"It should not be surprising that given a correct assembly the bacteria reproduced - by design the experiment only replaced codons with a different equivalent c

"It should not be surprising that given a correct assembly the bacteria reproduced - by design the experiment only replaced codons with a different equivalent codon" Codons are never really equivalent because of differences in tRNA abundances. So replacing a codon with another that codes for same amino acid can disrupt the rate of translation, and downstream processes like protein folding.