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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%.