Table 1.

Performance evaluation of HANDS

	Chromosome 1			Chromosome 5
	A	B	D	A	B	D
HSP positions	32,993	32,993	32,993	40,783	40,783	40,783
Positions ignored	4,669	5,540	4,205	6,230	7,284	4,420
Diploid coverage low	831	1,318	523	969	1,768	753
Diploid ambiguous	45	202	59	60	1,095	77
NT unassigned	2,627	2,627	2,627	2,866	2,866	2,866
Sub genome silenced	1,166	1,393	996	2,335	1,555	724
Position considered	28,324	27,453	28,788	34,553	33,499	36,363
Correct assignment	27,268 (96.27%)	25,746 (93.78%)	28,185 (97.91%)	33,371 (96.58%)	31,448 (93.88%)	35,565 (97.81%)
Incorrect assignment	882 (3.11%)	1,252 (4.56%)	470 (1.63%)	966 (2.80%)	1,518 (4.53%)	598 (1.64%)
No assignment	174 (0.61%)	455 (1.66%)	133 (0.46%)	216 (0.63%)	533 (1.59%)	200 (0.55%)

HSP bases were characterized for wheat chromosomes 1 and 5 using the T. aestivum nullisomic-tetrasomic lines and compared against the results obtained from HANDS. HANDS assigned the subgenome-specific base-identify with accuracy between 94% and 98%.