Table 1.

Effect of Amplicon Length and Zygosity on Assay Performance

Amplicon length (bp)
Detection, characterization, and mappinga
Detection and characterizationb
Detectionc
No detection
Homozygous replacements
      100 95.47 ± 3.64 4.40 ± 3.25 0.05 ± 0.38 0.08 ± 0.72
      200 93.74 ± 2.90 6.01 ± 2.56 0.11 ± 0.37 0.14 ± 0.62
      300 92.09 ± 2.51 7.43 ± 2.08 0.25 ± 0.46 0.23 ± 0.75
      400 90.43 ± 2.72 8.88 ± 2.17 0.41 ± 0.52 0.29 ± 0.77
      500 88.69 ± 2.70 10.30 ± 2.16 0.64 ± 0.62 0.38 ± 0.75
      600 87.04 ± 2.73 11.56 ± 2.17 0.93 ± 0.75 0.49 ± 0.78
      700 85.40 ± 2.40 12.77 ± 1.94 1.20 ± 0.71 0.64 ± 0.86
      800 83.83 ± 2.26 13.85 ± 1.69 1.54 ± 0.90 0.77 ± 0.95
      900 82.10 ± 2.58 14.90 ± 1.73 2.06 ± 1.04 0.94 ± 0.85
   1000 80.72 ± 2.49 15.79 ± 1.64 2.40 ± 1.18 1.09 ± 1.04
Heterozygous replacements
      100 94.24 ± 4.25 5.28 ± 3.48 0.22 ± 0.97 0.26 ± 1.16
      200 91.63 ± 3.43 7.23 ± 2.61 0.62 ± 1.09 0.51 ± 1.00
      300 88.97 ± 3.11 8.93 ± 2.13 1.24 ± 1.27 0.88 ± 1.12
      400 86.31 ± 3.26 10.42 ± 2.09 2.04 ± 1.36 1.24 ± 1.18
      500 83.36 ± 3.20 11.81 ± 1.96 3.14 ± 1.59 1.68 ± 1.20
      600 80.66 ± 3.49 12.71 ± 1.97 4.46 ± 1.79 2.17 ± 1.34
      700 77.77 ± 3.31 13.54 ± 1.85 5.91 ± 1.95 2.78 ± 1.38
      800 75.28 ± 3.13 14.25 ± 1.59 7.31 ± 1.92 3.17 ± 1.42
      900 72.56 ± 3.71 14.75 ± 1.51 8.87 ± 2.36 3.82 ± 1.50
   1000
70.43 ± 3.41
15.20 ± 1.49
10.08 ± 2.35
4.29 ± 1.66

a % SNPs (±sd) that can be detected, characterized (i.e., determination of the nature of the substitution), and unambiguously mapped

b % SNPs (±sd) that can be detected and characterized but not unambiguously positioned; typically, the ambiguity is restricted to a few (in many cases two) nearby positions

c % SNPs (±sd) that can be detected but not characterized; only a minor fraction of these SNPs can be positioned (i.e., the one uncertainty is the nature of the substitute base)