coverage in amplicon sequecing method

Question

[Picasa]

Hi,

There is a point I don't really understand. It's about coverage of amplicons (obtained via amplicon sequencing).

For example, in this figure (at the top):

that the coverage is not the same along the region. What can explan this ? I don't understand why we don't have a homogene distribution such as this figure :

Because an amplicon sequencing uses a pcr amplification, so you should have same ammount of data ?

Thanks in advance.

[Fabio Marroni]

1. They plotted in log10 scale, you didn't. Also, Why don't they give you a measure, instead of an "arbitrary linear scale"? It's impossible to understand what you have in hand.

2. Not all amplicon sequencing experiments have the same efficiency. Uneven coverage may also depend on mappability/repetitiveness of the region you are sequencing. I would not be too much worried about (not too big) variations in coverage, if all of the interesting regions are covered to a decent level.