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Table 3 Effect of mismatch sites and SNP types on the specificity of allele-specific PCR

From: An improved allele-specific PCR primer design method for SNP marker analysis and its application

Mismatch sites closest to the 3’end of primers

Polymorphism percent of SNP primers

Polymorphism percent of primers for every SNP type

A/G, C/T

A/C, G/T

A/T, T/A

C/G, G/C

The 2 nd base

25.1%

23.0%

26.8%

26.6%

43.3%

(139/554)

(32/139)

(37/138)

(38/143)

(58/134)

The 3 rd base

32.9%

30.7%

37.4%

45.9%

39.4%

(189/575)

(42/137)

(52/139)

(72/157)

(56/142)

The 4 th base

29.1%

25.7%

29.8%

28.1%

29.9%

(162/557)

(37/144)

(42/141)

(38/135)

(41/137)

Total number

29.1%

26.4%

31.3%

34%

37.5%

(490/1686)

(111/420)

(131/418)

(148/435)

(155/413)