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Mapping difference with BWA

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?

variant-calling samtools bam bwa genomics
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updated by ATpoint ATpoint • written by rj.rezwan • rj.rezwan

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

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written by ATpoint ATpoint

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