Somaclonal variation is a phenomenon that results in phenotypic variation in plants regenerated from cell culture. The large part of the molecular mechanism about somaclonal variation is unclear. One of reason of somaclonal variation is the transposition of an endogenous retrotransposon Tos17. However, contribution of Tos17 for the somaclonal variation is estimated at 10% or less by co-segregation analysis of phenotype and transposed Tos17. The other unknown factor(s) for somaclonal variation are expected. The past several years, we analyzed whole genome sequences from individuals of regenerated rice. We developed an efficient method to detect line specific SNPs from whole genome sequence data. Focusing to homozygous line-specific mutations enable to screen SNP candidates with high accuracy from whole-genome sequence data. The frequency of the SNPs was at 100-times higher than the spontaneous mutation of Arabidopsis thaliana. The mutation spectrum of validated SNPs shows similar to the spectrum for the spontaneous mutation of Arabidopsis except relatively low level of Cytosine to Thymine transversion. In addition, we have developed a pipeline of programs to detect transposition of transposons in regenerated rice with high accuracy. We already developed a mutant panel of 50,000 regenerated individuals of rice. SNPs in the mutant panel will be a powerful tool for functional analysis of rice genes as well as the gene knockout by insertion of Tos17.