Python package or CLI tool outputting mutations of sequence with respect to reference
If it's just a comparison of two sequences that you're looking for, then diffseq from the emboss toolkit should be okay:
https://www.bioinformatics.nl/cgi-bin/emboss/diffseq
I think this tool requires the sequences to be oriented in the same direction. If you discover a lot more variants than you expect, try reverse-complementing one of the sequences.