Calculation Of Quality Of The Consensus Genotype

Question

[Elisa]

Hi everybody. I am analyzing SOAP data from exome-sequencing, and I have a quality of consensus genotype. Because we do not see a correspondence between coverage and this quality value (for example I have high coverage and low consensus quality), I ask how is this calculated? In the file .cns where I have the creation of consensus and information about the best bases, I have always a so high difference between the best bases uniquely mapped and the total bases mapped. This is only due to the presence of pseudogenes or are there other reasons? Thank you very much for your help! Elisa

Answer 1

[Larry_Parnell]

As a partial answer I can offer that the quality of the genotype arises from the quality of the individual sequence reads. The region can be low coverage but of high-quality reads, or vice versa, or a combination. The quality of the sequence read is derived from detection signals from the sequencer itself.