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Table 2 Single feature polymorphism (SFP) comparison with sequence-characterized SNPs

From: Single-feature polymorphism discovery in the barley transcriptome

   GeneChip
   mxSFP nonSFP gpSFP
RNA sequence   5,301 240,307 5,203
MX 178 115 45 18
Non-polymorphic 2,200 27 2,045 128
GP 223 7 61 155
Chi-square = 2,049.2, df = 4, p-value = 0
  1. The categories for SFP calls from RNA data are shown in columns: mxSFP, SFP in Morex; nonSFP, no SFP at the 0.1% FDR; gpSFP, SFP in Golden Promise. The categories of sequence-characterized probes are in rows: MX, polymorphism in Morex; non-polymorphic, no polymorphism between probe and any of the two genotypes; GP, polymorphism in Golden Promise. Intersections of the columns and rows indicate different combinations of sequence-verified polymorphisms and SFP.