Table AI.
Summary of X chromosome SNPs
| OOA | CEU | Overlap | |
|---|---|---|---|
| Total genotyped | 10,525 | 10,525 | 10,525 |
| >1 duplicate inconsistencya | 1,061 | NA | NA |
| >5% missing datab | 547 | 461 | 261 |
| Mendelian inconsistenciesb,c | 44 | 246 | 10 |
| P<10−6 for HWE testd | 0 | 0 | 0 |
| Passed QC filtere | 9,139 | 10,064 | 8,972 |
| Passed QC in both OOA and CEU | |||
| Monomorphicd | 2,272 | 1,905 | 1,805 |
| Polymorphicd | |||
| MAF≥0.05 | 5,763 | 6,106 | 5,516 |
| MAF≥0.10 | 4,971 | 5,376 | 4,449 |
| MAF≥0.20 | 3,571 | 3,925 | 2,929 |
OOA, Old Order Amish; CEU, US Utah residents from HapMap; MAF, minor allele frequency. 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=5,516) were used for LD analysis.
a
Based on the 61 OOA individuals who were also genotyped on the Affymetrix 5.0 array; SNPs with more than one duplicated genotype discrepancy were excluded.
b
Based on 837 OOA and 90 CEU individuals (30 trios).
c
SNPs with >5 and >1 Mendelian inconsistencies in OOA and CEU, respectively.
d
Based on 60 unrelated individuals (30 men and 30 women) from each sample.
e
SNPs may fail QC in more than one way, so rows do not sum to the subtotal passing QC.