Table 3.

Summary of correctly called structural variations by Astrolabe, Aldy, and Stargazer in set 2.

Set 2	Truth	Astrolabe			Aldy			Stargazer
		30×	60×	100×	30×	60×	100×	30×	60×	100×
Full gene deletion (*5)	20	10	5	10	15	14	15	15	15	15
Copy number gaina	52	29	25	25	52	50	52	47	45	45
Resolved duplicated/ multiplicated alleles	61	4c	4c	4c	53	49	51	54	51	48
Hybridsb	107	3	8	8	72	66	67	31	30	28
Non-hybrid tandem	4	0	0	0	4	4	4	0	0	0
Ungenotyped (defaults)		0	0	0	1	3	2	18	16	19

The complete list of genotypes called per sample is provided in Supplementary Data Set 4.

^aDue to gene duplications/multiplications.

^bCollectively representing exon conversions and gene hybrids involving CYP2D6 and CYP2D7.

^cDetermined only for homozygous allele cases.