Although the answer to this question may be found in Mitochondrial Genetic code, because that answer is primarily about mitochondrial genetic codes, I shall give a more directed answer here.
Because the same genetic code that was elucidated in bacteria was found to apply to higher eukaryotes, it was initially assumed that the genetic code was universal, and was referred to as such. Subsequently it was discovered that mitochondria did not generally employ this ‘universal’ code, which is now usually referred to as the ‘standard’ code — indeed different mitochondrial codes were found in different organisms.
However the question seems to be more concerned with the genetic codes of bacteria and the nuclear genetic codes of eukaryotes. Here also there are deviations from the standard genetic code, which can be found listed either on this Wikipedia page or at NCBI.
Below are some examples from the NCBI list (where references may be found) with the standard coding in parentheses:
UGA Trp (Ter)
Ciliates, Dasycladacean and Hexamita
UAA Gln (Ter)
UAG Gln (Ter)
UGA Cys (Ter)
Candidate Division SR1, Gracilibacteria
UGA Gly (Ter)
CUG Ala (Leu)
Finally, tRNAs for the ‘additional’ amino acids, selenocysteine and pyrrolysine recognize, respectively, the UGA and UAG stop codons in specific contexts.