Table 1.
Summary of autosomal SNPs
| OOA | CEU | Overlap | |
|---|---|---|---|
| Total genotyped | 489,922 | 489,922 | 489,922 |
| >1 duplicate inconsistency1 | 51,459 | NA | NA |
| >5% missing data2 | 50,085 | 16,896 | 8,973 |
| Mendelian inconsistencies2,3 | 3,188 | 1,168 | 202 |
| p<10−6 for HWE test4 | 379 | 217 | 116 |
| Passed QC filter5 | 415,440 | 472,851 | 409,071 |
| Passed QC in both OOA and CEU | |||
| Monomorphic4 | 68,869 | 57,669 | 52,467 |
| Polymorphic4 | |||
| MAF≥0.05 | 297,605 | 310,704 | 287,476 |
| MAF≥0.10 | 256,614 | 267,149 | 240,375 |
| MAF≥0.20 | 182,941 | 189,133 | 161,062 |
OOA = Old Order Amish
CEU = U.S. Utah residents from HapMap
MAF = Minor Allele Frequency
Note: SNPs that failed a QC measure in either sample were excluded from further analysis, and SNPs with MAF≥0.05 passing QC in both samples (n=287,476) were used for LD analysis.
1
Based on the 61 OOA individuals who were also genotyped on the Affymetrix 6.0 array; SNPs with more than one duplicated genotype discrepancy were excluded.
2
Based on 837 OOA and 90 CEU individuals (30 trios).
3
SNPs with >5 and >1 Mendelian inconsistencies in OOA and CEU, respectively.
4
Based on 60 unrelated individuals (30 men and 30 women) from each sample.
5
SNPs may fail QC in more than one way, so rows do not sum to the subtotal passing QC.