Hello,
I was wondering was coverage you need to do genome re-sequencing in illumina (Illumina HighSeq 2000) ?
I was told 100x, which seems high, but I read that people often seem to use a 20-30x coverage.
Moreover, is it necessary to have a higher coverage to look for intra-population selective sweeps (from individual samples), than to investigate the genomic architecture of differenciation between sister species ?
Thank you by advance for you answer.
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helene.badouin •
Just an example of whole genome coverage:
Rather than giving you a hard number here are two articles that answer your questions.
Assessing the accuracy and power of population genetic inference from low-pass next-generation sequencing data. Crawford & Lazzro 2012.
Low-coverage sequencing: Implications for design of complex trait association studies. Li et al 2011.
Whole genome depth modeling:
Exome dist:
Thank you for the link. The first one in particular is very relevant for my interests (non human populations with small sample sizes).
Coverage should follow a Poisson distribution, so if your mean coverage is 30X, you will fall below 20X about 3.5% of the time. In theory to get 30X at 99% of locations you will need a mean of 45X coverage.
Unfortunately the genome does not respect this distribution and you will often see deserts and hotspots with thousands of reads, although this is largely a mappability issue.
Yup, it is naughty data. I Often see that a negative binomial is a better fit.
using the negative binomial, what mean coverage is necessary to have 99% of bases covered at 30X?
I guess I should have been more clear: this was for exome data. I also added a plot for WG data in my original post.
Exome depth histograms often look more like:
n<-100000 hist(rpois(n,rgamma(n,2,0.0333)))
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In which species do you intend to work? You know what's the quality of their genome?
It's a phytopathogen fungi genome, with a high GC-rate, so I think we're going to re-sequence several individuals at a high coverage at first (100x). Then we'll do some sampling, to see how much we can lower the coverage for further experiments without decreasing sensitivity.