Comparing Read Depth between 2016 and first plate of 2017

I realized that I did not really know how the average read depth per individual compared between 2016 and 2017. So I checked it out using the VCF files built from the 2016 and 2017 data separately. I then pulled out average read depth (DP) per scaffold and graphed that against length, separating out scaffolds based on blast information.

Here is the data for 2016. You can see average log10 read depth for the good Daphnia scaffolds falls out a little above 2.5 (~2.65). This equates to an average read depth of 446 per scaffold, which gives about 8X per individual (55 individuals).

Here is the data for 2017. You can see that average log10 read depth for the good Daphnia scaffolds falls out a little above 3 (~3.15). This equates to an average read depth of 1400 per scaffold, which gives about 15X per individual (92 individuals). This is better than the 2016 individuals. Part of that is due to doing a bit more sequencing, but also due to the fact that we are not losing reads to microbes.