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) |