Table 1.
GiSNP statistics for SNPs genotyped across Chromosome 20 in four population samples
|
Population |
African American |
Asian |
CEPH |
UK Unrelateds |
|---|---|---|---|---|
| Sample size | 97 | 42 | 47 Founders | 91 |
| Total SNPs | 33,206 | 25,719 | 28,223 | 28,460 |
| Total giSNPs | 10,081 | 16,506 | 17,464 | 15,680 |
| % of all SNPs that are giSNPs | 30.3% | 64.2% | 61.9% | 55.1% |
| Total giSNP clusters | 3527 | 4060 | 4527 | 4313 |
| Mean giSNP cluster length | 11.6 kb | 14.8 kb | 15.3 kb | 13.7 kb |
| Median giSNP cluster length | 3.5 kb | 5.5 kb | 5.7 kb | 5.1 kb |
| Mean number of giSNPs per cluster | 2.9 | 4.1 | 3.9 | 3.6 |
| MAF 0-10% giSNPs | 2473 (24.5%) | 2704 (16.4%) | 3108 (17.8%) | 3423 (21.8%) |
| MAF 10-20% giSNPs | 2376 (23.6%) | 3764 (22.8%) | 3883 (22.2%) | 3125 (19.9%) |
| MAF 20-30% giSNPs | 1994 (19.8%) | 3571 (21.6%) | 3848 (22.0%) | 3248 (20.7%) |
| MAF 30-40% giSNPs | 1736 (17.2%) | 3571 (21.6%) | 3607 (20.7%) | 2983 (19.0%) |
| MAF 40-50% giSNPs
|
1499 (14.9%)
|
2894 (17.5%)
|
3018 (17.3%)
|
2901 (18.5%)
|
-
SNPs with only one or two heterozygotes were removed from the analysis, resulting in lowered levels of MAF <10% SNPs.
