Sequencing has errors - some in the PCR stage so not corrected by greater read depth for short reads (long reads are much more error prone). Genomes are dynami

Sequencing has errors - some in the PCR stage so not corrected by greater read depth for short reads (long reads are much more error prone). Genomes are dynamic - they change. You are looking at the progeny or regenerated plant, not the original plant. Exact matching will not get you far.