When I use BWA(version 0.7.15-r1140), I select the BWA-MEM algorithm and here is my command:

`bwa mem -t 2 reference_file fastq1.fq.gz fastq2.fq.gz > result1.sam`

This works well and then I use this command to improve the threads:

`bwa mem -t 10 reference_file fastq1.fq.gz fastq2.fq.gz > result2.sam`

This also works well but when I compare the result1.sam with result2.sam, they are different! I also test with `-t 6, -t 16`, and all the results are different. However, when I run with the same threads twice, the results are identical. So I found that BWA-MEM will get different results with different threads.  

Then I read the source code and found this:

    kt_for(opt->n_threads, worker1, &w, (opt->flag&MEM_F_PE)? n>>1 : n); // find mapping positions
	    for (i = 0; i < opt->n_threads; ++i) smem_aux_destroy(w.aux[i]);
    free(w.aux);
    if (opt->flag&MEM_F_PE) { // infer insert sizes if not provided
        if (pes0) memcpy(pes, pes0, 4 * sizeof(mem_pestat_t));
        else mem_pestat(opt, bns->l_pac, n, w.regs, pes);
    }
    kt_for(opt->n_threads, worker2, &w, (opt->flag&MEM_F_PE)? n>>1 : n);

That is, BWA-MEM use n_threads(such as -t 6, n = 6) to find mapping positions, but use only 1 thread to execute the function `mem_pestat` to calculate `avg`(average of the insert size) and `std`(standard deviation of the insert size), which are important to find pair information. According to BWA, every thread will process around 10000000bp, so:

If I use -t 2, BWA will calculate avg and std with 2 x 10000000bp

If I use -t 10, BWA will calculate avg and std with 10 x 10000000bp

If I use -t 16, BWA will calculate avg and std with 16 x 10000000bp

So I know why the results are different with different threads.

I wonder to know if there is anything wrong with my opinion? If it's correct, I want to know how to evaluate the difference? The difference will change which filed of the SAM record( such as RNAME or POS)? If it's wrong, I want to know the real reason to make the difference.

Any reply will be much appreciated!
It's almost guaranteed that the differences are in alignments with low (0 or so) MAPQs. I have [a little C program](https://github.com/dpryan79/Misc/blob/master/CompareBAMs.c) that uses htslib to compare two name sorted BAM files (or at the very least they need to be in the same order). It'll print out differences due to chromosome/position/cigar. If you then looked at a couple of those my guess would be that the differences are only occurring at low confidence alignments, which is wholly unsurprising.