One read of the pair-ended reads is not able to map to the region when the reference is shorter using BWA

Question

[Louis Kok]

Hi All, I am not sure if anyone has the same experience as mine. When I perform BWA mapping using whole genome as reference, I could get both of a specific pair-ended reads mapped to the desired regions. However, when I extracted the regions from the target site (extended 500 bp front and back) and performed BWA mapping, one of the pair-ended reads is unable to map to it. The only difference is for whole genome as reference, I used -a bwtsw option and for short sequence as reference, I used -a is option. I wonder what the reason is behind it. Appreciate if anyone may know the answer. Thanks.