Figure 1

Observation of HMM: the illustration for alignment at position t for the sequence in study. The observation sets ${\left\{r_i^t\right\}}_{i=1}^{L_t}$ and ${\left\{q_i^t\right\}}_{i=1}^{L_t}$ are considered as the observation of o _t  in HMM. For the bases on the covered reads, blue color denotes the base is the same as reference allele, yellow color denotes the base is different from reference allele while purple color denotes the base is undecided on the genome in study.