Mapping difference with BWA

Question

[rj.rezwan]

Hi, I mapped the two accessions A and B to the reference genome using BWA. Reference genome is closely related species to A than B. But after mapping, I found that accession A has 97.78% and accession B 98.28% mapped to the reference genome. Why B has higher mapping % than A. Could someone explain this reason?

[ATpoint]

Cannot be answered without more details. At least add accessions and commands.