Question: Whole exome sequencing coverage
0
gravatar for alok.helix
13 months ago by
alok.helix80
India
alok.helix80 wrote:

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

sequencing exons alignment gene • 499 views
ADD COMMENTlink modified 13 months ago by WouterDeCoster39k • written 13 months ago by alok.helix80
1
gravatar for Vijay Lakhujani
13 months ago by
Vijay Lakhujani4.2k
India
Vijay Lakhujani4.2k wrote:

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
ADD COMMENTlink written 13 months ago by Vijay Lakhujani4.2k
1
gravatar for WouterDeCoster
13 months ago by
Belgium
WouterDeCoster39k wrote:

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.

ADD COMMENTlink written 13 months ago by WouterDeCoster39k

Thank WouterDeCoster for adding this. I agree on that!

ADD REPLYlink written 13 months ago by Vijay Lakhujani4.2k
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