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

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

	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

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).

ISSN: 1471-2164