Observed SFS, confidence intervals from bootstrap procedures and simulated SFS #---------------------------------- #---- Rscripts #---------------------------------- Main script plots_SFS.R which uses - functions.R Observed SFS are done be launching makeSFS.sh (which calls *.py files) while CI are by launching makeSFSbootstrap.sh (which calls - bootstrap.R) #---------------------------------- #--- SFS files #---------------------------------- - *extension* #Header SFS YRI LWK IBS GBR PJL BEB KHV JPT CLM PEL There are 11 columns with headers 1 Recombination and SFS category There are 20 recombination bins (from 0 to 19) + a bin for recombination above 1.5 cM/Mb (nb. 20) The SFS is unfolded and goes from 0 to 20 (10 individuals per populations). 2-11 the 10 populations of 1000G *extension* - limites_rec.txt all SNPs with 20 bins of recombinations - limites_rec_noBGC.txt all WW+SS - limites_rec_NTR50kb.txt same as above with more than 50kb from transcribed regions - limites_rec_SW.txt Strong to Weak polymorphisms - limites_rec_WS.txt Weak to Strong - neutral_all all WW+SS with RR>=1.5cM/Mb - neutral_[NTR/TR/NTR.50kb/syn/nonsyn] with also filtering on syn,nonsyn,NTR50kb,TR,NTR regions - syn synonymous polymorphisms - nonsyn nonsynonymous - NTR.50kb - neutral_exonic either within or outside exons - neutral_ConsElt46.0p0003cM above or below 0.0003cM from conserved elements - neutral_ConsElt46_quantile.cM 1st or 4t quartile of distance to conserved elements - neutral_DisHotspot_quantile.cM same for ditance to hotspots - bstat0p9 B>0.9 - gronau 35,574 neutral 1kg regions #---------------------------------- #--- Confidence intervals #---------------------------------- Confidence intervals from bootstrap procedures: bootstrap_standardDeviation estimates.* These files are available in confidenceIntervals.zip There are 21 columns (21 bins for the unfolded SFS) Rows have names that correspond to: - standard deviation - confidence interval 2.5% - confidence interval 97.5% - the recombination category (2,10 or 20, the represented ones) - the type of sites : synonymous, NTR50kb or WW+SS>=1.5cM/Mb pvalues are obtain using p_values_SFS.R #---------------------------------- #--- Simulated SFS from SLiM #---------------------------------- Simulated SFS from SLiM simulations - summary_neu_twoBtln* for YRI and JPT populations #Header freq.cat sfs.aver sfs.2.5 sfs.97.5 sfs.25 sfs.75 There are 6 columns with the average SFS from the simulations (sfs.aver) and confidence intervals (at 5% --> sfs.2.5 and sfs.97.5 or at 50% --> sfs.25 and sfs.75) while freq.cat is the observed sfs.