Table 3.
HapMap Phase I genotyping success measures
| Analysis panel
|
|||
|---|---|---|---|
| SNP categories | YRI | CEU | CHB + JPT |
| Assays submitted | 1,273,716 | 1,302,849 | 1,273,703 |
| Passed QC filters | 1,123,296 (88%) | 1,157,650 (89%) | 1,134,726 (89%) |
|
| |||
| Did not pass QC filters* | 150,420 (12%) | 145,199 (11%) | 138,977 (11%) |
| > 20% missing data | 98,116 (65%) | 107,626 (74%) | 93,710 (67%) |
| > 1 duplicate inconsistent | 7,575 (5%) | 6,254 (4%) | 10,725 (8%) |
| > 1 mendelian error | 22,815 (15%) | 13,600 (9%) | 0 (0%) |
| < 0.001 Hardy–Weinberg P-value | 12,052 (8%) | 9,721 (7%) | 16,176 (12%) |
| Other failures† | 23,478 (16%) | 17,692 (12%) | 23,722 (17%) |
|
| |||
| Non-redundant (unique) SNPs | 1,076,392 | 1,104,980 | 1,087,305 |
| Monomorphic | 156,290 (15%) | 234,482 (21%) | 268,325 (25%) |
| Polymorphic | 920,102 (85%) | 870,498 (79%) | 818,980 (75%) |
|
| |||
| All analysis panels | |||
|
| |||
| Unique QC-passed SNPs | 1,156,772 | ||
| Passed in one analysis panel | 52,204 (5%) | ||
| Passed in two analysis panels | 97,231 (8%) | ||
| Passed in three analysis panels | 1,007,337 (87%) | ||
|
| |||
| Monomorphic across three analysis panels | 75,997 | ||
| Polymorphic in all three analysis panels | 682,397 | ||
|
| |||
| MAF ≥ 0.05 in at least one of three analysis panels | 877,351 | ||
*
Out of 95 samples in CEU, YRI; 94 samples in CHB + JPT.
†
‘Other failures’ includes SNPs with discrepancies during the data transmission process. Some SNPs failed in more than one way, so these percentages add up to more than 100%.