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Table 1 Performance evaluation of HANDS

From: HANDS: a tool for genome-wide discovery of subgenome- specific base-identity in polyploids

 

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%)

  1. 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%.