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Table 1 Percentages of successful SNPs using an Axiom genotyping array in Douglas-fir

From: An Axiom SNP genotyping array for Douglas-fir

SNP categorybFinal SNP call rate thresholdaAffymetrix abbreviation [11]
DefaultRescue
97%90%80%70%60%
Off-target variant11111OTV
Other3029262423Other
Call rate below threshold83222CallRateBelowThreshold
Not Converted4034302726OTV + Other + CallRateBelowThreshold
No minor homozygote1313131313NoMinorHom
Monomorphic high resolution1616161616MonoHighResolution
Polymorphic high resolution3131313131PolyHighResolution
Rescued6101313Rescued from Other and CallRateBelowThreshold
Convertedc6066707374PolyHighResolution + NoMinorHom + MonoHighResolution + Rescued
Percent successful (population ave)31.537.541.644.044.9PolyHighResolution + Rescued
Number successful (population ave)17,55520,92623,22324,54825,037PolyHighResolution + Rescued
Percent successful (population sum)37.142.946.949.550.4PolyHighResolution + Rescued
Number successful (population sum)20,66923,91726,18027,61628,094PolyHighResolution + Rescued
  1. aWe applied QC thresholds in one or two phases of analysis. The Default protocol consisted of the default Affymetrix parameters, including a CR threshold of 97%. In the Rescue protocols, we used the Default thresholds for phase 1, but then applied lower CR thresholds (60–90%) to the Other and CallRateBelowThreshold categories in phase 2
  2. bSNPs (N = 55,766) were classified into six categories (OTV, Other, CallRateBelowThreshold, NoMinorHom, MonoHighResolution, PolyHighResolution) and one Rescued category. Successful SNPs were those that were polymorphic with a call rate (CR) exceeding the indicated CR threshold after one or two phases of analysis with alternative quality control (QC) thresholds. Table values are averages from two populations (C1/I1 and C2) that were analyzed separately, except for the ‘population sum’ rows, which are based on sums. The C1/I1 population consisted of coastal Douglas-fir (N = 1682) and interior Douglas-fir (N = 12) samples that passed QC thresholds and were analyzed together. The C2 population consisted of coastal Douglas-fir (N = 348) samples that passed QC thresholds and were analyzed independently
  3. cConverted SNPs were those that were successfully assayed using the Default or Rescue protocol, but not necessarily polymorphic