Table 1.

Reference allele frequency panels used for estimating contamination

Population	Number of sites	Number of sites (filtered)a	Number of individuals
HapMap_ASW	38 703	31 324	90
HapMap_CEU	73 562	58 190	180
HapMap_CHB	67 307	51 494	90
HapMap_GIH	34 158	26 098	100
HapMap_JPT	64 290	49 715	91
HapMap_LWK	39 992	31 119	100
HapMap_MEX	34 360	23 190	90
HapMap_MKK	37 935	29 612	180
HapMap_TSI	33 928	25 097	100
HapMap_YRI	89 604	72 546	180

^aNumber of single nucleotide polymorphism (SNPs) included for each population after applying the filtering described in the text. Data were downloaded from http://hapmap.ncbi.nlm.nih.gov/downloads/frequencies/2010-08_phaseII+III/allele_freqs_chrX_CEU_r28_nr.b36_fwd.txt.gz.