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Table 3 Variants from each category submitted to Affymetrix, classified by Affymetrix, and tiled on the final array

From: Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa

  SNP mSNP Indel SNP-SNP Indel-SNP SNP-in-Insertion F1D Codon-based
Submitted candidates 159,721 1,940 12,801 7,764 2,937 4,921 17,518 28,646
Affymetrix classification         
Recommended (F) 81,792 380   3,598 433 487 3,185 5,327
Recommended (R) 7,576 359   2,441 541 1,465 3,262 4,876
Recommended (F & R) 23,556 470     296 1,013 12,928
Neutral (F) 815 170 1,035 464 125 355 1,356 939
Neutral (R) 834 147 3,520 589 107 216 1,225 886
Neutral (F & R) 2,298 476 4,999    41 109 1,774
Tiled on array         
No. of target sites 63,263 1,761 9,528 7,092 1,177 2,843 3,751 5,648
No of probesets 86,817 19,050 10,558 7,092 1,206 3,376 4,000 6,000
  1. Filtered candidates from each variant category were classified by the Affymetrix’ in silico design scores into ‘recommended’ and ‘neutral’ in the forward (F) strand, in the reverse (R) strand, and in both forward and reverse (F&R) strands. A ‘not-recommended’ class is not listed here as none of the candidates in this category were tiled on the array. Also listed are the number of markers or polymorphisms tiled on the array and the corresponding number of probe sets (one or more probes whose intensities are combined to interrogate a marker).
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