Table 2.

Validation of polymorphism predictions in Est-1

			Graph analysis		Single-reference analysis
		N a	Recallb	FDRc	Recallb	FDR†
SNPs		2,316	85.2%	0.4%	77.5%	0.4%
Deletions	All	183	53.6%	2.0%	38.8%	2.7%
	1-3 bp	132	68.2%	2.2%	53.8%	2.7%
	≥ 4 bp	51	15.7%	0.0	0	n/a
Insertions	All	167	53.9%	2.2%	45.5%	1.3%
	1-3 bp	128	66.4%	2.3%	59.4%	1.3%
	≥ 4 bp	39	12.8%	0.0	0	n/a

^aNumber of known variants in 600 kb of dideoxy sequence data from [38]. ^bRatio of confirmed to the sum of confirmed and missed predictions of the respective kind; indicates sensitivity of method. ^cFalse discovery rate, percentage of erroneous calls.