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 |