeks ago by Pierre Lindenbaum113k
3
gravatar for Gabriel R.
10 weeks ago by
Gabriel R.2.5k
Center for Geogenetik KĂžbenhavns Universitet
Gabriel R.2.5k wrote:

These are probabilities of mismapping on a PHRED scale. For the first one, the probability of mismapping is:

(10^(-(39/10)) = 0.0001258925

For the second it is:

10^(-(50/10)) =  1e-05

So on average, your probability of mismapping is:

(0.0001258925+1e-05)/2 =  6.794627e-05

On a PHRED scale it is:

 -10*log10(6.794625e-05) =  41.67835
ADD COMMENTlink written 10 weeks ago by Gabriel R.2.5k

Thanks! By the way, do you know what kind of probability distribution do mapping qualities have?

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by hpapoli70
1

it depends on the aligner but it in any case, it's a bit of a scam: https://sequencing.qcfail.com/articles/mapq-values-are-really-useful-but-their-implementation-is-a-mess/ The link above has a plot of the distribution of mapping qualities.

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by Gabriel R.2.5k
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