Table 1.

Recovery of Est-1 variants by using SHORE

		Predicted by both analysesa	Private to genome graph analysis	Private to reference-only analysis	Total gain in genome graph analysis
SNPs		401,158	66,264	5,423	15.0%
Deletions	All	25,926	6,807	778	22.6%
	1-3 bp	25,865	5,256	778	16.8%
	≥ 4 bp	61	1,551	0	2,542%
Insertions	All	22,305	9,220	678	37.2%
	1-3 bp	22,285	7,379	678	29.2%
	≥ 4 bp	20	1,841	0	9,205%

^aIncludes variants predicted by graph analysis that have been found in the single-reference analysis in the same sequence context, although with a differing position, resulting from ambiguous alignments. Some of the variants longer than 3 bp could be reassembled in the single-reference analysis, by combining shorter indels.