Table 1.

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.