TABLE 2.

Validation of large-insertion mapping strategies with real experimental data.

References	Sequenced sample	Results obtained by Easymap
Wilson-Sánchez et al. (2014)	Pool of 10 SALK mutants	17 of 19 known insertions were detected by Easymap; the remaining 2 were filtered out as false positives due to very few supporting reads (average RD per sample was 4.5×, instead of the recommended 10×)
Lup and Micol, unpublished	Pool of 6 SALK mutants	9 insertions detected
Yang et al. (2013)	Mutagenized T1c-19 rice	2 of 2 insertions detected; 2 clearly distinguishable false positives
	Mutagenized TT51-1 rice	2 of 2 insertions detected; 47 clearly distinguishable false positives due to the presence of an endogenous sequence in the insertion sequence
Li W.X. et al. (2016)	Mutant T027	2 of 2 insertions detected; 1 false positive common to all lines from this article (omitted below)
	Mutant T182	1 of 1 insertion detected; 1 false positive
	Mutant T204	1 of 1 insertion detected
	Mutant T273	1 of 1 insertion detected split in two clusters due to a large deletion in the mutagenized genome
	Mutant T400	1 of 1 insertion detected

See Supplementary Table 1 for more detailed information.