pvmsp1DeepSeek - christianparobek/cambodiaWGS GitHub Wiki

These documents are in my dropbox. Maybe consider reanalyzing the clustering data once through just to make sure I have good records of what was done?

####19 May 2016 Ended up reclustering a while ago and finding good concordance between our pvmsp1 data and our Fws data, using a 10% cutoff.

Jon wants to calculate average MOI for our WGS samples. We should use the same cutoff as Jess's 2015 pvmsp1 deep-sequencing paper: 0.5%. Additionally, I want to set very stringent cutoffs for coverage and missing data.

In summary, we have WGS-derived Fws values for 55 OM samples.

• Of these 55, 47 we have pvmsp1 data.
• Of these 47, 41 have both R1 and R2 data.
• Of these 41, 27 we have 1000x coverage for both reps.