The present invention relates to highly efficient ligase-based SNP analysis using DNA ligation fragments which includes non-binding modified nucleobases. More specifically, for the ligase-based SNP analysis, only when front sequencing is G:C matching regardless of base pairing of the non-binding modified nucleobases, ligation is specifically possible by introducing the non-binding modified nucleobases to 5' terminals of downstream ligation fragments and utilizing as substrates of ligase so that successful C/T type polymorphism analysis can be possible.;COPYRIGHT KIPO 2014;[Reference numerals] (AA) Fragment template; (BB) Modified nucleobases (Nm); (CC) Lane; (DD) 20 mer (Upstream); (EE,HH) Match; (FF,II) Mismatch; (GG,JJ) C/T type identification
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