Next-generation short read sequencing is widely utilized in genome wide association study. However, as an indirect measurement technique, short read sequencing requires alignment step to map all sequencing reads to reference genome before acquiring interested genomic information. Facing to huge quantity of whole genome sequences, efficiency of sequence alignment becomes a key factor to achieve satisfied sequencing result. To improve efficiency of short read sequencing alignment, we propose a method to retrieve more reliable aligned reads with Bayesian inference. In detail, we firstly deduce the occurrence pattern of sequencing errors from mismatches collected in already aligned reads. Then, in addition to already aligned reads, with the deduced pattern, we evaluate alignment reliability of the left reads and eventually extract more reliable aligned reads to improve alignment efficiency. The experiment with E. coli short read DNA sequencing data proves the validity of the proposed method.