"Quantification of GC-biased gene conversion in the human genome"
S. Glémin, P.F. Arndt, P.W. Messer, D. Petrov, N. Galtier, and L. Duret.


To use the Mathematica file, gBGCEstimation.nb.txt, first remove the .txt extension.

Legend of the column names for the B_estimates files

.POP = .AFR, .EUR or .EAS as function of the population
Average around SNPs are computed specifically for each population so the value are not exactly the same.
Columns 1 and 2 are the same for all populations and can be used to merge the three population files.


chromosome	:	Chromosome number
window_inMb	:	Window's poistion in Mb
localGC_100bp.POP	:	GC content of the 100bp around each SNP was computed and average over the window
rec1KG_YRI.5kb.POP	:	Recombination rate at 5kb (1KG YRI map) around each SNP was computed and average over the window
rec1KG_CEU.5kb.POP	:	Recombination rate at 5kb (1KG CEU map) around each SNP was computed and average over the window
rec1KG_CHBJPT.5kb.POP	:	Recombination rate at 5kb (1KG CHBJPT map) around each SNP was computed and average over the window
recHM_5kb.POP	:	Recombination rate at 5kb (HapMap map) around each SNP was computed and average over the window
recDECODE.5kb.POP	:	Recombination rate at 5kb (deCODE map) around each SNP was computed and average over the window
fracHotPop.POP	:	Fraction of hotspot in the window (population specific hotspots)
recHotPop.POP	:	Average recombination rate in hotspots in the window (population specific hotspots)
recColdPop.POP	:	Average recombination rate in coldspots in the window (population specific hotpsots)
ratiorecPop.POP	:	Ratio of recombination rate in hotpsots and coldspots in the window (population specific hotspots)
fracHotHM.POP	:	Fraction of hotspot in the window (HapMap hotspots)
recHotHM.POP	:	Average recombination rate in hotspots in the window (HapMap hotspots)
recColdHM.POP	:	Average recombination rate in coldspots in the window (HapMap hotspots)
ratiorecHM.POP	:	Ratio of recombination rate in hotpsots and coldspots in the window (HapMap hotspots)
fracHotHMT6.POP	:	Fraction of hotspot in the window (HapMap hotspots threshold 6cM/Mb)
recHotHMT6.POP	:	Average recombination rate in hotspots in the window (HapMap hotspots threshold 6cM/Mb)
recColdHMT6.POP	:	Average recombination rate in coldspots in the window (HapMap hotspots threshold 6cM/Mb)
ratiorecHMT6.POP	:	Ratio of recombination rate in hotpsots and coldspots in the window (HapMap hotspots threshold 6cM/Mb)
B_M1.POP	:	B estimate model M1
lambda_M1.POP	:	lambda estimate model M1
B_M1star.POP	:	B estimate model M1*
lambda_M1star.POP	:	lambda estimate model M1*
eN_M1star.POP	:	neutral error estimate model M1*
eWS_M1star.POP	:	WS error estimate model M1*
eSW_M1star.POP	:	SW error estimate model M1*
B0_M3starPop.POP	:	B0 estimate model M3* (population specific hotspots)
B1_M3starPop.POP	:	B1 estimate model M3* (population specific hotspots)
Bmean_M3starPop.POP	:	mean B estimate model M3* (population specific hotspots)
lambda_M3starPop.POP	:	lambda estimate model M3* (population specific hotspots)
B0_M3starHM.POP	:	B0 estimate model M3* (HapMap hotspots)
B1_M3starHM.POP	:	B1 estimate model M3* (HapMap hotspots)
Bmean_M3starHM.POP	:	mean B estimate model M3* (HapMap hotspots)
lambda_M3starHM.POP	:	lambda estimate model M3* (HapMap hotspots)
B0_M3starHMT6.POP	:	B0 estimate model M3* (HapMap hotspots threshold 6cM/Mb)
B1_M3starHMT6.POP	:	B1 estimate model M3* (HapMap hotspots threshold 6cM/Mb)
Bmean_M3starHMT6.POP	:	mean B estimate model M3* (HapMap hotspots threshold 6cM/Mb)
lambda_M3starHMT6.POP	:	lambda estimate model M3* (HapMap hotspots threshold 6cM/Mb)
lnLM0.POP	:	log-likelihood model M0
lnLM1.POP	:	log-likelihood model M1
lnLM0star.POP	:	log-likelihood model M0*
lnLM1star.POP	:	log-likelihood model M1*
lnLM3starHMPop.POP	:	log-likelihood model M3* (population specific hotspots)
lnLM3starHM.POP	:	log-likelihood model M3* (HapMap hotspots)
lnLM3starHMT6.POP	:	log-likelihood model M3* (HapMap hotspots threshold 6cM/Mb)
lnLmax.POP	:	log-likelihood saturated model