Whole exome sequencing coverage

Question

[alok.helix]

Kit used: Agilent Sureselect all exon V6 what does 200 fold average coverage mean in whole exome sequencing?

Answer 1

[lakhujanivijay]

Fold average coverage is used to describe the sequencing depth. For example, if your genome has a size of 100 Mb and you have 1 Gb of sequencing data (Total bases of all the reads) then you have

1000,000,000 (1 Gb) / 100,000,000 (100 mb) = 10x coverage

Answer 2

[WouterDeCoster]

Coverage refers to the number of independent sequencing reads spanning a locus or nucleotide.

The answer of Vijay Lakhujani is correct for genome sequencing, but since you are asking about exome sequencing the situation is slightly different. You are obviously only targetting a subset of the genome. Since you are using PCR amplification your coverage will biased, for example, the coverage of GC rich regions, such as 5' UTR sequences, will be less because those regions amplify less well.

So the average locus has 200 reads covering the locus, but some will have more and other will have less.

[lakhujanivijay]

Thank WouterDeCoster for adding this. I agree on that!