Table 1.

The Number of Variants Detected by Illumina Short Reads, PacBio Long Reads, and Genome Alignment.

Variant Type	Illumina	PacBio	Genome Alignment
			LASTZ	MUMmer
Number of samples	347	10	14	14
TRA	76,835	85,279		1,332
DUP	48,132	213	3,700	2
DEL	72,930	60,747	62,953	48,153
INV	341,752	11,532	159	343
INS		103,447	70,065	113
MEI	284,741	270,708	246,340
Total	824,390	531,926	390,823