Table 2

Pre-processing statistics of HapMap phase III datasets and sub-continental population classification problems
Dataset/Problem Samples All SNPs SNPs with call rate < 100% SNPs on Non-autosomal Chr. SNPs deviated from HWE Filtered SNPs Unfiltered SNPs
ASW 87 1458387 214898 34554 94234 298524 1159863
CEU 165 1458387 376531 34554 81633 427638 1030749
CHB 137 1458387 353208 34554 77028 423270 1035117
CHD 109 1458387 352031 34554 77111 421328 1037059
GIH 101 1458387 234863 34554 85463 314376 1144011
JPT 113 1458387 271105 34554 75502 337033 1121354
LWK 110 1458387 365638 34554 97174 425375 1033012
MKK 184 1458387 411395 34554 105490 471384 987003
MXL 86 1458387 311704 34554 86910 387207 1071180
TSI 102 1458387 268916 34554 81919 326585 1131802
YRI 203 1458387 423100 34554 94449 476513 981874
European 267 1458387 493449 34554 137488 575492 882895
East Asian 250 1458387 475217 34554 129695 565554 892833
African 497 1458387 742671 34554 228268 841790 616597
North American 548 1458387 803678 34554 306572 931993 526394
Kenyan 294 1458387 590202 34554 170547 677326 781061
Chinese 246 1458387 538224 34554 131394 629023 829364

Hajiloo et al.

Hajiloo et al. BMC Bioinformatics 2013 14:61   doi:10.1186/1471-2105-14-61

Open Data