Table 1.

Effect of Amplicon Length and Zygosity on Assay Performance

Amplicon length (bp)	Detection, characterization, and mapping^a	Detection and characterization^b	Detection^c	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)

High-Throughput MALDI-TOF Discovery of Genomic Sequence Polymorphisms