Understanding the values in a VCF

[lre1234]

Hi all,

In my generated VCF file (from samtools mpileup) some of my info fields are these:

##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">

My question is in regarding the Mann-Whitney U test. I know it says that higher is better, but generally, is considered a good cut-off for a Mann-Whitney test. From what I have been able to find about these statistics is that it is essentially a pValue, so wouldn't a value <=0.05 be better? I am probably completely misunderstanding this.

[dpryan]

A number <= 0.05 would indicate significant bias, which is the opposite of what you want.