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why allelic count on forward and reverse strand do not add up to depth in the results of samtools mpileup?
dmel_mitochondrion_genome       2878    .       A       <*>     0       .       DP=15;I16=0,9,0,0,347,13419,0,0,180,3600,0,0,140,2570,0,0;QS=1,0;MQ0F=0 PL:ADF:ADR      0,27,86:0,0:9,0

See the above line for example. Here the depth is DP=15, however allelic count on forward strand and reverse stand is 0, 0 and 9, 0, and sum up to 9 < 15. Why this happens?

Thanks in advance.

samtools vcf mpileup
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updated by Tom_L Tom_L • written by mt1022 mt1022

1 answer

The first four values of the I16 tags are depths at Q13 threshold, corresponding to 10^(-13/10) base calling error, which is 5% (documentation: http://samtools.sourceforge.net/mpileup.shtml).

Would it be possible that 15 is the total depth without taking into account any base calling threshold whereas 9 passed the given threshold? Can you check that into the corresponding BAM file?

Cheers.

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written by Tom_L Tom_L

the quality of base calling for those reads is ~30 at that position. I guess this is not the main problem.

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written by mt1022 mt1022

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