When we construct phylogenetic trees, there might be discordance of topologies in different genomic regions. In order to address this issue, Bayesian Concordance Analysis (BCA) can be utilized to perform a phylogenetic analysis across whole genome and statistically quantification of the discordance. Supplemented some Perl scripts, the pipeline takes the genomic sequence files as input and calls several bioinformatics software (e.g. VCFtools, RepeatMasker, PAUP*4.0, MrModelTest, Mr.Bayes and so on) to mask their repeat sequences, align sequences and so on, and whereby we can obtain the phylogenetic discordance information of various locus across whole genome, which can contribute to the further research about the evolutionary history of different genome regions. At last, we applied this method into 129S1 mouse which is originated from the backcross of several generation between C3H/Hu mouse and 129/Sv mouse, finding that the contribution of C3H/Hu mouse to the mosaic genome of 129S1 mouse is less than that of 129/Sv.