Will the ordering of fasta references influence bwa mem alignment result?

Question

[hanschen]

Hi all! I'm just learning to use bwa and I am wondering if the ordering of fasta reference sequences affects the alignment result.

I have two databases prepared and they are identical except for the ordering of reference sequences. And I just encountered an issue that using bwa mem to align the read to two databases gives me different results. Is that possible?

The parameter I set is:

bwa mem -x ont2d -a

Thanks!

[WouterDeCoster]

gives me different results

Please elaborate.

[hanschen]

Sorry for being unclear. The numbers of alignments reported are different. a read can have alignments using one database but not using the other.

[Titus]

There is different result if you change number of threads because solution searched change. I'm not sure the order of the fasta change something at the end you still have same motif/reads.