Hi,

If you want the coordinates for the "same" region across the references, you can perform a genomic multiple alignment. You could use this tool : https://www.biorxiv.org/content/10.1101/730531v1

To be sure of the context what are your 5 references from ? Different species ?

To avoid multi-alignment at the genome level (that would be quite difficult to manage and to use after in your analysis), I would propose the following strategy.

1. Choose a reference above all, let's call it THE reference
2. perform SNP analysis against THE reference (see GATK guidelines: https://www.broadinstitute.org/partnerships/education/broade/best-practices-variant-calling-gatk-1) based on DNA-Seq reads for your 3 varieties.
3. Align your other references vs. THE reference and extract per-position variations... you could use the combination of samtools mpileup and bcftools without any filter... see samtools mpileup VCF output
4. Finally, you can merge 2 and 3 to compare variants from references and varieties to THE references and between them with a multi-sample vcf analysis.

Of note, you will need an alignment tool that works with "assembly to assembly" alignment; you could use this: https://github.com/lh3/minimap2

Good luck,