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Table 1 Single-feature polymorphisms (SFPs) discovered in Golden Promise and Morex1

From: Single-feature polymorphism discovery by computing probe affinity shape powers

 

Probes

Polymorphic

Non-polymorphic

GeneChip2

250,811

401

2,200

SAM FDR0.13

15,026

305

84

Weight score2.54

9,603

284

48

Rate (%)5

3.82

70.82

2.18

  1. 1 Barley1 GeneChip transcript data obtained from two genotypes (Morex and Golden Promise) from six tissue types [47] were used in this analysis.
  2. 2 GeneChip indicates the Barley1 GeneChip which contains 250,811 probes. There are 401 polymorphic probes and 2200 non-polymorphic probes sequence verified between Morex and Golden Promise in this dataset [47].
  3. 3 SAM FDR0.1 indicates the number of SFPs detected using a false discovery rate (FDR) 0.1 in the SAM (significance analysis of microarray) analysis of the bioconductor siggenes package.
  4. 4 Weight score 2.5 indicates the number of SFPs detected after a weight score cutoff value of 2.5 was applied.
  5. 5 Rate (%) indicates the percent SFPs with a weight score cutoff of 2.5 divided by the number of polymorphic, non-polymorphic, or all probes.