PHRED quality score

[EvaRei]

hello everbody,

I have following vcf file:

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 56700
chr1 14653 . C T 27 VARQ AC1=1;AF1=0.5;DP4=7,0,6,0;DP=15;FQ=29.9;FUNC=noncoding;MED=39;MQ=23;PV4=1,0.32,1,0.21;SF=0.33;VDB=0.0044;VP=0.35 GT:PL : DP:SP:GQ 0/1:57,0,72:13:0:60

can somebody please explain the QUAL column (phred quality score) of my vcf file. in the column QUAL I have values ranging from 3 to 225 (in this case 27). I guess the higher the value the more confident the calls are. but does anyone can help me with some reasonable cut offs?

thanx

[mbblack]

Generally, a base QV is

Q = -10log10(e) where e is the expectation of a base being called incorrectly

So, a QV of 10 means a probability of 1 in 10 of calling a base incorrectly, or a Base Call Accuracy of 90%. A QV of 20 means a 1 in 20 probability, or 99% accuracy. QV = 30 would be 1 in 1000, or 99.9% accuracy, and so on.

The values range from 0 to 255, but 0 really means the base was absent or undetected, and 255 means it was detected, but the QV could not be assigned (basically, the detector saw something but the signal was not good enough or clean enough to assign a quality score).

QV > 10 is a pretty common cutoff for both base calls and for mapping QVs.