Genetic maps generated from the 1000G phased OMNI data. OMNI haplotypes were obtained from the Phase 1 dataset (/vol1/ftp/phase1/analysis_results/supporting/omni_haplotypes/). Genetic maps were generated for each population separately using LDhat (http://ldhat.sourceforge.net/). Haplotypes were split into 2000 SNP windows with an overlap of 200 SNPs between each window. The recombination rate was estimated for each window independently, using a block penalty of 5 for a total of 22.5 million iterations with a sample being taken from the MCMC chain every 15,000 iterations. The first 7.5 million iterations were discarded as burn in. Once rates were estimated, windows were merged by splicing the estimates at the mid-point of the overlapping regions. LDhat estimates the population genetic recombination rate, rho = 4Ner. In order to convert to per-generation rates (measured in cM/Mb), the LDhat rates were compared to pedigree-based rates from Kong et al. (2010). Specifically, rates were binned at the 5Mb scale, and a linear regression performed between the two datasets. The gradient of this line gives an estimate of 4Ne, allowing the population based rates to be converted to per-generation rates. Using the above method, the effective population sizes for each population were estimated as follows. ACB 17939.993963 ASW 17150.137312 CDX 12255.652372 CEU 11490.672741 CHB 13038.180071 CHS 11962.133624 CLM 10862.696703 FIN 9648.177725 GBR 11314.802435 GIH 12990.359505 IBS 11635.830405 JPT 11600.019740 KHV 12339.783775 LWK 18861.336542 MKK 16951.674498 MXL 9995.936127 PEL 8315.793426 PUR 11946.510129 TSI 12787.027208 YRI 15898.782067 Adam Auton (adam.auton@einstein.yu.edu) May 7th, 2013