Table 1.
Genotyping Accuracy
|
|
Sampled SNPs |
Total SNPs |
Individuals or families |
Genotypes compared |
Discordances or inheritance errors |
Discordant SNPs |
Concordance |
|---|---|---|---|---|---|---|---|
| Single base extension | 543 | 11,560 | 40 | 21,191 | 98 | 33 | 99.5% ± 0.2% |
| Dideoxy sequencing | 60 | 11,555 | 6 | 341 | 1 | 1 | 99.7% ± 0.7% |
| Mendelian inheritance
|
11,555
|
11,555
|
5 trios
|
167,649
|
61
|
60
|
99.96% ± 0.01%
|
-
Discordances were based on comparisons to reference genotypes. No calls or missing reference genotypes were omitted from the comparisons. For inheritance analysis, discordances refer to the occurrence of inheritance errors in family trios as determined by PEDCHECK (O'Connell and Weeks 1998). Discordant SNPs had at least one discordance or inheritance error. Standard deviations represent the variance among individuals in the case of concordance measures, and families in the case of inheritance analysis.
