Table 2. Comparison of GINDEL, two versions of Genome STRiP (with different setting of the effective length threshold), Pindel and Clever-sv on simulated data.

Coverage	Length	Del. Num.	GINDEL	Genome STRiP v1	Genome STRiP v2	Pindel	Clever-sv
10×	50–200	70	0.9869	0.0000	0.6254	0.5476	0.9857
	200–400	46	0.9769	0.4423	0.8349	0.5502	0.9859
	400–500	13	1.0000	0.8516	0.9327	0.3333	1.0000
	500–1500	34	1.0000	0.9942	0.9942	0.5830	0.9948
	>1500	58	0.9979	0.9805	0.9805	0.5950	0.9540
6.4×	50–200	70	0.9791	0.0000	0.5679	-	0.8867
	200–400	46	0.9697	0.3927	0.7869	-	0.9754
	400–500	13	1.0000	0.8496	0.9162	-	0.9915
	500–1500	34	1.0000	0.9542	0.9542	-	0.9699
	>1500	58	0.9967	0.9548	0.9667	-	0.9345
4.2×	50–200	70	0.9645	0.0000	0.4429	-	0.6756
	200–400	46	0.9651	0.3562	0.6984	-	0.9068
	400–500	13	1.0000	0.8308	0.8940	-	0.9538
	500–1500	34	0.9979	0.9144	0.9144	-	0.9458
	>1500	58	0.9963	0.9686	0.9801	-	0.8966

Results on the percentage of correctly called genotypes are given for deletions with different lengths. Del. Num. indicates the number of deletions in specific length (the number of genotypes is Del. Num. multiply the number of individuals), and because Pindel discovers 104 out of the 221 deletions, so the number of deletions in each specific length (from small to large) are: 24, 21, 5, 20, and 34 respectively. Pindel does not call genotype for data with lower coverages. So no results are reported.