A summary of the genotyping for two representative batches of the HapMap study
|
Batch |
Detection scheme |
Probes designed |
Base-call parameters |
Probes converted |
Conversion |
Repeatability |
Trio accuracy |
Completeness |
|---|---|---|---|---|---|---|---|---|
| 4 | 2 color | 6072 | 1 | 5469 | 90.1% | 99.5% | 99.6% | 98.0% |
| 6072 | 2 | 5127 | 84.4% | 99.6% | 99.7% | 99.3% | ||
|
|
6072
|
3
|
4706
|
77.5%
|
99.8%
|
99.9%
|
99.25%
|
|
| 4 color | 6072 | 1 | 5729 | 94.4% | 99.6% | 99.6% | 98.6% | |
| 6072 | 2 | 5416 | 89.2% | 99.6% | 99.7% | 99.7% | ||
|
|
|
6072
|
3
|
4984
|
82.1%
|
99.9%
|
99.96%
|
99.5%
|
| 6 | 2 color | 12234 | 1 | 10924 | 89.3% | 99.5% | 99.7% | 98.6% |
| 12234 | 2 | 10341 | 84.5% | 99.7% | 99.7% | 99.6% | ||
|
|
|
12234
|
3
|
9517
|
77.5%
|
99.95%
|
99.9%
|
99.5%
|
-
Batch 4 contains 6072 probes and was genotyped across the population using a two-color detection method and then repeated using a four-color detection method. Batch 6 contained 12,234 probes and was only genotyped using a two-color assay. The performance metrics are defined in the text. Results are shown for each data set with varying choices of base-calling parameters. “Parameter set 1” optimizes the conversion rate, “Parameter set 2” optimizes the completeness of the set of converted markers and “Parameter set 3” optimizes the concordance metrics as a surrogate for accuracy.
