I have a question regarding coverage levels of different scaffolds in an assembly to better my understanding of genome assemblies. Say my species of interest is the one shown in the orange points in the below example blobplot (produced using Blobtools), how can the coverage vary so much for scaffolds of the same species (for example the majority of orange points are around 10^3, but then there are some that are around coverage of 10^1). Is this due to uneven coverage that this genome has? Or do these lower coverage reads just have a lot of errors in them?
I know there are only a few orange point around 10^1 but I have seen other examples where there is basically two clusters for the same species (one at high and one at lower coverage)
Thanks for any input!