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Table 2 Transcript and probeset ranking variables versus genotyping success using an Axiom genotyping array

From: An Axiom SNP genotyping array for Douglas-fir

VariableNo. of probesetsCategory or meanPercent or meanNumber
SuccessFailSuccessFail
Transcript ranking variablesa
 No. of hits to scaffoldsb (transcript mean) (v0.5)58,350158.541.518,74513,286
> 141.558.5940313,242
027.572.510112663
 Transcript confidence scoreb (absent for UH SNPs)54,625Higher55.844.213,98711,087
Lower49.650.414,66314,888
 No. of SNPs per transcriptc58,350Mean12.0010.3629,15929,191
Q356.243.892027173
Q143.556.573759570
 Combined rankc (transcripts)58,350Mean27,252.231,096.529,15929,191
Q152.547.576596930
Q335.764.352149375
Probeset-within-transcript ranking variables
 Infinium successb,d6173SNP success74.525.545981575
 Probability of flanking SNPsb,e58,350Low50.849.227,73226,844
Moderate37.862.214272347
 No. of perfect allelesb (percent identity = 100%)(v0.5)58,350153.546.523,91620,799
039.260.850427810
225.774.3201582
 pConvertc57,381Mean0.6150.59528,50828,873
Q357.742.383196087
Q141.558.564299059
 Target SNP probabilityb,f (OSU SNPs)53,958P < 0.000155.045.024,60020,138
P < 0.00139.760.336585562
 Target SNP probabilityb (UH SNPs)37253 programs23.376.7128422
2 programs12.088.03812794
Final rankc,g (transcripts and probesets-within-transcripts)58,350Mean27,891.830,457.629,15929,191
Q161.538.589665622
Q346.653.468007788
Other variables
 Recommendationb,h57,295Recommended54.745.317,77914,748
Neutral43.256.810,69114,078
  1. aTranscripts refer to the Newbler isotigs [17] or putative transcripts [32] used for SNP discovery. v0.5 is version 0.5 of the Douglas-fir reference genome. UH SNPs were those detected by Müller et al. [32], whereas OSU SNPs were those detected by Howe et al. [17]
  2. bFor the categorical variables, percentages and numbers of probesets are reported for each category and means are absent. All differences among categories were highly significant (P <  0.0001) using a likelihood ratio chi-square test
  3. cFor the ranks and continuous variables, means are reported in bold, and percentages and numbers of probesets are reported for the upper (Q3) and lower (Q1) quartiles. Categories are ranked by probeset success. Successful SNPs were those that had a call rate > 60% and were polymorphic. All differences between means were highly significant (P <  0.0001) using a T-test (non-rank variables) or a Wilcoxon rank test (Combined rank and Final rank variables)
  4. dFor SNPs successfully genotyped with the Infinium platform, Axiom probeset success (74.5%) was significantly greater than the overall probeset success rate of 50.0% (P <  0.0001)
  5. eLow (rank = 1) or moderate (rank = 2) chance of having flanking SNPs or indels
  6. fThe P <  0.001 category indicates that 0.0001 ≤ P <  0.001
  7. gThe final probeset rank was based on the combined transcript rank plus the probeset-within-transcript variables
  8. hThe Affymetrix Recommendation variable was not used to select probesets because it is a categorical variable derived from pConvert